NameTypeDateCenterInitiativeDescription
G-DOC: a systems medicine platform for personalized oncology.Publications2011-09-01Data WranglingG-DOC: a systems medicine platform for personalized oncology.

Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM.

Neoplasia. 2011 Sep;13(9):771-83. pmid: 21969811.
In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers.Publications2013-01-01Data WranglingIn silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers.

Gusev Y, Riggins RB, Bhuvaneshwar K, Gauba R, Sheahan L, Clarke R, Madhavan S.

Cancer Inform. 2013;12:31-51. doi: 10.4137/CIN.S10329.
Platform for Personalized Oncology: Integrative analyses reveal novel molecular signatures associated with colorectal cancer relapse.Publications2013-03-18Data WranglingPlatform for Personalized Oncology: Integrative analyses reveal novel molecular signatures associated with colorectal cancer relapse.

Madhavan S, Gauba R, Song L, Bhuvaneshwar K, Gusev Y, Byers S, Juhl H, Weiner L.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:118. pmid: 24303318.
Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse.Publications2013-11-20Data WranglingGenome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse.

Madhavan S, Gusev Y, Natarajan TG, Song L, Bhuvaneshwar K, Gauba R, Pandey A, Haddad BR, Goerlitz D, Cheema AK, Juhl H, Kallakury B, Marshall JL, Byers SW, Weiner LM.

Front Genet. 2013 Nov 20;4:236. doi: 10.3389/fgene.2013.00236.
Algebraic connectivity of brain networks shows patterns of segregation leading to reduced network robustness in Alzheimer's disease.Publications2014-01-01ENIGMAAlgebraic connectivity of brain networks shows patterns of segregation leading to reduced network robustness in Alzheimer's disease.

Daianu M, Jahanshad N, Nir TM, Leonardo CD, Jack CR Jr, Weiner MW, Bernstein MA, Thompson PM.

Comput Diffus MRI (2014). 2014;2014:55-64. doi: 10.1007/978-3-319-11182-7_6.
Neuroanatomical correlates of emotional blunting in behavioral variant frontotemporal dementia and early-onset Alzheimer's disease.Publications2014-01-01ENIGMANeuroanatomical correlates of emotional blunting in behavioral variant frontotemporal dementia and early-onset Alzheimer's disease.

Lee GJ, Lu PH, Mather MJ, Shapira J, Jimenez E, Leow AD, Thompson PM, Mendez MF.

J Alzheimers Dis. 2014;41(3):793-800. doi: 10.3233/JAD-132219.
Verbal memory declines more rapidly with age in HIV infected versus uninfected adults.Publications2014-01-01ENIGMAVerbal memory declines more rapidly with age in HIV infected versus uninfected adults.

Seider TR, Luo X, Gongvatana A, Devlin KN, de la Monte SM, Chasman JD, Yan P, Tashima KT, Navia B, Cohen RA.

J Clin Exp Neuropsychol. 2014;36(4):356-67. doi: 10.1080/13803395.2014.892061.
Rich club network analysis shows distinct patterns of disruption in frontotemporal dementia and Alzheimer's disease.Publications2014-01-01ENIGMARich club network analysis shows distinct patterns of disruption in frontotemporal dementia and Alzheimer's disease.

Daianu M, Jahanshad N, Villalon-Reina JE, Mendez MF, Bartzokis G, Jimenez EE, Joshi A, Barsuglia J, Thompson PM.

Math Vis. 2014;2014:13-22. doi: 10.1007/978-3-319-11182-7_2.
Dynamic Treatment Regimes.Publications2014-01-01MD2KDynamic Treatment Regimes.

Chakraborty B, Murphy SA.

Annu Rev Stat Appl. 2014;1:447-464. doi: 10.1146/annurev-statistics-022513-115553.
Dynamic treatment regimes: technical challenges and applications.Publications2014-01-01MD2KDynamic treatment regimes: technical challenges and applications.

Laber EB, Lizotte DJ, Qian M, Pelham WE, Murphy SA.

Electron J Stat. 2014;8(1):1225-1272. pmid: 25356091.
Assessing the Availability of Users to Engage in Just-in-Time Intervention in the Natural Environment.Publications2014-01-01MD2KAssessing the Availability of Users to Engage in Just-in-Time Intervention in the Natural Environment.

Sarker H, Sharmin M, Ali AA, Rahman MM, Bari R, Hossain SM, Kumar S.

Proc ACM Int Conf Ubiquitous Comput. 2014;2014:909-920. doi: 10.1145/2632048.2636082.
Identifying Drug (Cocaine) Intake Events from Acute Physiological Response in the Presence of Free-living Physical Activity.Publications2014-01-01MD2KIdentifying Drug (Cocaine) Intake Events from Acute Physiological Response in the Presence of Free-living Physical Activity.

Hossain SM, Ali AA, Rahman M, Ertin E, Epstein D, Kennedy A, Preston K, Umbricht A, Chen Y, Kumar S.

IPSN. 2014;2014:71-82. pmid: 25531010.
Are We There Yet? Feasibility of Continuous Stress Assessment via Wireless Physiological Sensors.Publications2014-01-01MD2KAre We There Yet? Feasibility of Continuous Stress Assessment via Wireless Physiological Sensors.

Rahman M, Bari R, Ali AA, Sharmin M, Raij A, Hovsepian K, Hossain SM, Ertin E, Kennedy A, Epstein DH, Preston KL, Jobes M, Beck JG, Kedia S, Ward KD, al'Absi M, Kumar S.

ACM BCB. 2014;2014:479-488. doi: 10.1145/2649387.2649433.
A group-mediated, home-based physical activity intervention for patients with peripheral artery disease: effects on social and psychological function.Publications2014-01-28MD2KA group-mediated, home-based physical activity intervention for patients with peripheral artery disease: effects on social and psychological function.

Rejeski WJ, Spring B, Domanchuk K, Tao H, Tian L, Zhao L, McDermott MM.

J Transl Med. 2014 Jan 28;12:29. doi: 10.1186/1479-5876-12-29.
Altered relationships between age and functional brain activation in adolescents at clinical high risk for psychosis.Publications2014-01-30ENIGMAAltered relationships between age and functional brain activation in adolescents at clinical high risk for psychosis.

Karlsgodt KH, van Erp TG, Bearden CE, Cannon TD.

Psychiatry Res. 2014 Jan 30;221(1):21-9. doi: 10.1016/j.pscychresns.2013.08.004.
The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data.Publications2014-06-01ENIGMAThe ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data.

Thompson PM, Stein JL, Medland SE, Hibar DP, Vasquez AA, Renteria ME, Toro R, Jahanshad N, Schumann G, Franke B, Wright MJ, Martin NG, Agartz I, Alda M, Alhusaini S, Almasy L, Almeida J, Alpert K, Andreasen NC, Andreassen OA, Apostolova LG, Appel K, Armstrong NJ, Aribisala B, Bastin ME, Bauer M, Bearden CE, Bergmann O, Binder EB, Blangero J, Bockholt HJ, Bøen E, Bois C, Boomsma DI, Booth T, Bowman IJ, Bralten J, Brouwer RM, Brunner HG, Brohawn DG, Buckner RL, Buitelaar J, Bulayeva K, Bustillo JR, Calhoun VD, Cannon DM, Cantor RM, Carless MA, Caseras X, Cavalleri GL, Chakravarty MM, Chang KD, Ching CR, Christoforou A, Cichon S, Clark VP, Conrod P, Coppola G, Crespo-Facorro B, Curran JE, Czisch M, Deary IJ, de Geus EJ, den Braber A, Delvecchio G, Depondt C, de Haan L, de Zubicaray GI, Dima D, Dimitrova R, Djurovic S, Dong H, Donohoe G, Duggirala R, Dyer TD, Ehrlich S, Ekman CJ, Elvsåshagen T, Emsell L, Erk S, Espeseth T, Fagerness J, Fears S, Fedko I, Fernández G, Fisher SE, Foroud T, Fox PT, Francks C, Frangou S, Frey EM, Frodl T, Frouin V, Garavan H, Giddaluru S, Glahn DC, Godlewska B, Goldstein RZ, Gollub RL, Grabe HJ, Grimm O, Gruber O, Guadalupe T, Gur RE, Gur RC, Göring HH, Hagenaars S, Hajek T, Hall GB, Hall J, Hardy J, Hartman CA, Hass J, Hatton SN, Haukvik UK, Hegenscheid K, Heinz A, Hickie IB, Ho BC, Hoehn D, Hoekstra PJ, Hollinshead M, Holmes AJ, Homuth G, Hoogman M, Hong LE, Hosten N, Hottenga JJ, Hulshoff Pol HE, Hwang KS, Jack CR Jr, Jenkinson M, Johnston C, Jönsson EG, Kahn RS, Kasperaviciute D, Kelly S, Kim S, Kochunov P, Koenders L, Krämer B, Kwok JB, Lagopoulos J, Laje G, Landen M, Landman BA, Lauriello J, Lawrie SM, Lee PH, Le Hellard S, Lemaître H, Leonardo CD, Li CS, Liberg B, Liewald DC, Liu X, Lopez LM, Loth E, Lourdusamy A, Luciano M, Macciardi F, Machielsen MW, Macqueen GM, Malt UF, Mandl R, Manoach DS, Martinot JL, Matarin M, Mather KA, Mattheisen M, Mattingsdal M, Meyer-Lindenberg A, McDonald C, McIntosh AM, McMahon FJ, McMahon KL, Meisenzahl E, Melle I, Milaneschi Y, Mohnke S, Montgomery GW, Morris DW, Moses EK, Mueller BA, Muñoz Maniega S, Mühleisen TW, Müller-Myhsok B, Mwangi B, Nauck M, Nho K, Nichols TE, Nilsson LG, Nugent AC, Nyberg L, Olvera RL, Oosterlaan J, Ophoff RA, Pandolfo M, Papalampropoulou-Tsiridou M, Papmeyer M, Paus T, Pausova Z, Pearlson GD, Penninx BW, Peterson CP, Pfennig A, Phillips M, Pike GB, Poline JB, Potkin SG, Pütz B, Ramasamy A, Rasmussen J, Rietschel M, Rijpkema M, Risacher SL, Roffman JL, Roiz-Santiañez R, Romanczuk-Seiferth N, Rose EJ, Royle NA, Rujescu D, Ryten M, Sachdev PS, Salami A, Satterthwaite TD, Savitz J, Saykin AJ, Scanlon C, Schmaal L, Schnack HG, Schork AJ, Schulz SC, Schür R, Seidman L, Shen L, Shoemaker JM, Simmons A, Sisodiya SM, Smith C, Smoller JW, Soares JC, Sponheim SR, Sprooten E, Starr JM, Steen VM, Strakowski S, Strike L, Sussmann J, Sämann PG, Teumer A, Toga AW, Tordesillas-Gutierrez D, Trabzuni D, Trost S, Turner J, Van den Heuvel M, van der Wee NJ, van Eijk K, van Erp TG, van Haren NE, van 't Ent D, van Tol MJ, Valdés Hernández MC, Veltman DJ, Versace A, Völzke H, Walker R, Walter H, Wang L, Wardlaw JM, Weale ME, Weiner MW, Wen W, Westlye LT, Whalley HC, Whelan CD, White T, Winkler AM, Wittfeld K, Woldehawariat G, Wolf C, Zilles D, Zwiers MP, Thalamuthu A, Schofield PR, Freimer NB, Lawrence NS, Drevets W, Alzheimer’s Disease Neuroimaging Initiative, EPIGEN Consortium, IMAGEN Consortium, Saguenay Youth Study (SYS) Group..

Brain Imaging Behav. 2014 Jun;8(2):153-82. doi: 10.1007/s11682-013-9269-5.
RisQ: Recognizing Smoking Gestures with Inertial Sensors on a Wristband.Publications2014-06-01MD2KRisQ: Recognizing Smoking Gestures with Inertial Sensors on a Wristband.

Parate A, Chiu MC, Chadowitz C, Ganesan D, Kalogerakis E.

MobiSys. 2014 Jun;2014:149-161. doi: 10.1145/2594368.2594379.
Whole-genome analyses of whole-brain data: working within an expanded search space.Publications2014-06-01ENIGMAWhole-genome analyses of whole-brain data: working within an expanded search space.

Medland SE, Jahanshad N, Neale BM, Thompson PM.

Nat Neurosci. 2014 Jun;17(6):791-800. doi: 10.1038/nn.3718.
Predictors of CNS injury as measured by proton magnetic resonance spectroscopy in the setting of chronic HIV infection and CART.Publications2014-06-01ENIGMAPredictors of CNS injury as measured by proton magnetic resonance spectroscopy in the setting of chronic HIV infection and CART.

Harezlak J, Cohen R, Gongvatana A, Taylor M, Buchthal S, Schifitto G, Zhong J, Daar ES, Alger JR, Brown M, Singer EJ, Campbell TB, McMahon D, So YT, Yiannoutsos CT, Navia BA, HIV Neuroimaging Consortium..

J Neurovirol. 2014 Jun;20(3):294-303. doi: 10.1007/s13365-014-0246-6.
iShadow: Design of a Wearable, Real-Time Mobile Gaze Tracker.Publications2014-06-01MD2KiShadow: Design of a Wearable, Real-Time Mobile Gaze Tracker.

Mayberry A, Hu P, Marlin B, Salthouse C, Ganesan D.

MobiSys. 2014 Jun;2014:82-94. doi: 10.1145/2594368.2594388.
Multivariate General Linear Models (MGLM) on Riemannian Manifolds with Applications to Statistical Analysis of Diffusion Weighted Images.Publications2014-06-23CPCPMultivariate General Linear Models (MGLM) on Riemannian Manifolds with Applications to Statistical Analysis of Diffusion Weighted Images.

Kim HJ, Adluru N, Collins MD, Chung MK, Bendlin BB, Johnson SC, Davidson RJ, Singh V.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2014 Jun 23;2014:2705-2712. doi: 10.1109/CVPR.2014.352.
Impact of family structure and common environment on heritability estimation for neuroimaging genetics studies using Sequential Oligogenic Linkage Analysis Routines.Publications2014-06-27ENIGMAImpact of family structure and common environment on heritability estimation for neuroimaging genetics studies using Sequential Oligogenic Linkage Analysis Routines.

Koran ME, Thornton-Wells TA, Jahanshad N, Glahn DC, Thompson PM, Blangero J, Nichols TE, Kochunov P, Landman BA.

J Med Imaging (Bellingham). 2014 Jun 27;1(1):014005. doi: 10.1117/1.JMI.1.1.014005.
Optimization of remotely delivered intensive lifestyle treatment for obesity using the Multiphase Optimization Strategy: Opt-IN study protocol.Publications2014-07-01MD2KOptimization of remotely delivered intensive lifestyle treatment for obesity using the Multiphase Optimization Strategy: Opt-IN study protocol.

Pellegrini CA, Hoffman SA, Collins LM, Spring B.

Contemp Clin Trials. 2014 Jul;38(2):251-9. doi: 10.1016/j.cct.2014.05.007.
Relationship between salivary cortisol and depression in adolescent survivors of a major natural disaster.Publications2014-07-01MD2KRelationship between salivary cortisol and depression in adolescent survivors of a major natural disaster.

Yonekura T, Takeda K, Shetty V, Yamaguchi M.

J Physiol Sci. 2014 Jul;64(4):261-7. doi: 10.1007/s12576-014-0315-x.
A latent class analysis of cancer risk behaviors among U.S. college students.Publications2014-07-01MD2KA latent class analysis of cancer risk behaviors among U.S. college students.

Kang J, Ciecierski CC, Malin EL, Carroll AJ, Gidea M, Craft LL, Spring B, Hitsman B.

Prev Med. 2014 Jul;64:121-5. doi: 10.1016/j.ypmed.2014.03.023.
Healthy lifestyle change and subclinical atherosclerosis in young adults: Coronary Artery Risk Development in Young Adults (CARDIA) study.Publications2014-07-01MD2KHealthy lifestyle change and subclinical atherosclerosis in young adults: Coronary Artery Risk Development in Young Adults (CARDIA) study.

Spring B, Moller AC, Colangelo LA, Siddique J, Roehrig M, Daviglus ML, Polak JF, Reis JP, Sidney S, Liu K.

Circulation. 2014 Jul 1;130(1):10-7. doi: 10.1161/CIRCULATIONAHA.113.005445.
Neural dysregulation during a working memory task in human immunodeficiency virus-seropositive and hepatitis C coinfected individuals.Publications2014-08-01ENIGMANeural dysregulation during a working memory task in human immunodeficiency virus-seropositive and hepatitis C coinfected individuals.

Caldwell JZ, Gongvatana A, Navia BA, Sweet LH, Tashima K, Ding M, Cohen RA.

J Neurovirol. 2014 Aug;20(4):398-411. doi: 10.1007/s13365-014-0257-3.
Automated-immunosensor with centrifugal fluid valves for salivary cortisol measurement.Publications2014-08-01MD2KAutomated-immunosensor with centrifugal fluid valves for salivary cortisol measurement.

Yamaguchi M, Katagata H, Tezuka Y, Niwa D, Shetty V.

Sens Biosensing Res. 2014 Aug;1:15-20. doi: 10.1016/j.sbsr.2014.07.001.
Introduction to SMART designs for the development of adaptive interventions: with application to weight loss research.Publications2014-09-01MD2KIntroduction to SMART designs for the development of adaptive interventions: with application to weight loss research.

Almirall D, Nahum-Shani I, Sherwood NE, Murphy SA.

Transl Behav Med. 2014 Sep;4(3):260-74. doi: 10.1007/s13142-014-0265-0.
Medial temporal atrophy in early and late-onset Alzheimer's disease.Publications2014-09-01ENIGMAMedial temporal atrophy in early and late-onset Alzheimer's disease.

Cavedo E, Pievani M, Boccardi M, Galluzzi S, Bocchetta M, Bonetti M, Thompson PM, Frisoni GB.

Neurobiol Aging. 2014 Sep;35(9):2004-12. doi: 10.1016/j.neurobiolaging.2014.03.009.
Lean Big Data integration in systems biology and systems pharmacology.Publications2014-09-01LINCS-DCICLean Big Data integration in systems biology and systems pharmacology.

Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y.

Trends Pharmacol Sci. 2014 Sep;35(9):450-60. doi: 10.1016/j.tips.2014.07.001.
Functional connectivity in autosomal dominant and late-onset Alzheimer disease.Publications2014-09-01ENIGMAFunctional connectivity in autosomal dominant and late-onset Alzheimer disease.

Thomas JB, Brier MR, Bateman RJ, Snyder AZ, Benzinger TL, Xiong C, Raichle M, Holtzman DM, Sperling RA, Mayeux R, Ghetti B, Ringman JM, Salloway S, McDade E, Rossor MN, Ourselin S, Schofield PR, Masters CL, Martins RN, Weiner MW, Thompson PM, Fox NC, Koeppe RA, Jack CR Jr, Mathis CA, Oliver A, Blazey TM, Moulder K, Buckles V, Hornbeck R, Chhatwal J, Schultz AP, Goate AM, Fagan AM, Cairns NJ, Marcus DS, Morris JC, Ances BM.

JAMA Neurol. 2014 Sep;71(9):1111-22. doi: 10.1001/jamaneurol.2014.1654.
Structural abnormality of the corticospinal tract in major depressive disorder.Publications2014-09-10ENIGMAStructural abnormality of the corticospinal tract in major depressive disorder.

Sacchet MD, Prasad G, Foland-Ross LC, Joshi SH, Hamilton JP, Thompson PM, Gotlib IH.

Biol Mood Anxiety Disord. 2014 Sep 10;4:8. doi: 10.1186/2045-5380-4-8.
Estimating Drivers' Stress from GPS Traces.Publications2014-09-17MD2KEstimating Drivers' Stress from GPS Traces.

Vhaduri S, Ali A, Sharmin M, Hovsepian K, Kumar S.

Proc Int Conf Automot User Interfaces Interact Veh Appl (2014). 2014 Sep 17;2014:. doi: 10.1145/2667317.2667335.
Towards Scalable Graph Computation on Mobile Devices.Publications2014-10-01MD2KTowards Scalable Graph Computation on Mobile Devices.

Chen Y, Lin Z, Pienta R, Kahng M, Chau DH.

Proc IEEE Int Conf Big Data. 2014 Oct;2014:29-35. doi: 10.1109/BigData.2014.7004353.
MAGE: Matching Approximate Patterns in Richly-Attributed Graphs.Publications2014-10-01MD2KMAGE: Matching Approximate Patterns in Richly-Attributed Graphs.

Pienta R, Tamersoy A, Tong H, Chau DH.

Proc IEEE Int Conf Big Data. 2014 Oct;2014:585-590. doi: 10.1109/BigData.2014.7004278.
A blueprint of cell identity.Publications2014-10-01LINCS-DCICA blueprint of cell identity.

Ma'ayan A, Duan Q.

Nat Biotechnol. 2014 Oct;32(10):1007-8. doi: 10.1038/nbt.3035.
Regular fish consumption and age-related brain gray matter loss.Publications2014-10-01ENIGMARegular fish consumption and age-related brain gray matter loss.

Raji CA, Erickson KI, Lopez OL, Kuller LH, Gach HM, Thompson PM, Riverol M, Becker JT.

Am J Prev Med. 2014 Oct;47(4):444-51. doi: 10.1016/j.amepre.2014.05.037.
Designing adaptive intensive interventions using methods from engineering.Publications2014-10-01MD2KDesigning adaptive intensive interventions using methods from engineering.

Lagoa CM, Bekiroglu K, Lanza ST, Murphy SA.

J Consult Clin Psychol. 2014 Oct;82(5):868-78. doi: 10.1037/a0037736.
MMap: Fast Billion-Scale Graph Computation on a PC via Memory Mapping.Publications2014-10-01MD2KMMap: Fast Billion-Scale Graph Computation on a PC via Memory Mapping.

Lin Z, Kahng M, Sabrin KM, Chau DH, Lee H, Kang U.

Proc IEEE Int Conf Big Data. 2014 Oct;2014:159-164. doi: 10.1109/BigData.2014.7004226.
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease.Publications2014-10-03ENIGMAJoint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease.

Ashbrook DG, Williams RW, Lu L, Stein JL, Hibar DP, Nichols TE, Medland SE, Thompson PM, Hager R.

BMC Genomics. 2014 Oct 3;15:850. doi: 10.1186/1471-2164-15-850.
Investigating brain connectivity heritability in a twin study using diffusion imaging data.Publications2014-10-15ENIGMAInvestigating brain connectivity heritability in a twin study using diffusion imaging data.

Shen KK, Rose S, Fripp J, McMahon KL, de Zubicaray GI, Martin NG, Thompson PM, Wright MJ, Salvado O.

Neuroimage. 2014 Oct 15;100:628-41. doi: 10.1016/j.neuroimage.2014.06.041.
Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics.Publications2014-10-15ENIGMAAutomatic clustering of white matter fibers in brain diffusion MRI with an application to genetics.

Jin Y, Shi Y, Zhan L, Gutman BA, de Zubicaray GI, McMahon KL, Wright MJ, Toga AW, Thompson PM.

Neuroimage. 2014 Oct 15;100:75-90. doi: 10.1016/j.neuroimage.2014.04.048.
Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis.Publications2014-10-29ENIGMANovel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis.

Benyamin B, Esko T, Ried JS, Radhakrishnan A, Vermeulen SH, Traglia M, Gögele M, Anderson D, Broer L, Podmore C, Luan J, Kutalik Z, Sanna S, van der Meer P, Tanaka T, Wang F, Westra HJ, Franke L, Mihailov E, Milani L, Hälldin J, Winkelmann J, Meitinger T, Thiery J, Peters A, Waldenberger M, Rendon A, Jolley J, Sambrook J, Kiemeney LA, Sweep FC, Sala CF, Schwienbacher C, Pichler I, Hui J, Demirkan A, Isaacs A, Amin N, Steri M, Waeber G, Verweij N, Powell JE, Nyholt DR, Heath AC, Madden PA, Visscher PM, Wright MJ, Montgomery GW, Martin NG, Hernandez D, Bandinelli S, van der Harst P, Uda M, Vollenweider P, Scott RA, Langenberg C, Wareham NJ, InterAct Consortium., van Duijn C, Beilby J, Pramstaller PP, Hicks AA, Ouwehand WH, Oexle K, Gieger C, Metspalu A, Camaschella C, Toniolo D, Swinkels DW, Whitfield JB.

Nat Commun. 2014 Oct 29;5:4926. doi: 10.1038/ncomms5926.
A multiple imputation strategy for sequential multiple assignment randomized trials.Publications2014-10-30MD2KA multiple imputation strategy for sequential multiple assignment randomized trials.

Shortreed SM, Laber E, Scott Stroup T, Pineau J, Murphy SA.

Stat Med. 2014 Oct 30;33(24):4202-14. doi: 10.1002/sim.6223.
Skull-stripping with machine learning deformable organisms.Publications2014-10-30ENIGMASkull-stripping with machine learning deformable organisms.

Prasad G, Joshi AA, Feng A, Toga AW, Thompson PM, Terzopoulos D.

J Neurosci Methods. 2014 Oct 30;236:114-24. doi: 10.1016/j.jneumeth.2014.07.023.
Associations between depression and anxiety symptoms and retinal vessel caliber in adolescents and young adults.Publications2014-11-01ENIGMAAssociations between depression and anxiety symptoms and retinal vessel caliber in adolescents and young adults.

Meier MH, Gillespie NA, Hansell NK, Hewitt AW, Hickie IB, Lu Y, MacGregor S, Medland SE, Sun C, Wong TY, Wright MJ, Zhu G, Martin NG, Mackey DA.

Psychosom Med. 2014 Nov-Dec;76(9):732-8. doi: 10.1097/PSY.0000000000000117.
Genetic architecture of subcortical brain regions: common and region-specific genetic contributions.Publications2014-11-01ENIGMAGenetic architecture of subcortical brain regions: common and region-specific genetic contributions.

Rentería ME, Hansell NK, Strike LT, McMahon KL, de Zubicaray GI, Hickie IB, Thompson PM, Martin NG, Medland SE, Wright MJ.

Genes Brain Behav. 2014 Nov;13(8):821-30. doi: 10.1111/gbb.12177.
Serum cholesterol and variant in cholesterol-related gene CETP predict white matter microstructure.Publications2014-11-01ENIGMASerum cholesterol and variant in cholesterol-related gene CETP predict white matter microstructure.

Warstadt NM, Dennis EL, Jahanshad N, Kohannim O, Nir TM, McMahon KL, de Zubicaray GI, Montgomery GW, Henders AK, Martin NG, Whitfield JB, Jack CR Jr, Bernstein MA, Weiner MW, Toga AW, Wright MJ, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2014 Nov;35(11):2504-13. doi: 10.1016/j.neurobiolaging.2014.05.024.
Mediodorsal and visual thalamic connectivity differ in schizophrenia and bipolar disorder with and without psychosis history.Publications2014-11-01ENIGMAMediodorsal and visual thalamic connectivity differ in schizophrenia and bipolar disorder with and without psychosis history.

Anticevic A, Yang G, Savic A, Murray JD, Cole MW, Repovs G, Pearlson GD, Glahn DC.

Schizophr Bull. 2014 Nov;40(6):1227-43. doi: 10.1093/schbul/sbu100.
A case study for cloud based high throughput analysis of NGS data using the globus genomics system.Publications2014-11-07Data WranglingA case study for cloud based high throughput analysis of NGS data using the globus genomics system.

Bhuvaneshwar K, Sulakhe D, Gauba R, Rodriguez A, Madduri R, Dave U, Lacinski L, Foster I, Gusev Y, Madhavan S.

Comput Struct Biotechnol J. 2014 Nov 7;13:64-74. doi: 10.1016/j.csbj.2014.11.001.
Altered white matter microstructure is associated with social cognition and psychotic symptoms in 22q11.2 microdeletion syndrome.Publications2014-11-11ENIGMAAltered white matter microstructure is associated with social cognition and psychotic symptoms in 22q11.2 microdeletion syndrome.

Jalbrzikowski M, Villalon-Reina JE, Karlsgodt KH, Senturk D, Chow C, Thompson PM, Bearden CE.

Front Behav Neurosci. 2014 Nov 11;8:393. doi: 10.3389/fnbeh.2014.00393.
Histone H3.3 and its proteolytically processed form drive a cellular senescence programme.Publications2014-11-14LINCS-DCICHistone H3.3 and its proteolytically processed form drive a cellular senescence programme.

Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E.

Nat Commun. 2014 Nov 14;5:5210. doi: 10.1038/ncomms6210.
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.Publications2014-11-15LINCS-DCICDrug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.

Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A.

Bioinformatics. 2014 Nov 15;30(22):3289-90. doi: 10.1093/bioinformatics/btu526.
Obesity gene NEGR1 associated with white matter integrity in healthy young adults.Publications2014-11-15ENIGMAObesity gene NEGR1 associated with white matter integrity in healthy young adults.

Dennis EL, Jahanshad N, Braskie MN, Warstadt NM, Hibar DP, Kohannim O, Nir TM, McMahon KL, de Zubicaray GI, Montgomery GW, Martin NG, Toga AW, Wright MJ, Thompson PM.

Neuroimage. 2014 Nov 15;102 Pt 2:548-57. doi: 10.1016/j.neuroimage.2014.07.041.
Heritability of head motion during resting state functional MRI in 462 healthy twins.Publications2014-11-15ENIGMAHeritability of head motion during resting state functional MRI in 462 healthy twins.

Couvy-Duchesne B, Blokland GA, Hickie IB, Thompson PM, Martin NG, de Zubicaray GI, McMahon KL, Wright MJ.

Neuroimage. 2014 Nov 15;102 Pt 2:424-34. doi: 10.1016/j.neuroimage.2014.08.010.
Connectopathy in ageing and dementia.Publications2014-12-01ENIGMAConnectopathy in ageing and dementia.

Toga AW, Thompson PM.

Brain. 2014 Dec;137(Pt 12):3104-6. doi: 10.1093/brain/awu276.
ExpertBayes: Automatically refining manually built Bayesian networks.Publications2014-12-01CPCPExpertBayes: Automatically refining manually built Bayesian networks.

Almeida E, Ferreira P, Vinhoza T, Dutra I, Li J, Wu Y, Burnside E.

Proc Int Conf Mach Learn Appl. 2014 Dec;2014:362-366. doi: 10.1109/ICMLA.2014.64.
Genome-Wide Analyses of Working-Memory Ability: A Review.Publications2014-12-01ENIGMAGenome-Wide Analyses of Working-Memory Ability: A Review.

Knowles EE, Mathias SR, McKay DR, Sprooten E, Blangero J, Almasy L, Glahn DC.

Curr Behav Neurosci Rep. 2014 Dec;1(4):224-233. doi: 10.1007/s40473-014-0028-8.
Genetics of microstructure of the corpus callosum in older adults.Publications2014-12-16ENIGMAGenetics of microstructure of the corpus callosum in older adults.

Kanchibhotla SC, Mather KA, Thalamuthu A, Zhuang L, Schofield PR, Kwok JB, Ames D, Wright MJ, Trollor JN, Wen W, Sachdev PS.

PLoS One. 2014 Dec 16;9(12):e113181. doi: 10.1371/journal.pone.0113181.
Multitask learning of signaling and regulatory networks with application to studying human response to flu.Publications2014-12-18LINCS-DCICMultitask learning of signaling and regulatory networks with application to studying human response to flu.

Jain S, Gitter A, Bar-Joseph Z.

PLoS Comput Biol. 2014 Dec 18;10(12):e1003943. doi: 10.1371/journal.pcbi.1003943.
GLO-STIX: Graph-Level Operations for Specifying Techniques and Interactive eXploration.Publications2014-12-31MD2KGLO-STIX: Graph-Level Operations for Specifying Techniques and Interactive eXploration.

Stolper CD, Kahng M, Lin Z, Foerster F, Goel A, Stasko J, Chau DH.

IEEE Trans Vis Comput Graph. 2014 Dec 31;2014:2320-2328. doi: 10.1109/TVCG.2014.2346444.
Using the laws of thermodynamics to understand how matrix metalloproteinases coordinate the myocardial response to injury.Publications2015-01-01HeartBD2KUsing the laws of thermodynamics to understand how matrix metalloproteinases coordinate the myocardial response to injury.

Iyer RP, Jung M, Lindsey ML.

Metalloproteinases Med. 2015;2:75-82. doi: 10.2147/MNM.S74093.
Shared genetic factors influence amygdala volumes and risk for alcoholism.Publications2015-01-01ENIGMAShared genetic factors influence amygdala volumes and risk for alcoholism.

Dager AD, McKay DR, Kent JW Jr, Curran JE, Knowles E, Sprooten E, Göring HH, Dyer TD, Pearlson GD, Olvera RL, Fox PT, Lovallo WR, Duggirala R, Almasy L, Blangero J, Glahn DC.

Neuropsychopharmacology. 2015 Jan;40(2):412-20. doi: 10.1038/npp.2014.187.
Hippocampal and amygdalar local structural differences in elderly patients with schizophrenia.Publications2015-01-01ENIGMAHippocampal and amygdalar local structural differences in elderly patients with schizophrenia.

Prestia A, Cavedo E, Boccardi M, Muscio C, Adorni A, Geroldi C, Bonetti M, Thompson PM, Frisoni GB.

Am J Geriatr Psychiatry. 2015 Jan;23(1):47-58. doi: 10.1016/j.jagp.2014.01.006.
Left atrial decompression through unidirectional left-to-right interatrial shunt for the treatment of left heart failure: first-in-man experience with the V-Wave device.Publications2015-01-01MD2KLeft atrial decompression through unidirectional left-to-right interatrial shunt for the treatment of left heart failure: first-in-man experience with the V-Wave device.

Amat-Santos IJ, Bergeron S, Bernier M, Allende R, Barbosa Ribeiro H, Urena M, Pibarot P, Verheye S, Keren G, Yaacoby M, Nitzan Y, Abraham WT, Rodés-Cabau J.

EuroIntervention. 2015 Jan;10(9):1127-31. doi: 10.4244/EIJY14M05_07.
X-ray crystallography over the past decade for novel drug discovery - where are we heading next?Publications2015-01-01Data WranglingX-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W.

Expert Opin Drug Discov. 2015;10(9):975-89. doi: 10.1517/17460441.2015.1061991.
Gene interactions and structural brain change in early-onset Alzheimer's disease subjects using the pipeline environment.Publications2015-01-01BDDS, ENIGMAGene interactions and structural brain change in early-onset Alzheimer's disease subjects using the pipeline environment.

Moon SW, Dinov ID, Zamanyan A, Shi R, Genco A, Hobel S, Thompson PM, Toga AW, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Psychiatry Investig. 2015 Jan;12(1):125-35. doi: 10.4306/pi.2015.12.1.125.
Efficient Learning of Continuous-Time Hidden Markov Models for Disease Progression.Publications2015-01-01MD2KEfficient Learning of Continuous-Time Hidden Markov Models for Disease Progression.

Liu YY, Li S, Li F, Song L, Rehg JM.

Adv Neural Inf Process Syst. 2015;28:3599-3607. pmid: 27019571.
Binary Classifier Calibration Using a Bayesian Non-Parametric Approach.Publications2015-01-01CCDBinary Classifier Calibration Using a Bayesian Non-Parametric Approach.

Naeini MP, Cooper GF, Hauskrecht M.

Proc SIAM Int Conf Data Min. 2015;2015:208-216. doi: 10.1137/1.9781611974010.24.
Tissue Inhibitor of Metalloproteinase-1: Actions beyond Matrix Metalloproteinase Inhibition.Publications2015-01-01HeartBD2KTissue Inhibitor of Metalloproteinase-1: Actions beyond Matrix Metalloproteinase Inhibition.

Lindsey ML, Yabluchanskiy A, Ma Y.

Cardiology. 2015;132(3):147-50. doi: 10.1159/000433419.
Brain connectivity and novel network measures for Alzheimer's disease classification.Publications2015-01-01ENIGMABrain connectivity and novel network measures for Alzheimer's disease classification.

Prasad G, Joshi SH, Nir TM, Toga AW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S121-31. doi: 10.1016/j.neurobiolaging.2014.04.037.
Genome-wide interaction analysis reveals replicated epistatic effects on brain structure.Publications2015-01-01ENIGMAGenome-wide interaction analysis reveals replicated epistatic effects on brain structure.

Hibar DP, Stein JL, Jahanshad N, Kohannim O, Hua X, Toga AW, McMahon KL, de Zubicaray GI, Martin NG, Wright MJ, Alzheimer's Disease Neuroimaging Initiative., Weiner MW, Thompson PM.

Neurobiol Aging. 2015 Jan;36 Suppl 1:S151-8. doi: 10.1016/j.neurobiolaging.2014.02.033.
Diffusion weighted imaging-based maximum density path analysis and classification of Alzheimer's disease.Publications2015-01-01ENIGMADiffusion weighted imaging-based maximum density path analysis and classification of Alzheimer's disease.

Nir TM, Villalon-Reina JE, Prasad G, Jahanshad N, Joshi SH, Toga AW, Bernstein MA, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S132-40. doi: 10.1016/j.neurobiolaging.2014.05.037.
Achieving human and machine accessibility of cited data in scholarly publications.Publications2015-01-01CEDARAchieving human and machine accessibility of cited data in scholarly publications.

Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Proell S, Rauber A, Sacchi S, Smith A, Taylor M, Clark T.

PeerJ Comput Sci. 2015;1:. doi: 10.7717/peerj-cs.1.
Connectivity network measures predict volumetric atrophy in mild cognitive impairment.Publications2015-01-01ENIGMAConnectivity network measures predict volumetric atrophy in mild cognitive impairment.

Nir TM, Jahanshad N, Toga AW, Bernstein MA, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S113-20. doi: 10.1016/j.neurobiolaging.2014.04.038.
Higher homocysteine associated with thinner cortical gray matter in 803 participants from the Alzheimer's Disease Neuroimaging Initiative.Publications2015-01-01ENIGMAHigher homocysteine associated with thinner cortical gray matter in 803 participants from the Alzheimer's Disease Neuroimaging Initiative.

Madsen SK, Rajagopalan P, Joshi SH, Toga AW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S203-10. doi: 10.1016/j.neurobiolaging.2014.01.154.
Does MRI scan acceleration affect power to track brain change?Publications2015-01-01ENIGMADoes MRI scan acceleration affect power to track brain change?

Ching CR, Hua X, Hibar DP, Ward CP, Gunter JL, Bernstein MA, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S167-77. doi: 10.1016/j.neurobiolaging.2014.05.039.
Seemingly unrelated regression empowers detection of network failure in dementia.Publications2015-01-01ENIGMASeemingly unrelated regression empowers detection of network failure in dementia.

Jahanshad N, Nir TM, Toga AW, Jack CR Jr, Bernstein MA, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S103-12. doi: 10.1016/j.neurobiolaging.2014.02.032.
Mapping ventricular expansion onto cortical gray matter in older adults.Publications2015-01-01ENIGMAMapping ventricular expansion onto cortical gray matter in older adults.

Madsen SK, Gutman BA, Joshi SH, Toga AW, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S32-41. doi: 10.1016/j.neurobiolaging.2014.03.044.
Simultaneous Longitudinal Registration with Group-Wise Similarity Prior.Publications2015-01-01ENIGMASimultaneous Longitudinal Registration with Group-Wise Similarity Prior.

Fleishman GM, Gutman BA, Fletcher PT, Thompson PM.

Inf Process Med Imaging. 2015;24:746-57. doi: 10.1007/978-3-319-19992-4_59.
Controlling False Discovery Rate in Signal Space for Transformation-Invariant Thresholding of Statistical Maps.Publications2015-01-01BDDSControlling False Discovery Rate in Signal Space for Transformation-Invariant Thresholding of Statistical Maps.

Li J, Shi Y, Toga AW.

Inf Process Med Imaging. 2015;24:125-36. doi: 10.1007/978-3-319-19992-4_10.
Predicting malignancy from mammography findings and image-guided core biopsies.Publications2015-01-01CPCPPredicting malignancy from mammography findings and image-guided core biopsies.

Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.

Int J Data Min Bioinform. 2015;11(3):257-76. pmid: 26333262.
A randomized controlled trial to evaluate the safety and efficacy of cardiac contractility modulation in patients with moderately reduced left ventricular ejection fraction and a narrow QRS duration: study rationale and design.Publications2015-01-01MD2KA randomized controlled trial to evaluate the safety and efficacy of cardiac contractility modulation in patients with moderately reduced left ventricular ejection fraction and a narrow QRS duration: study rationale and design.

Abraham WT, Lindenfeld J, Reddy VY, Hasenfuss G, Kuck KH, Boscardin J, Gibbons R, Burkhoff D, FIX-HF-5C Investigators and Coordinators..

J Card Fail. 2015 Jan;21(1):16-23. doi: 10.1016/j.cardfail.2014.09.011.
A Riemannian Framework for Intrinsic Comparison of Closed Genus-Zero Shapes.Publications2015-01-01ENIGMAA Riemannian Framework for Intrinsic Comparison of Closed Genus-Zero Shapes.

Gutman BA, Fletcher PT, Cardoso MJ, Fleishman GM, Lorenzi M, Thompson PM, Ourselin S.

Inf Process Med Imaging. 2015;24:205-18. pmid: 26221675.
Low plasma ApoE levels are associated with smaller hippocampal size in the Alzheimer's disease neuroimaging initiative cohort.Publications2015-01-01ENIGMALow plasma ApoE levels are associated with smaller hippocampal size in the Alzheimer's disease neuroimaging initiative cohort.

Teng E, Chow N, Hwang KS, Thompson PM, Gylys KH, Cole GM, Jack CR Jr, Shaw LM, Trojanowski JQ, Soares HD, Weiner MW, Apostolova LG, Alzheimer’s Disease Neuroimaging Initiative..

Dement Geriatr Cogn Disord. 2015;39(3-4):154-66. doi: 10.1159/000368982.
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.Publications2015-01-01LINCS-DCICPhosphoSitePlus, 2014: mutations, PTMs and recalibrations.

Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E.

Nucleic Acids Res. 2015 Jan;43(Database issue):D512-20. doi: 10.1093/nar/gku1267.
Structural Neuroimaging Genetics Interactions in Alzheimer's Disease.Publications2015-01-01BDDSStructural Neuroimaging Genetics Interactions in Alzheimer's Disease.

Moon SW, Dinov ID, Kim J, Zamanyan A, Hobel S, Thompson PM, Toga AW.

J Alzheimers Dis. 2015;48(4):1051-63. doi: 10.3233/JAD-150335.
Sex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead.Publications2015-01-01LINCS-DCICSex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead.

Sánchez-Martín FJ, Lindquist DM, Landero-Figueroa J, Zhang X, Chen J, Cecil KM, Medvedovic M, Puga A.

Neurotoxicology. 2015 Jan;46:92-100. doi: 10.1016/j.neuro.2014.12.004.
T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes.Publications2015-01-01CCDT-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes.

Huang GT, Tsamardinos I, Raghu V, Kaminski N, Benos PV.

Pac Symp Biocomput. 2015;:431-42. pmid: 25592602.
Empowering imaging biomarkers of Alzheimer's disease.Publications2015-01-01ENIGMAEmpowering imaging biomarkers of Alzheimer's disease.

Gutman BA, Wang Y, Yanovsky I, Hua X, Toga AW, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Neurobiol Aging. 2015 Jan;36 Suppl 1:S69-80. doi: 10.1016/j.neurobiolaging.2014.05.038.
Relationship between Systemic and Cerebral Vascular Disease and Brain Structure Integrity in Normal Elderly Individuals.Publications2015-01-01ENIGMARelationship between Systemic and Cerebral Vascular Disease and Brain Structure Integrity in Normal Elderly Individuals.

Riverol M, Becker JT, López OL, Raji CA, Thompson PM, Carmichael OT, Gach HM, Longstreth WT Jr, Fried L, Tracy RP, Kuller LH.

J Alzheimers Dis. 2015;44(1):319-28. doi: 10.3233/JAD-141077.
Physical activity, body mass index, and brain atrophy in Alzheimer's disease.Publications2015-01-01ENIGMAPhysical activity, body mass index, and brain atrophy in Alzheimer's disease.

Boyle CP, Raji CA, Erickson KI, Lopez OL, Becker JT, Gach HM, Longstreth WT Jr, Teverovskiy L, Kuller LH, Carmichael OT, Thompson PM.

Neurobiol Aging. 2015 Jan;36 Suppl 1:S194-202. doi: 10.1016/j.neurobiolaging.2014.05.036.
SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information.Publications2015-01-01BDDSSOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information.

Husain SS, Kalinin A, Truong A, Dinov ID.

J Big Data. 2015;2:. doi: 10.1186/s40537-015-0018-z.
Visual hallucinations are associated with hyperconnectivity between the amygdala and visual cortex in people with a diagnosis of schizophrenia.Publications2015-01-01ENIGMAVisual hallucinations are associated with hyperconnectivity between the amygdala and visual cortex in people with a diagnosis of schizophrenia.

Ford JM, Palzes VA, Roach BJ, Potkin SG, van Erp TG, Turner JA, Mueller BA, Calhoun VD, Voyvodic J, Belger A, Bustillo J, Vaidya JG, Preda A, McEwen SC, Functional Imaging Biomedical Informatics Research Network., Mathalon DH.

Schizophr Bull. 2015 Jan;41(1):223-32. doi: 10.1093/schbul/sbu031.
Rapid Sampling for Visualizations with Ordering Guarantees.Publications2015-01-01KnowEnGRapid Sampling for Visualizations with Ordering Guarantees.

Kim A, Blais E, Parameswaran A, Indyk P, Madden S, Rubinfeld R.

Proceedings VLDB Endowment. 2015 Jan;8(5):521-532. pmid: 26779380.
Sharing big biomedical data.Publications2015-01-01BDDSSharing big biomedical data.

Toga AW, Dinov ID.

J Big Data. 2015;2:. doi: 10.1186/s40537-015-0016-1.
Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry.Publications2015-01-01BDDS, ENIGMAStudying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry.

Shi J, Stonnington CM, Thompson PM, Chen K, Gutman B, Reschke C, Baxter LC, Reiman EM, Caselli RJ, Wang Y, Alzheimer's Disease Neuroimaging Initiative..

Neuroimage. 2015 Jan 1;104:1-20. doi: 10.1016/j.neuroimage.2014.09.062.
Tensor Spectral Clustering for Partitioning Higher-order Network Structures.Publications2015-01-01MobilizeTensor Spectral Clustering for Partitioning Higher-order Network Structures.

Benson AR, Gleich DF, Leskovec J.

Proc SIAM Int Conf Data Min. 2015;2015:118-126. doi: 10.1137/1.9781611974010.14.
Machine Reading for Extraction of Bacteria and Habitat Taxonomies.Publications2015-01-01KnowEnGMachine Reading for Extraction of Bacteria and Habitat Taxonomies.

Kordjamshidi P, Massa W, Provoost T, Moens MF.

Biomed Eng Syst Technol Int Jt Conf BIOSTEC Revis Sel Pap. 2015 Jan;574:239-255. doi: 10.1007/978-3-319-27707-3_15.
Mechanisms and clinical consequences of untreated central sleep apnea in heart failure.Publications2015-01-06MD2KMechanisms and clinical consequences of untreated central sleep apnea in heart failure.

Costanzo MR, Khayat R, Ponikowski P, Augostini R, Stellbrink C, Mianulli M, Abraham WT.

J Am Coll Cardiol. 2015 Jan 6;65(1):72-84. doi: 10.1016/j.jacc.2014.10.025.
Progressive reduction in cortical thickness as psychosis develops: a multisite longitudinal neuroimaging study of youth at elevated clinical risk.Publications2015-01-15ENIGMAProgressive reduction in cortical thickness as psychosis develops: a multisite longitudinal neuroimaging study of youth at elevated clinical risk.

Cannon TD, Chung Y, He G, Sun D, Jacobson A, van Erp TG, McEwen S, Addington J, Bearden CE, Cadenhead K, Cornblatt B, Mathalon DH, McGlashan T, Perkins D, Jeffries C, Seidman LJ, Tsuang M, Walker E, Woods SW, Heinssen R, North American Prodrome Longitudinal Study Consortium..

Biol Psychiatry. 2015 Jan 15;77(2):147-57. doi: 10.1016/j.biopsych.2014.05.023.
Investigating the genetics of hippocampal volume in older adults without dementia.Publications2015-01-27ENIGMAInvestigating the genetics of hippocampal volume in older adults without dementia.

Mather KA, Armstrong NJ, Wen W, Kwok JB, Assareh AA, Thalamuthu A, Reppermund S, Duesing K, Wright MJ, Ames D, Trollor JN, Brodaty H, Schofield PR, Sachdev PS.

PLoS One. 2015 Jan 27;10(1):e0116920. doi: 10.1371/journal.pone.0116920.
Abnormalities in cortical gray matter density in borderline personality disorder.Publications2015-02-01ENIGMAAbnormalities in cortical gray matter density in borderline personality disorder.

Rossi R, Lanfredi M, Pievani M, Boccardi M, Rasser PE, Thompson PM, Cavedo E, Cotelli M, Rosini S, Beneduce R, Bignotti S, Magni LR, Rillosi L, Magnaldi S, Cobelli M, Rossi G, Frisoni GB.

Eur Psychiatry. 2015 Feb;30(2):221-7. doi: 10.1016/j.eurpsy.2014.11.009.
Single nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents.Publications2015-02-01ENIGMASingle nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents.

Desrivières S, Lourdusamy A, Tao C, Toro R, Jia T, Loth E, Medina LM, Kepa A, Fernandes A, Ruggeri B, Carvalho FM, Cocks G, Banaschewski T, Barker GJ, Bokde AL, Büchel C, Conrod PJ, Flor H, Heinz A, Gallinat J, Garavan H, Gowland P, Brühl R, Lawrence C, Mann K, Martinot ML, Nees F, Lathrop M, Poline JB, Rietschel M, Thompson P, Fauth-Bühler M, Smolka MN, Pausova Z, Paus T, Feng J, Schumann G, IMAGEN Consortium..

Mol Psychiatry. 2015 Feb;20(2):263-74. doi: 10.1038/mp.2013.197.
Occipital sources of resting-state alpha rhythms are related to local gray matter density in subjects with amnesic mild cognitive impairment and Alzheimer's disease.Publications2015-02-01ENIGMAOccipital sources of resting-state alpha rhythms are related to local gray matter density in subjects with amnesic mild cognitive impairment and Alzheimer's disease.

Babiloni C, Del Percio C, Boccardi M, Lizio R, Lopez S, Carducci F, Marzano N, Soricelli A, Ferri R, Triggiani AI, Prestia A, Salinari S, Rasser PE, Basar E, Famà F, Nobili F, Yener G, Emek-Savaş DD, Gesualdo L, Mundi C, Thompson PM, Rossini PM, Frisoni GB.

Neurobiol Aging. 2015 Feb;36(2):556-70. doi: 10.1016/j.neurobiolaging.2014.09.011.
Pleiotropic locus for emotion recognition and amygdala volume identified using univariate and bivariate linkage.Publications2015-02-01ENIGMAPleiotropic locus for emotion recognition and amygdala volume identified using univariate and bivariate linkage.

Knowles EE, McKay DR, Kent JW Jr, Sprooten E, Carless MA, Curran JE, de Almeida MA, Dyer TD, Göring HH, Olvera RL, Duggirala R, Fox PT, Almasy L, Blangero J, Glahn DC.

Am J Psychiatry. 2015 Feb 1;172(2):190-9. doi: 10.1176/appi.ajp.2014.14030311.
Prevalence of metabolic syndrome and its association with physical capacity, disability, and self-rated health in Lifestyle Interventions and Independence for Elders Study participants.Publications2015-02-01MD2KPrevalence of metabolic syndrome and its association with physical capacity, disability, and self-rated health in Lifestyle Interventions and Independence for Elders Study participants.

Botoseneanu A, Ambrosius WT, Beavers DP, de Rekeneire N, Anton S, Church T, Folta SC, Goodpaster BH, King AC, Nicklas BJ, Spring B, Wang X, Gill TM, LIFE Study Groups..

J Am Geriatr Soc. 2015 Feb;63(2):222-32. doi: 10.1111/jgs.13205.
Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.Publications2015-02-01BDDSProcessing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.

Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380.
White matter disruption in moderate/severe pediatric traumatic brain injury: advanced tract-based analyses.Publications2015-02-12ENIGMAWhite matter disruption in moderate/severe pediatric traumatic brain injury: advanced tract-based analyses.

Dennis EL, Jin Y, Villalon-Reina JE, Zhan L, Kernan CL, Babikian T, Mink RB, Babbitt CJ, Johnson JL, Giza CC, Thompson PM, Asarnow RF.

Neuroimage Clin. 2015 Feb 12;7:493-505. doi: 10.1016/j.nicl.2015.02.002.
Shared genetic variance between obesity and white matter integrity in Mexican Americans.Publications2015-02-13ENIGMAShared genetic variance between obesity and white matter integrity in Mexican Americans.

Spieker EA, Kochunov P, Rowland LM, Sprooten E, Winkler AM, Olvera RL, Almasy L, Duggirala R, Fox PT, Blangero J, Glahn DC, Curran JE.

Front Genet. 2015 Feb 13;6:26. doi: 10.3389/fgene.2015.00026.
Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.Publications2015-02-13CCDEvolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

Priedigkeit N, Wolfe N, Clark NL.

PLoS Genet. 2015 Feb 13;11(2):e1004967. doi: 10.1371/journal.pgen.1004967.
Partial volume correction in quantitative amyloid imaging.Publications2015-02-15ENIGMAPartial volume correction in quantitative amyloid imaging.

Su Y, Blazey TM, Snyder AZ, Raichle ME, Marcus DS, Ances BM, Bateman RJ, Cairns NJ, Aldea P, Cash L, Christensen JJ, Friedrichsen K, Hornbeck RC, Farrar AM, Owen CJ, Mayeux R, Brickman AM, Klunk W, Price JC, Thompson PM, Ghetti B, Saykin AJ, Sperling RA, Johnson KA, Schofield PR, Buckles V, Morris JC, Benzinger TL, Dominantly Inherited Alzheimer Network..

Neuroimage. 2015 Feb 15;107:55-64. doi: 10.1016/j.neuroimage.2014.11.058.
Effects of changing from non-accelerated to accelerated MRI for follow-up in brain atrophy measurement.Publications2015-02-15ENIGMAEffects of changing from non-accelerated to accelerated MRI for follow-up in brain atrophy measurement.

Leung KK, Malone IM, Ourselin S, Gunter JL, Bernstein MA, Thompson PM, Jack CR Jr, Weiner MW, Fox NC, Alzheimer's Disease Neuroimaging Initiative..

Neuroimage. 2015 Feb 15;107:46-53. doi: 10.1016/j.neuroimage.2014.11.049.
Medical data transformation using rewriting.Publications2015-02-20BDDSMedical data transformation using rewriting.

Ashish N, Toga AW.

Front Neuroinform. 2015 Feb 20;9:1. doi: 10.3389/fninf.2015.00001.
Developing a clinical utility framework to evaluate prediction models in radiogenomics.Publications2015-02-21CPCPDeveloping a clinical utility framework to evaluate prediction models in radiogenomics.

Wu Y, Liu J, Del Rio AM, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES.

Proc SPIE Int Soc Opt Eng. 2015 Feb 21;9416:. doi: 10.1117/12.2081954.
Inferring Meal Eating Activities in Real World Settings from Ambient Sounds: A Feasibility Study.Publications2015-03-01MD2KInferring Meal Eating Activities in Real World Settings from Ambient Sounds: A Feasibility Study.

Thomaz E, Zhang C, Essa I, Abowd GD.

IUI. 2015 Mar-Apr;2015:427-431. doi: 10.1145/2678025.2701405.
Interactive Querying over Large Network Data: Scalability, Visualization, and Interaction Design.Publications2015-03-01MD2KInteractive Querying over Large Network Data: Scalability, Visualization, and Interaction Design.

Pienta R, Tamersoy A, Tong H, Endert A, Chau DH.

IUI. 2015 Mar-Apr;2015(Companion):61-64. doi: 10.1145/2732158.2732192.
Contributions of Feature Binding During Encoding and Functional Connectivity of the Medial Temporal Lobe Structures to Episodic Memory Deficits Across the Prodromal and First-Episode Phases of Schizophrenia.Publications2015-03-01ENIGMAContributions of Feature Binding During Encoding and Functional Connectivity of the Medial Temporal Lobe Structures to Episodic Memory Deficits Across the Prodromal and First-Episode Phases of Schizophrenia.

Haut KM, van Erp TG, Knowlton B, Bearden CE, Subotnik K, Ventura J, Nuechterlein KH, Cannon TD.

Clin Psychol Sci. 2015 Mar;3(2):159-174. doi: 10.1177/2167702614533949.
Sparse kernel machine regression for ordinal outcomes.Publications2015-03-01PIC-SURESparse kernel machine regression for ordinal outcomes.

Shen Y, Liao KP, Cai T.

Biometrics. 2015 Mar;71(1):63-70. doi: 10.1111/biom.12223.
Design and protocol of a randomized multiple behavior change trial: Make Better Choices 2 (MBC2).Publications2015-03-01MD2KDesign and protocol of a randomized multiple behavior change trial: Make Better Choices 2 (MBC2).

Pellegrini CA, Steglitz J, Johnston W, Warnick J, Adams T, McFadden HG, Siddique J, Hedeker D, Spring B.

Contemp Clin Trials. 2015 Mar;41:85-92. doi: 10.1016/j.cct.2015.01.009.
Query-Based Outlier Detection in Heterogeneous Information Networks.Publications2015-03-01KnowEnGQuery-Based Outlier Detection in Heterogeneous Information Networks.

Kuck J, Zhuang H, Yan X, Cam H, Han J.

Adv Database Technol. 2015 Mar;2015:325-336. doi: 10.5441/002/edbt.2015.29.
The effect of reverse remodeling on long-term survival in mildly symptomatic patients with heart failure receiving cardiac resynchronization therapy: results of the REVERSE study.Publications2015-03-01MD2KThe effect of reverse remodeling on long-term survival in mildly symptomatic patients with heart failure receiving cardiac resynchronization therapy: results of the REVERSE study.

Gold MR, Daubert C, Abraham WT, Ghio S, St John Sutton M, Hudnall JH, Cerkvenik J, Linde C.

Heart Rhythm. 2015 Mar;12(3):524-30. doi: 10.1016/j.hrthm.2014.11.014.
Heart failure and respiratory hospitalizations are reduced in patients with heart failure and chronic obstructive pulmonary disease with the use of an implantable pulmonary artery pressure monitoring device.Publications2015-03-01MD2KHeart failure and respiratory hospitalizations are reduced in patients with heart failure and chronic obstructive pulmonary disease with the use of an implantable pulmonary artery pressure monitoring device.

Krahnke JS, Abraham WT, Adamson PB, Bourge RC, Bauman J, Ginn G, Martinez FJ, Criner GJ, Champion Trial Study Group..

J Card Fail. 2015 Mar;21(3):240-9. doi: 10.1016/j.cardfail.2014.12.008.
Stratifying patients at the risk of heart failure hospitalization using existing device diagnostic thresholds.Publications2015-03-01MD2KStratifying patients at the risk of heart failure hospitalization using existing device diagnostic thresholds.

Sharma V, Rathman LD, Small RS, Whellan DJ, Koehler J, Warman E, Abraham WT.

Heart Lung. 2015 Mar-Apr;44(2):129-36. doi: 10.1016/j.hrtlng.2014.07.007.
Social embeddedness in an online weight management programme is linked to greater weight loss.Publications2015-03-06MD2KSocial embeddedness in an online weight management programme is linked to greater weight loss.

Poncela-Casasnovas J, Spring B, McClary D, Moller AC, Mukogo R, Pellegrini CA, Coons MJ, Davidson M, Mukherjee S, Nunes Amaral LA.

J R Soc Interface. 2015 Mar 6;12(104):20140686. doi: 10.1098/rsif.2014.0686.
Subcortical shape and volume abnormalities in an elderly HIV+ cohort.Publications2015-03-17ENIGMASubcortical shape and volume abnormalities in an elderly HIV+ cohort.

Wade BS, Valcour V, Busovaca E, Esmaeili-Firidouni P, Joshi SH, Wang Y, Thompson PM.

Proc SPIE Int Soc Opt Eng. 2015 Mar 17;9417:. doi: 10.1117/12.2082241.
A Transformation Similarity Constraint for Groupwise Nonlinear Registration in Longitudinal Neuro Imaging Studies.Publications2015-03-20ENIGMAA Transformation Similarity Constraint for Groupwise Nonlinear Registration in Longitudinal Neuro Imaging Studies.

Fleishman GM, Gutman BA, Fletcher PT, Thompson P.

Proc SPIE Int Soc Opt Eng. 2015 Mar 20;9413:. doi: 10.1117/12.2080841.
7T Multi-shell Hybrid Diffusion Imaging (HYDI) for Mapping Brain Connectivity in Mice.Publications2015-03-20ENIGMA7T Multi-shell Hybrid Diffusion Imaging (HYDI) for Mapping Brain Connectivity in Mice.

Daianu M, Jahanshad N, Villalon-Reina JE, Prasad G, Jacobs RE, Barnes S, Zlokovic BV, Montagne A, Thompson PM.

Proc SPIE Int Soc Opt Eng. 2015 Mar 20;9413:. doi: 10.1117/12.2081491.
Communication of brain network core connections altered in behavioral variant frontotemporal dementia but possibly preserved in early-onset Alzheimer's disease.Publications2015-03-20ENIGMACommunication of brain network core connections altered in behavioral variant frontotemporal dementia but possibly preserved in early-onset Alzheimer's disease.

Daianu M, Jahanshad N, Mendez MF, Bartzokis G, Jimenez EE, Thompson PM.

Proc SPIE Int Soc Opt Eng. 2015 Mar 20;9413:. doi: 10.1117/12.2082352.
Leveraging Interaction between Genetic Variants and Mammographic Findings for Personalized Breast Cancer Diagnosis.Publications2015-03-25CPCPLeveraging Interaction between Genetic Variants and Mammographic Findings for Personalized Breast Cancer Diagnosis.

Liu J, Wu Y, Ong I, Page D, Peissig P, McCarty C, Onitilo AA, Burnside E.

AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:107-11. pmid: 26306250.
Harnessing the heart of big data.Publications2015-03-27HeartBD2KHarnessing the heart of big data.

Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR 3rd, Lindsey ML, Ping P.

Circ Res. 2015 Mar 27;116(7):1115-9. doi: 10.1161/CIRCRESAHA.115.306013.
Frontal and striatal alterations associated with psychopathic traits in adolescents.Publications2015-03-30ENIGMAFrontal and striatal alterations associated with psychopathic traits in adolescents.

Yang Y, Narr KL, Baker LA, Joshi SH, Jahanshad N, Raine A, Thompson PM.

Psychiatry Res. 2015 Mar 30;231(3):333-40. doi: 10.1016/j.pscychresns.2015.01.017.
Cognitive decline preceding the onset of psychosis in patients with 22q11.2 deletion syndrome.Publications2015-04-01ENIGMACognitive decline preceding the onset of psychosis in patients with 22q11.2 deletion syndrome.

Vorstman JA, Breetvelt EJ, Duijff SN, Eliez S, Schneider M, Jalbrzikowski M, Armando M, Vicari S, Shashi V, Hooper SR, Chow EW, Fung WL, Butcher NJ, Young DA, McDonald-McGinn DM, Vogels A, van Amelsvoort T, Gothelf D, Weinberger R, Weizman A, Klaassen PW, Koops S, Kates WR, Antshel KM, Simon TJ, Ousley OY, Swillen A, Gur RE, Bearden CE, Kahn RS, Bassett AS, International Consortium on Brain and Behavior in 22q11.2 Deletion Syndrome..

JAMA Psychiatry. 2015 Apr;72(4):377-85. doi: 10.1001/jamapsychiatry.2014.2671.
Improved data analysis for the MinION nanopore sequencer.Publications2015-04-01BDTGImproved data analysis for the MinION nanopore sequencer.

Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M.

Nat Methods. 2015 Apr;12(4):351-6. doi: 10.1038/nmeth.3290.
AUTOMATED MULTI-ATLAS LABELING OF THE FORNIX AND ITS INTEGRITY IN ALZHEIMER'S DISEASE.Publications2015-04-01ENIGMAAUTOMATED MULTI-ATLAS LABELING OF THE FORNIX AND ITS INTEGRITY IN ALZHEIMER'S DISEASE.

Jin Y, Shi Y, Zhan L, Thompson PM, Alzheimer’s Disease Neuroimaging Initiative (ADNI)..

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:140-143. doi: 10.1109/ISBI.2015.7163835.
Boosting Classification Accuracy of Diffusion MRI Derived Brain Networks for the Subtypes of Mild Cognitive Impairment Using Higher Order Singular Value Decomposition.Publications2015-04-01ENIGMABoosting Classification Accuracy of Diffusion MRI Derived Brain Networks for the Subtypes of Mild Cognitive Impairment Using Higher Order Singular Value Decomposition.

Zhan L, Liu Y, Zhou J, Ye J, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:131-135. doi: 10.1109/ISBI.2015.7163833.
FEATURE SELECTION IMPROVES THE ACCURACY OF CLASSIFYING ALZHEIMER DISEASE USING DIFFUSION TENSOR IMAGES.Publications2015-04-01ENIGMAFEATURE SELECTION IMPROVES THE ACCURACY OF CLASSIFYING ALZHEIMER DISEASE USING DIFFUSION TENSOR IMAGES.

Demirhan A, Nir TM, Zavaliangos-Petropulu A, Jack CR Jr, Weiner MW, Bernstein MA, Thompson PM, Jahanshad N, Alzheimer’s Disease Neuroimaging Initiative (ADNI)..

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:126-130. doi: 10.1109/ISBI.2015.7163832.
Random Forest Classification of Depression Status Based On Subcortical Brain Morphometry Following Electroconvulsive Therapy.Publications2015-04-01ENIGMARandom Forest Classification of Depression Status Based On Subcortical Brain Morphometry Following Electroconvulsive Therapy.

Wade BS, Joshi SH, Pirnia T, Leaver AM, Woods RP, Thompson PM, Espinoza R, Narr KL.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:92-96. doi: 10.1109/ISBI.2015.7163824.
MAPPING ABNORMAL SUBCORTICAL BRAIN MORPHOMETRY IN AN ELDERLY HIV+ COHORT.Publications2015-04-01ENIGMAMAPPING ABNORMAL SUBCORTICAL BRAIN MORPHOMETRY IN AN ELDERLY HIV+ COHORT.

Wade BS, Valcour VG, Wendelken-Riegelhaupt L, Esmaeili-Firidouni P, Joshi SH, Wang Y, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:971-975. doi: 10.1109/ISBI.2015.7164033.
WHITE MATTER INTEGRITY IN TRAUMATIC BRAIN INJURY: EFFECTS OF PERMISSIBLE FIBER TURNING ANGLE.Publications2015-04-01ENIGMAWHITE MATTER INTEGRITY IN TRAUMATIC BRAIN INJURY: EFFECTS OF PERMISSIBLE FIBER TURNING ANGLE.

Dennis EL, Jin Y, Kernan C, Babikian T, Mink R, Babbitt C, Johnson J, Giza CC, Asarnow RF, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:930-933. doi: 10.1109/ISBI.2015.7164023.
SPECTRAL GRAPH THEORY AND GRAPH ENERGY METRICS SHOW EVIDENCE FOR THE ALZHEIMER'S DISEASE DISCONNECTION SYNDROME IN APOE-4 RISK GENE CARRIERS.Publications2015-04-01ENIGMASPECTRAL GRAPH THEORY AND GRAPH ENERGY METRICS SHOW EVIDENCE FOR THE ALZHEIMER'S DISEASE DISCONNECTION SYNDROME IN APOE-4 RISK GENE CARRIERS.

Daianu M, Mezher A, Jahanshad N, Hibar DP, Nir TM, Jack CR Jr, Weiner MW, Bernstein MA, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:458-461. doi: 10.1109/ISBI.2015.7163910.
HERITABILITY OF BRAIN NETWORK TOPOLOGY IN 853 TWINS AND SIBLINGS.Publications2015-04-01ENIGMAHERITABILITY OF BRAIN NETWORK TOPOLOGY IN 853 TWINS AND SIBLINGS.

Zhan L, Jahanshad N, Faskowitz J, Zhu D, Prasad G, Martin NG, de Zubicaray GI, McMahon KL, Wright MJ, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:449-453. doi: 10.1109/ISBI.2015.7163908.
Medial Demons Registration Localizes The Degree of Genetic Influence Over Subcortical Shape Variability: An N= 1480 Meta-Analysis.Publications2015-04-01ENIGMAMedial Demons Registration Localizes The Degree of Genetic Influence Over Subcortical Shape Variability: An N= 1480 Meta-Analysis.

Gutman BA, Jahanshad N, Ching CR, Wang Y, Kochunov PV, Nichols TE, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:1402-1406. doi: 10.1109/ISBI.2015.7164138.
GENETIC ANALYSIS OF STRUCTURAL BRAIN CONNECTIVITY USING DICCCOL MODELS OF DIFFUSION MRI IN 522 TWINS.Publications2015-04-01ENIGMAGENETIC ANALYSIS OF STRUCTURAL BRAIN CONNECTIVITY USING DICCCOL MODELS OF DIFFUSION MRI IN 522 TWINS.

Zhu D, Zhan L, Faskowitz J, Daianu M, Jahanshad N, de Zubicaray GI, McMahon KL, Martin NG, Wright MJ, Thompson PM.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:1167-1171. doi: 10.1109/ISBI.2015.7164080.
Bias correction in species distribution models: pooling survey and collection data for multiple species.Publications2015-04-01MobilizeBias correction in species distribution models: pooling survey and collection data for multiple species.

Fithian W, Elith J, Hastie T, Keith DA.

Methods Ecol Evol. 2015 Apr;6(4):424-438. doi: 10.1111/2041-210X.12242.
Detecting Genetic Risk Factors for Alzheimer's Disease in Whole Genome Sequence Data via Lasso Screening.Publications2015-04-01ENIGMADetecting Genetic Risk Factors for Alzheimer's Disease in Whole Genome Sequence Data via Lasso Screening.

Yang T, Wang J, Sun Q, Hibar DP, Jahanshad N, Liu L, Wang Y, Zhan L, Thompson PM, Ye J.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:985-989. doi: 10.1109/ISBI.2015.7164036.
Information-Theoretic Characterization of Blood Panel Predictors for Brain Atrophy and Cognitive Decline in the Elderly.Publications2015-04-01ENIGMAInformation-Theoretic Characterization of Blood Panel Predictors for Brain Atrophy and Cognitive Decline in the Elderly.

Madsen SK, Ver Steeg G, Mezher A, Jahanshad N, Nir TM, Hua X, Gutman BA, Galstyan A, Thompson PM, Alzheimer’s Disease Neuroimaging Initiative (ADNI)..

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:980-984. doi: 10.1109/ISBI.2015.7164035.
MULTI-RESOLUTION STATISTICAL ANALYSIS ON GRAPH STRUCTURED DATA IN NEUROIMAGING.Publications2015-04-01CPCPMULTI-RESOLUTION STATISTICAL ANALYSIS ON GRAPH STRUCTURED DATA IN NEUROIMAGING.

Kim WH, Singh V, Chung MK, Adluru N, Bendlin BB, Johnson SC.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:1548-1551. doi: 10.1109/ISBI.2015.7164173.
Barriers and Negative Nudges: Exploring Challenges in Food Journaling.Publications2015-04-01MD2KBarriers and Negative Nudges: Exploring Challenges in Food Journaling.

Cordeiro F, Epstein DA, Thomaz E, Bales E, Jagannathan AK, Abowd GD, Fogarty J.

Proc SIGCHI Conf Hum Factor Comput Syst. 2015 Apr;2015:1159-1162. doi: 10.1145/2702123.2702155.
cDREM: inferring dynamic combinatorial gene regulation.Publications2015-04-01LINCS-DCICcDREM: inferring dynamic combinatorial gene regulation.

Wise A, Bar-Joseph Z.

J Comput Biol. 2015 Apr;22(4):324-33. doi: 10.1089/cmb.2015.0010.
Spatial and temporal dynamics of the cardiac mitochondrial proteome.Publications2015-04-01HeartBD2KSpatial and temporal dynamics of the cardiac mitochondrial proteome.

Lau E, Huang D, Cao Q, Dincer TU, Black CM, Lin AJ, Lee JM, Wang D, Liem DA, Lam MP, Ping P.

Expert Rev Proteomics. 2015 Apr;12(2):133-46. doi: 10.1586/14789450.2015.1024227.
Multiset Statistics for Gene Set Analysis.Publications2015-04-01CPCPMultiset Statistics for Gene Set Analysis.

Newton MA, Wang Z.

Annu Rev Stat Appl. 2015 Apr;2:95-111. doi: 10.1146/annurev-statistics-010814-020335.
Graph Regularized Meta-path Based Transductive Regression in Heterogeneous Information Network.Publications2015-04-01KnowEnGGraph Regularized Meta-path Based Transductive Regression in Heterogeneous Information Network.

Wan M, Ouyang Y, Kaplan L, Han J.

Proc SIAM Int Conf Data Min. 2015 Apr-May;2015:918-926. doi: 10.1137/1.9781611974010.103.
Common genetic variants influence human subcortical brain structures.Publications2015-04-09ENIGMACommon genetic variants influence human subcortical brain structures.

Hibar DP, Stein JL, Renteria ME, Arias-Vasquez A, Desrivières S, Jahanshad N, Toro R, Wittfeld K, Abramovic L, Andersson M, Aribisala BS, Armstrong NJ, Bernard M, Bohlken MM, Boks MP, Bralten J, Brown AA, Chakravarty MM, Chen Q, Ching CR, Cuellar-Partida G, den Braber A, Giddaluru S, Goldman AL, Grimm O, Guadalupe T, Hass J, Woldehawariat G, Holmes AJ, Hoogman M, Janowitz D, Jia T, Kim S, Klein M, Kraemer B, Lee PH, Olde Loohuis LM, Luciano M, Macare C, Mather KA, Mattheisen M, Milaneschi Y, Nho K, Papmeyer M, Ramasamy A, Risacher SL, Roiz-Santiañez R, Rose EJ, Salami A, Sämann PG, Schmaal L, Schork AJ, Shin J, Strike LT, Teumer A, van Donkelaar MM, van Eijk KR, Walters RK, Westlye LT, Whelan CD, Winkler AM, Zwiers MP, Alhusaini S, Athanasiu L, Ehrlich S, Hakobjan MM, Hartberg CB, Haukvik UK, Heister AJ, Hoehn D, Kasperaviciute D, Liewald DC, Lopez LM, Makkinje RR, Matarin M, Naber MA, McKay DR, Needham M, Nugent AC, Pütz B, Royle NA, Shen L, Sprooten E, Trabzuni D, van der Marel SS, van Hulzen KJ, Walton E, Wolf C, Almasy L, Ames D, Arepalli S, Assareh AA, Bastin ME, Brodaty H, Bulayeva KB, Carless MA, Cichon S, Corvin A, Curran JE, Czisch M, de Zubicaray GI, Dillman A, Duggirala R, Dyer TD, Erk S, Fedko IO, Ferrucci L, Foroud TM, Fox PT, Fukunaga M, Gibbs JR, Göring HH, Green RC, Guelfi S, Hansell NK, Hartman CA, Hegenscheid K, Heinz A, Hernandez DG, Heslenfeld DJ, Hoekstra PJ, Holsboer F, Homuth G, Hottenga JJ, Ikeda M, Jack CR Jr, Jenkinson M, Johnson R, Kanai R, Keil M, Kent JW Jr, Kochunov P, Kwok JB, Lawrie SM, Liu X, Longo DL, McMahon KL, Meisenzahl E, Melle I, Mohnke S, Montgomery GW, Mostert JC, Mühleisen TW, Nalls MA, Nichols TE, Nilsson LG, Nöthen MM, Ohi K, Olvera RL, Perez-Iglesias R, Pike GB, Potkin SG, Reinvang I, Reppermund S, Rietschel M, Romanczuk-Seiferth N, Rosen GD, Rujescu D, Schnell K, Schofield PR, Smith C, Steen VM, Sussmann JE, Thalamuthu A, Toga AW, Traynor BJ, Troncoso J, Turner JA, Valdés Hernández MC, van 't Ent D, van der Brug M, van der Wee NJ, van Tol MJ, Veltman DJ, Wassink TH, Westman E, Zielke RH, Zonderman AB, Ashbrook DG, Hager R, Lu L, McMahon FJ, Morris DW, Williams RW, Brunner HG, Buckner RL, Buitelaar JK, Cahn W, Calhoun VD, Cavalleri GL, Crespo-Facorro B, Dale AM, Davies GE, Delanty N, Depondt C, Djurovic S, Drevets WC, Espeseth T, Gollub RL, Ho BC, Hoffmann W, Hosten N, Kahn RS, Le Hellard S, Meyer-Lindenberg A, Müller-Myhsok B, Nauck M, Nyberg L, Pandolfo M, Penninx BW, Roffman JL, Sisodiya SM, Smoller JW, van Bokhoven H, van Haren NE, Völzke H, Walter H, Weiner MW, Wen W, White T, Agartz I, Andreassen OA, Blangero J, Boomsma DI, Brouwer RM, Cannon DM, Cookson MR, de Geus EJ, Deary IJ, Donohoe G, Fernández G, Fisher SE, Francks C, Glahn DC, Grabe HJ, Gruber O, Hardy J, Hashimoto R, Hulshoff Pol HE, Jönsson EG, Kloszewska I, Lovestone S, Mattay VS, Mecocci P, McDonald C, McIntosh AM, Ophoff RA, Paus T, Pausova Z, Ryten M, Sachdev PS, Saykin AJ, Simmons A, Singleton A, Soininen H, Wardlaw JM, Weale ME, Weinberger DR, Adams HH, Launer LJ, Seiler S, Schmidt R, Chauhan G, Satizabal CL, Becker JT, Yanek L, van der Lee SJ, Ebling M, Fischl B, Longstreth WT Jr, Greve D, Schmidt H, Nyquist P, Vinke LN, van Duijn CM, Xue L, Mazoyer B, Bis JC, Gudnason V, Seshadri S, Ikram MA, Alzheimer’s Disease Neuroimaging Initiative., CHARGE Consortium., EPIGEN., IMAGEN., SYS., Martin NG, Wright MJ, Schumann G, Franke B, Thompson PM, Medland SE.

Nature. 2015 Apr 9;520(7546):224-9. doi: 10.1038/nature14101.
Comparison of nine tractography algorithms for detecting abnormal structural brain networks in Alzheimer's disease.Publications2015-04-14ENIGMAComparison of nine tractography algorithms for detecting abnormal structural brain networks in Alzheimer's disease.

Zhan L, Zhou J, Wang Y, Jin Y, Jahanshad N, Prasad G, Nir TM, Leonardo CD, Ye J, Thompson PM, For The Alzheimer's Disease Neuroimaging Initiative.

Front Aging Neurosci. 2015 Apr 14;7:48. doi: 10.3389/fnagi.2015.00048.
Alterations in frontal white matter neurochemistry and microstructure in schizophrenia: implications for neuroinflammation.Publications2015-04-14ENIGMAAlterations in frontal white matter neurochemistry and microstructure in schizophrenia: implications for neuroinflammation.

Chiappelli J, Hong LE, Wijtenburg SA, Du X, Gaston F, Kochunov P, Rowland LM.

Transl Psychiatry. 2015 Apr 14;5:e548. doi: 10.1038/tp.2015.43.
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.Publications2015-04-15LINCS-DCICSMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.

Wise A, Bar-Joseph Z.

Bioinformatics. 2015 Apr 15;31(8):1250-7. doi: 10.1093/bioinformatics/btu800.
Structured learning for spatial information extraction from biomedical text: bacteria biotopes.Publications2015-04-25KnowEnGStructured learning for spatial information extraction from biomedical text: bacteria biotopes.

Kordjamshidi P, Roth D, Moens MF.

BMC Bioinformatics. 2015 Apr 25;16:129. doi: 10.1186/s12859-015-0542-z.
Cortical thickness and brain volumetric analysis in body dysmorphic disorder.Publications2015-04-30ENIGMACortical thickness and brain volumetric analysis in body dysmorphic disorder.

Madsen SK, Zai A, Pirnia T, Arienzo D, Zhan L, Moody TD, Thompson PM, Feusner JD.

Psychiatry Res. 2015 Apr 30;232(1):115-22. doi: 10.1016/j.pscychresns.2015.02.003.
Heritability of fractional anisotropy in human white matter: a comparison of Human Connectome Project and ENIGMA-DTI data.Publications2015-05-01ENIGMAHeritability of fractional anisotropy in human white matter: a comparison of Human Connectome Project and ENIGMA-DTI data.

Kochunov P, Jahanshad N, Marcus D, Winkler A, Sprooten E, Nichols TE, Wright SN, Hong LE, Patel B, Behrens T, Jbabdi S, Andersson J, Lenglet C, Yacoub E, Moeller S, Auerbach E, Ugurbil K, Sotiropoulos SN, Brouwer RM, Landman B, Lemaitre H, den Braber A, Zwiers MP, Ritchie S, van Hulzen K, Almasy L, Curran J, deZubicaray GI, Duggirala R, Fox P, Martin NG, McMahon KL, Mitchell B, Olvera RL, Peterson C, Starr J, Sussmann J, Wardlaw J, Wright M, Boomsma DI, Kahn R, de Geus EJ, Williamson DE, Hariri A, van 't Ent D, Bastin ME, McIntosh A, Deary IJ, Hulshoff Pol HE, Blangero J, Thompson PM, Glahn DC, Van Essen DC.

Neuroimage. 2015 May 1;111:300-11. doi: 10.1016/j.neuroimage.2015.02.050.
Mining Quality Phrases from Massive Text Corpora.Publications2015-05-01KnowEnGMining Quality Phrases from Massive Text Corpora.

Liu J, Shang J, Wang C, Ren X, Han J.

Proc ACM SIGMOD Int Conf Manag Data. 2015 May-Jun;2015:1729-1744. doi: 10.1145/2723372.2751523.
Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.Publications2015-05-01ENIGMAEfficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.

Furlotte NA, Eskin E.

Genetics. 2015 May;200(1):59-68. doi: 10.1534/genetics.114.171447.
Ringo: Interactive Graph Analytics on Big-Memory Machines.Publications2015-05-01MobilizeRingo: Interactive Graph Analytics on Big-Memory Machines.

Perez Y, Sosič R, Banerjee A, Puttagunta R, Raison M, Shah P, Leskovec J.

Proc ACM SIGMOD Int Conf Manag Data. 2015 May-Jun;2015:1105-1110. doi: 10.1145/2723372.2735369.
A Database Framework for Classifier Engineering.Publications2015-05-01MobilizeA Database Framework for Classifier Engineering.

Kimelfeld B, Ré C.

CEUR Workshop Proc. 2015 May;1378:. pmid: 27274719.
The digital phenotype.Publications2015-05-01PIC-SUREThe digital phenotype.

Jain SH, Powers BW, Hawkins JB, Brownstein JS.

Nat Biotechnol. 2015 May;33(5):462-3. doi: 10.1038/nbt.3223.
A novel cortical thickness estimation method based on volumetric Laplace-Beltrami operator and heat kernel.Publications2015-05-01ENIGMAA novel cortical thickness estimation method based on volumetric Laplace-Beltrami operator and heat kernel.

Wang G, Zhang X, Su Q, Shi J, Caselli RJ, Wang Y, Alzheimer’s Disease Neuroimaging Initiative..

Med Image Anal. 2015 May;22(1):1-20. doi: 10.1016/j.media.2015.01.005.
Association of BNP and Troponin Levels with Outcome among Cardiac Resynchronization Therapy Recipients.Publications2015-05-01MD2KAssociation of BNP and Troponin Levels with Outcome among Cardiac Resynchronization Therapy Recipients.

Shalaby AA, Abraham WT, Fonarow GC, Bersohn MM, Gorcsan J 3rd, Lee LY, Halilovic J, Saba S, Maisel A, Singh JP, Sonel A, Kadish A.

Pacing Clin Electrophysiol. 2015 May;38(5):581-90. doi: 10.1111/pace.12610.
Regional hippocampal damage in heart failure.Publications2015-05-01ENIGMARegional hippocampal damage in heart failure.

Woo MA, Ogren JA, Abouzeid CM, Macey PM, Sairafian KG, Saharan PS, Thompson PM, Fonarow GC, Hamilton MA, Harper RM, Kumar R.

Eur J Heart Fail. 2015 May;17(5):494-500. doi: 10.1002/ejhf.241.
Abnormal hippocampal morphology in dissociative identity disorder and post-traumatic stress disorder correlates with childhood trauma and dissociative symptoms.Publications2015-05-01ENIGMAAbnormal hippocampal morphology in dissociative identity disorder and post-traumatic stress disorder correlates with childhood trauma and dissociative symptoms.

Chalavi S, Vissia EM, Giesen ME, Nijenhuis ER, Draijer N, Cole JH, Dazzan P, Pariante CM, Madsen SK, Rajagopalan P, Thompson PM, Toga AW, Veltman DJ, Reinders AA.

Hum Brain Mapp. 2015 May;36(5):1692-704. doi: 10.1002/hbm.22730.
Caffe con Troll: Shallow Ideas to Speed Up Deep Learning.Publications2015-05-01MobilizeCaffe con Troll: Shallow Ideas to Speed Up Deep Learning.

Hadjis S, Abuzaid F, Zhang C, Ré C.

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REEF: Retainable Evaluator Execution Framework.Publications2015-05-01MD2KREEF: Retainable Evaluator Execution Framework.

Weimer M, Chen Y, Chun BG, Condie T, Curino C, Douglas C, Lee Y, Majestro T, Malkhi D, Matusevych S, Myers B, Narayanamurthy S, Ramakrishnan R, Rao S, Sears R, Sezgin B, Wang J.

Proc ACM SIGMOD Int Conf Manag Data. 2015 May-Jun;2015:1343-1355. doi: 10.1145/2723372.2742793.
Leveraging Pattern Semantics for Extracting Entities in Enterprises.Publications2015-05-01KnowEnGLeveraging Pattern Semantics for Extracting Entities in Enterprises.

Tao F, Zhao B, Fuxman A, Li Y, Han J.

Proc Int World Wide Web Conf. 2015 May;2015:1078-1088. pmid: 26705540.
Donor Retention in Online Crowdfunding Communities: A Case Study of DonorsChoose.org.Publications2015-05-01MobilizeDonor Retention in Online Crowdfunding Communities: A Case Study of DonorsChoose.org.

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Proc Int World Wide Web Conf. 2015 May;2015:34-44. doi: 10.1145/2736277.2741120.
CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations.Publications2015-05-15CCDCellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations.

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Bioinformatics. 2015 May 15;31(10):1584-91. doi: 10.1093/bioinformatics/btv015.
Delving into Egocentric Actions.Publications2015-06-01MD2KDelving into Egocentric Actions.

Li Y, Ye Z, Rehg JM.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2015 Jun;2015:287-295. doi: 10.1109/CVPR.2015.7298625.
Gaze-enabled Egocentric Video Summarization via Constrained Submodular Maximization.Publications2015-06-01CPCP, MD2KGaze-enabled Egocentric Video Summarization via Constrained Submodular Maximization.

Xut J, Mukherjee L, Li Y, Warner J, Rehg JM, Singht V.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2015 Jun;2015:2235-2244. doi: 10.1109/CVPR.2015.7298836.
Statistical Inference Models for Image Datasets with Systematic Variations.Publications2015-06-01CPCPStatistical Inference Models for Image Datasets with Systematic Variations.

Kim WH, Bendlin BB, Chung MK, Johnson SC, Singh V.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2015 Jun;2015:4795-4803. doi: 10.1109/CVPR.2015.7299112.
Development of an online, publicly accessible naive Bayesian decision support tool for mammographic mass lesions based on the American College of Radiology (ACR) BI-RADS lexicon.Publications2015-06-01CPCPDevelopment of an online, publicly accessible naive Bayesian decision support tool for mammographic mass lesions based on the American College of Radiology (ACR) BI-RADS lexicon.

Benndorf M, Kotter E, Langer M, Herda C, Wu Y, Burnside ES.

Eur Radiol. 2015 Jun;25(6):1768-75. doi: 10.1007/s00330-014-3570-6.
Novel Neuroimaging Methods to Understand How HIV Affects the Brain.Publications2015-06-01ENIGMANovel Neuroimaging Methods to Understand How HIV Affects the Brain.

Thompson PM, Jahanshad N.

Curr HIV/AIDS Rep. 2015 Jun;12(2):289-98. doi: 10.1007/s11904-015-0268-6.
D-ribose aids heart failure patients with preserved ejection fraction and diastolic dysfunction: a pilot study.Publications2015-06-01MD2KD-ribose aids heart failure patients with preserved ejection fraction and diastolic dysfunction: a pilot study.

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Ther Adv Cardiovasc Dis. 2015 Jun;9(3):56-65. doi: 10.1177/1753944715572752.
Association of Protein Phosphatase PPM1G With Alcohol Use Disorder and Brain Activity During Behavioral Control in a Genome-Wide Methylation Analysis.Publications2015-06-01ENIGMAAssociation of Protein Phosphatase PPM1G With Alcohol Use Disorder and Brain Activity During Behavioral Control in a Genome-Wide Methylation Analysis.

Ruggeri B, Nymberg C, Vuoksimaa E, Lourdusamy A, Wong CP, Carvalho FM, Jia T, Cattrell A, Macare C, Banaschewski T, Barker GJ, Bokde AL, Bromberg U, Büchel C, Conrod PJ, Fauth-Bühler M, Flor H, Frouin V, Gallinat J, Garavan H, Gowland P, Heinz A, Ittermann B, Martinot JL, Nees F, Pausova Z, Paus T, Rietschel M, Robbins T, Smolka MN, Spanagel R, Bakalkin G, Mill J, Sommer WH, Rose RJ, Yan J, Aliev F, Dick D, Kaprio J, Desrivières S, Schumann G, IMAGEN Consortium..

Am J Psychiatry. 2015 Jun;172(6):543-52. doi: 10.1176/appi.ajp.2014.14030382.
Toward a complete dataset of drug-drug interaction information from publicly available sources.Publications2015-06-01CEDARToward a complete dataset of drug-drug interaction information from publicly available sources.

Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD.

J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006.
Accurate and fast multiple-testing correction in eQTL studies.Publications2015-06-04ENIGMAAccurate and fast multiple-testing correction in eQTL studies.

Sul JH, Raj T, de Jong S, de Bakker PI, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B.

Am J Hum Genet. 2015 Jun 4;96(6):857-68. doi: 10.1016/j.ajhg.2015.04.012.
Dynamics of the discovery process of protein-protein interactions from low content studies.Publications2015-06-06LINCS-DCICDynamics of the discovery process of protein-protein interactions from low content studies.

Wang Z, Clark NR, Ma'ayan A.

BMC Syst Biol. 2015 Jun 6;9:26. doi: 10.1186/s12918-015-0173-z.
BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks.Publications2015-06-12ENIGMABRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks.

Richiardi J, Altmann A, Milazzo AC, Chang C, Chakravarty MM, Banaschewski T, Barker GJ, Bokde AL, Bromberg U, Büchel C, Conrod P, Fauth-Bühler M, Flor H, Frouin V, Gallinat J, Garavan H, Gowland P, Heinz A, Lemaître H, Mann KF, Martinot JL, Nees F, Paus T, Pausova Z, Rietschel M, Robbins TW, Smolka MN, Spanagel R, Ströhle A, Schumann G, Hawrylycz M, Poline JB, Greicius MD, IMAGEN consortium..

Science. 2015 Jun 12;348(6240):1241-4. doi: 10.1126/science.1255905.
Sleep disordered breathing and post-discharge mortality in patients with acute heart failure.Publications2015-06-14MD2KSleep disordered breathing and post-discharge mortality in patients with acute heart failure.

Khayat R, Jarjoura D, Porter K, Sow A, Wannemacher J, Dohar R, Pleister A, Abraham WT.

Eur Heart J. 2015 Jun 14;36(23):1463-9. doi: 10.1093/eurheartj/ehu522.
Identification of causal genes for complex traits.Publications2015-06-15ENIGMAIdentification of causal genes for complex traits.

Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E.

Bioinformatics. 2015 Jun 15;31(12):i206-13. doi: 10.1093/bioinformatics/btv240.
Exploiting ontology graph for predicting sparsely annotated gene function.Publications2015-06-15KnowEnGExploiting ontology graph for predicting sparsely annotated gene function.

Wang S, Cho H, Zhai C, Berger B, Peng J.

Bioinformatics. 2015 Jun 15;31(12):i357-64. doi: 10.1093/bioinformatics/btv260.
Personalized Modeling for Prediction with Decision-Path Models.Publications2015-06-22CCDPersonalized Modeling for Prediction with Decision-Path Models.

Visweswaran S, Ferreira A, Ribeiro GA, Oliveira AC, Cooper GF.

PLoS One. 2015 Jun 22;10(6):e0131022. doi: 10.1371/journal.pone.0131022.
The Alzheimer's Disease Neuroimaging Initiative informatics core: A decade in review.Publications2015-07-01BDDSThe Alzheimer's Disease Neuroimaging Initiative informatics core: A decade in review.

Toga AW, Crawford KL.

Alzheimers Dement. 2015 Jul;11(7):832-9. doi: 10.1016/j.jalz.2015.04.004.
Evaluation of an electronic health record-supported obesity management protocol implemented in a community health center: a cautionary note.Publications2015-07-01MD2KEvaluation of an electronic health record-supported obesity management protocol implemented in a community health center: a cautionary note.

Steglitz J, Sommers M, Talen MR, Thornton LK, Spring B.

J Am Med Inform Assoc. 2015 Jul;22(4):755-63. doi: 10.1093/jamia/ocu034.
Saul: Towards Declarative Learning Based Programming.Publications2015-07-01KnowEnGSaul: Towards Declarative Learning Based Programming.

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IJCAI (U S). 2015 Jul;2015:1844-1851. pmid: 26635465.
Striatal activity and reduced white matter increase frontal activity in youths with family histories of alcohol and other substance-use disorders performing a go/no-go task.Publications2015-07-01ENIGMAStriatal activity and reduced white matter increase frontal activity in youths with family histories of alcohol and other substance-use disorders performing a go/no-go task.

Acheson A, Tagamets MA, Winkler A, Rowland LM, Mathias CW, Wright SN, Hong LE, Kochunov P, Dougherty DM.

Brain Behav. 2015 Jul;5(7):e00352. doi: 10.1002/brb3.352.
Incremental Knowledge Base Construction Using DeepDive.Publications2015-07-01MobilizeIncremental Knowledge Base Construction Using DeepDive.

Shin J, Wu S, Wang F, De Sa C, Zhang C, Ré C.

Proceedings VLDB Endowment. 2015 Jul;8(11):1310-1321. doi: 10.14778/2809974.2809991.
Manifold-valued Dirichlet Processes.Publications2015-07-01CPCPManifold-valued Dirichlet Processes.

Kim HJ, Xu J, Vemuri BC, Singh V.

Proc Int Conf Mach Learn. 2015 Jul;2015:1199-1208. pmid: 26973982.
Smartphone applications to support weight loss: current perspectives.Publications2015-07-01MD2KSmartphone applications to support weight loss: current perspectives.

Pellegrini CA, Pfammatter AF, Conroy DE, Spring B.

Adv Health Care Technol. 2015 Jul;1:13-22. doi: 10.2147/AHCT.S57844.
Impact of Early and Late Visual Deprivation on the Structure of the Corpus Callosum: A Study Combining Thickness Profile with Surface Tensor-Based Morphometry.Publications2015-07-01ENIGMAImpact of Early and Late Visual Deprivation on the Structure of the Corpus Callosum: A Study Combining Thickness Profile with Surface Tensor-Based Morphometry.

Shi J, Collignon O, Xu L, Wang G, Kang Y, Leporé F, Lao Y, Joshi AA, Leporé N, Wang Y.

Neuroinformatics. 2015 Jul;13(3):321-36. doi: 10.1007/s12021-014-9259-9.
Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.Publications2015-07-02CPCPHematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.

Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson KD, Kang YA, Kim JS, Dewey CN, Keles S, Bresnick EH.

Mol Cell. 2015 Jul 2;59(1):62-74. doi: 10.1016/j.molcel.2015.05.020.
Big Data: Astronomical or Genomical?Publications2015-07-07KnowEnGBig Data: Astronomical or Genomical?

Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE.

PLoS Biol. 2015 Jul 7;13(7):e1002195. doi: 10.1371/journal.pbio.1002195.
Mesochronal Structure Learning.Publications2015-07-12CCDMesochronal Structure Learning.

Plis S, Danks D, Yang J.

Uncertain Artif Intell. 2015 Jul 12;31:. pmid: 27076793.
Prioritizing Proteomics Assay Development for Clinical Translation.Publications2015-07-14HeartBD2KPrioritizing Proteomics Assay Development for Clinical Translation.

Lam MP, Venkatraman V, Cao Q, Wang D, Dincer TU, Lau E, Su AI, Xing Y, Ge J, Ping P, Van Eyk JE.

J Am Coll Cardiol. 2015 Jul 14;66(2):202-4. doi: 10.1016/j.jacc.2015.04.072.
Muscle LIM Protein: Master regulator of cardiac and skeletal muscle functions.Publications2015-07-15HeartBD2KMuscle LIM Protein: Master regulator of cardiac and skeletal muscle functions.

Vafiadaki E, Arvanitis DA, Sanoudou D.

Gene. 2015 Jul 15;566(1):1-7. doi: 10.1016/j.gene.2015.04.077.
Fast and powerful heritability inference for family-based neuroimaging studies.Publications2015-07-15ENIGMAFast and powerful heritability inference for family-based neuroimaging studies.

Ganjgahi H, Winkler AM, Glahn DC, Blangero J, Kochunov P, Nichols TE.

Neuroimage. 2015 Jul 15;115:256-68. doi: 10.1016/j.neuroimage.2015.03.005.
Callosal Function in Pediatric Traumatic Brain Injury Linked to Disrupted White Matter Integrity.Publications2015-07-15ENIGMACallosal Function in Pediatric Traumatic Brain Injury Linked to Disrupted White Matter Integrity.

Dennis EL, Ellis MU, Marion SD, Jin Y, Moran L, Olsen A, Kernan C, Babikian T, Mink R, Babbitt C, Johnson J, Giza CC, Thompson PM, Asarnow RF.

J Neurosci. 2015 Jul 15;35(28):10202-11. doi: 10.1523/JNEUROSCI.1595-15.2015.
Boosting brain connectome classification accuracy in Alzheimer's disease using higher-order singular value decomposition.Publications2015-07-24ENIGMABoosting brain connectome classification accuracy in Alzheimer's disease using higher-order singular value decomposition.

Zhan L, Liu Y, Wang Y, Zhou J, Jahanshad N, Ye J, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Front Neurosci. 2015 Jul 24;9:257. doi: 10.3389/fnins.2015.00257.
Rsu1 regulates ethanol consumption in Drosophila and humans.Publications2015-07-28ENIGMARsu1 regulates ethanol consumption in Drosophila and humans.

Ojelade SA, Jia T, Rodan AR, Chenyang T, Kadrmas JL, Cattrell A, Ruggeri B, Charoen P, Lemaitre H, Banaschewski T, Büchel C, Bokde AL, Carvalho F, Conrod PJ, Flor H, Frouin V, Gallinat J, Garavan H, Gowland PA, Heinz A, Ittermann B, Lathrop M, Lubbe S, Martinot JL, Paus T, Smolka MN, Spanagel R, O'Reilly PF, Laitinen J, Veijola JM, Feng J, Desrivières S, Jarvelin MR, IMAGEN Consortium., Schumann G, Rothenfluh A.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4085-93. doi: 10.1073/pnas.1417222112.
External validation of a publicly available computer assisted diagnostic tool for mammographic mass lesions with two high prevalence research datasets.Publications2015-08-01CPCPExternal validation of a publicly available computer assisted diagnostic tool for mammographic mass lesions with two high prevalence research datasets.

Benndorf M, Burnside ES, Herda C, Langer M, Kotter E.

Med Phys. 2015 Aug;42(8):4987-96. doi: 10.1118/1.4927260.
TOPTRAC: Topical Trajectory Pattern Mining.Publications2015-08-01KnowEnGTOPTRAC: Topical Trajectory Pattern Mining.

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KDD. 2015 Aug;2015:587-596. doi: 10.1145/2783258.2783342.
DataSpread: Unifying Databases and Spreadsheets.Publications2015-08-01KnowEnGDataSpread: Unifying Databases and Spreadsheets.

Bendre M, Sun B, Zhang D, Zhou X, Chang KC, Parameswaran A.

Proceedings VLDB Endowment. 2015 Aug;8(12):2000-2003. pmid: 26900487.
Debiasing Crowdsourced Batches.Publications2015-08-01KnowEnGDebiasing Crowdsourced Batches.

Zhuang H, Parameswaran A, Roth D, Han J.

KDD. 2015 Aug;2015:1593-1602. doi: 10.1145/2783258.2783316.
Network Lasso: Clustering and Optimization in Large Graphs.Publications2015-08-01MobilizeNetwork Lasso: Clustering and Optimization in Large Graphs.

Hallac D, Leskovec J, Boyd S.

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Mindtagger: A Demonstration of Data Labeling in Knowledge Base Construction.Publications2015-08-01MobilizeMindtagger: A Demonstration of Data Labeling in Knowledge Base Construction.

Shin J, Ré C, Cafarella M.

Proceedings VLDB Endowment. 2015 Aug;8(12):1920-1923. doi: 10.14778/2824032.2824101.
Rich club analysis in the Alzheimer's disease connectome reveals a relatively undisturbed structural core network.Publications2015-08-01ENIGMARich club analysis in the Alzheimer's disease connectome reveals a relatively undisturbed structural core network.

Daianu M, Jahanshad N, Nir TM, Jack CR Jr, Weiner MW, Bernstein MA, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Hum Brain Mapp. 2015 Aug;36(8):3087-103. doi: 10.1002/hbm.22830.
Human paraoxonase-1 (PON1): Gene structure and expression, promiscuous activities and multiple physiological roles.Publications2015-08-01HeartBD2KHuman paraoxonase-1 (PON1): Gene structure and expression, promiscuous activities and multiple physiological roles.

Mackness M, Mackness B.

Gene. 2015 Aug 1;567(1):12-21. doi: 10.1016/j.gene.2015.04.088.
Smart Drill-Down: A New Data Exploration Operator.Publications2015-08-01KnowEnGSmart Drill-Down: A New Data Exploration Operator.

Joglekar M, Garcia-Molina H, Parameswaran A.

Proceedings VLDB Endowment. 2015 Aug;8(12):1928-1931. pmid: 26844008.
Collaborative Data Analytics with DataHub.Publications2015-08-01KnowEnGCollaborative Data Analytics with DataHub.

Bhardwaj A, Karger D, Subramanyam H, Deshpande A, Madden S, Wu E, Elmore A, Parameswaran A, Zhang R.

Proceedings VLDB Endowment. 2015 Aug;8(12):1916-1919. pmid: 26844007.
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.Publications2015-08-01BDDSTrans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.

Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164.
ClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering.Publications2015-08-01KnowEnGClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering.

Ren X, El-Kishky A, Wang C, Tao F, Voss CR, Ji H, Han J.

KDD. 2015 Aug;2015:995-1004. doi: 10.1145/2783258.2783362.
On the Discovery of Evolving Truth.Publications2015-08-01KnowEnGOn the Discovery of Evolving Truth.

Li Y, Li Q, Gao J, Su L, Zhao B, Fan W, Han J.

KDD. 2015 Aug;2015:675-684. doi: 10.1145/2783258.2783277.
Automatic Entity Recognition and Typing from Massive Text Corpora: A Phrase and Network Mining Approach.Publications2015-08-01KnowEnGAutomatic Entity Recognition and Typing from Massive Text Corpora: A Phrase and Network Mining Approach.

Ren X, El-Kishky A, Wang C, Han J.

KDD. 2015 Aug;2015:2319-2320. doi: 10.1145/2783258.2789988.
Modeling Truth Existence in Truth Discovery.Publications2015-08-01KnowEnGModeling Truth Existence in Truth Discovery.

Zhi S, Zhao B, Tong W, Gao J, Yu D, Ji H, Han J.

KDD. 2015 Aug;2015:1543-1552. doi: 10.1145/2783258.2783339.
Assembler: Efficient Discovery of Spatial Co-evolving Patterns in Massive Geo-sensory Data.Publications2015-08-01KnowEnGAssembler: Efficient Discovery of Spatial Co-evolving Patterns in Massive Geo-sensory Data.

Zhang C, Zheng Y, Ma X, Han J.

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Towards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach.Publications2015-08-01KnowEnGTowards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach.

Wang C, Liu X, Song Y, Han J.

KDD. 2015 Aug;2015:1225-1234. doi: 10.1145/2783258.2783288.
Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks.Publications2015-08-01KnowEnGIncorporating World Knowledge to Document Clustering via Heterogeneous Information Networks.

Wang C, Song Y, El-Kishky A, Roth D, Zhang M, Han J.

KDD. 2015 Aug;2015:1215-1224. doi: 10.1145/2783258.2783374.
The circular relationship between matrix metalloproteinase-9 and inflammation following myocardial infarction.Publications2015-08-01HeartBD2KThe circular relationship between matrix metalloproteinase-9 and inflammation following myocardial infarction.

Deleon-Pennell KY, Altara R, Yabluchanskiy A, Modesti A, Lindsey ML.

IUBMB Life. 2015 Aug;67(8):611-8. doi: 10.1002/iub.1408.
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.Publications2015-08-15CPCPEBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C.

Bioinformatics. 2015 Aug 15;31(16):2614-22. doi: 10.1093/bioinformatics/btv193.
Predicting the Naturalistic Course of Major Depressive Disorder Using Clinical and Multimodal Neuroimaging Information: A Multivariate Pattern Recognition Study.Publications2015-08-15ENIGMAPredicting the Naturalistic Course of Major Depressive Disorder Using Clinical and Multimodal Neuroimaging Information: A Multivariate Pattern Recognition Study.

Schmaal L, Marquand AF, Rhebergen D, van Tol MJ, Ruhé HG, van der Wee NJ, Veltman DJ, Penninx BW.

Biol Psychiatry. 2015 Aug 15;78(4):278-86. doi: 10.1016/j.biopsych.2014.11.018.
Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.Publications2015-08-28CCDIdentifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.

Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257.
Fast Inbound Top-K Query for Random Walk with Restart.Publications2015-09-01KnowEnGFast Inbound Top-K Query for Random Walk with Restart.

Zhang C, Jiang S, Chen Y, Sun Y, Han J.

Mach Learn Knowl Discov Databases. 2015 Sep;9285:608-624. doi: 10.1007/978-3-319-23525-7_37.
Characterizing Smoking and Drinking Abstinence from Social Media.Publications2015-09-01MD2KCharacterizing Smoking and Drinking Abstinence from Social Media.

Tamersoy A, De Choudhury M, Chau DH.

HT ACM Conf Hypertext Soc Media. 2015 Sep;2015:139-148. doi: 10.1145/2700171.2791247.
Fused Lasso Screening Rules via the Monotonicity of Subdifferentials.Publications2015-09-01ENIGMAFused Lasso Screening Rules via the Monotonicity of Subdifferentials.

Wang J, Fan W, Ye J.

IEEE Trans Pattern Anal Mach Intell. 2015 Sep;37(9):1806-20. doi: 10.1109/TPAMI.2014.2388203.
Multi-resolution statistical analysis of brain connectivity graphs in preclinical Alzheimer's disease.Publications2015-09-01CPCPMulti-resolution statistical analysis of brain connectivity graphs in preclinical Alzheimer's disease.

Kim WH, Adluru N, Chung MK, Okonkwo OC, Johnson SC, B Bendlin B, Singh V.

Neuroimage. 2015 Sep;118:103-17. doi: 10.1016/j.neuroimage.2015.05.050.
CIDER: Enabling Robustness-Power Tradeoffs on a Computational Eyeglass.Publications2015-09-01MD2KCIDER: Enabling Robustness-Power Tradeoffs on a Computational Eyeglass.

Mayberry A, Tun Y, Hu P, Smith-Freedman D, Ganesan D, Marlin B, Salthouse C.

Proc Annu Int Conf Mob Comput Netw. 2015 Sep;2015:400-412. doi: 10.1145/2789168.2790096.
Brain Imaging and Neurodevelopment in HIV-uninfected Thai Children Born to HIV-infected Mothers.Publications2015-09-01ENIGMABrain Imaging and Neurodevelopment in HIV-uninfected Thai Children Born to HIV-infected Mothers.

Jahanshad N, Couture MC, Prasitsuebsai W, Nir TM, Aurpibul L, Thompson PM, Pruksakaew K, Lerdlum S, Visrutaratna P, Catella S, Desai A, Kerr SJ, Puthanakit T, Paul R, Ananworanich J, Valcour VG, SEARCH 012 and PREDICT Study Groups..

Pediatr Infect Dis J. 2015 Sep;34(9):e211-6. doi: 10.1097/INF.0000000000000774.
Genomic structural variants are linked with intellectual disability.Publications2015-09-01ENIGMAGenomic structural variants are linked with intellectual disability.

Bulayeva K, Lesch KP, Bulayev O, Walsh C, Glatt S, Gurgenova F, Omarova J, Berdichevets I, Thompson PM.

J Neural Transm (Vienna). 2015 Sep;122(9):1289-301. doi: 10.1007/s00702-015-1366-8.
puffMarker: A Multi-Sensor Approach for Pinpointing the Timing of First Lapse in Smoking Cessation.Publications2015-09-01MD2KpuffMarker: A Multi-Sensor Approach for Pinpointing the Timing of First Lapse in Smoking Cessation.

Saleheen N, Ali AA, Hossain SM, Sarker H, Chatterjee S, Marlin B, Ertin E, al'Absi M, Kumar S.

Proc ACM Int Conf Ubiquitous Comput. 2015 Sep;2015:999-1010. pmid: 26543927.
Stress: Towards a Gold Standard for Continuous Stress Assessment in the Mobile Environment.Publications2015-09-01MD2KStress: Towards a Gold Standard for Continuous Stress Assessment in the Mobile Environment.

Hovsepian K, al'Absi M, Ertin E, Kamarck T, Nakajima M, Kumar S.

Proc ACM Int Conf Ubiquitous Comput. 2015 Sep;2015:493-504. doi: 10.1145/2750858.2807526.
Robust Classification of Information Networks by Consistent Graph Learning.Publications2015-09-01KnowEnGRobust Classification of Information Networks by Consistent Graph Learning.

Zhi S, Han J, Gu Q.

Mach Learn Knowl Discov Databases. 2015 Sep;9285:752-767. doi: 10.1007/978-3-319-23525-7_46.
Cortisol Reactivity to Stress and Its Association With White Matter Integrity in Adults With Schizophrenia.Publications2015-09-01ENIGMACortisol Reactivity to Stress and Its Association With White Matter Integrity in Adults With Schizophrenia.

Nugent KL, Chiappelli J, Sampath H, Rowland LM, Thangavelu K, Davis B, Du X, Muellerklein F, Daughters S, Kochunov P, Hong LE.

Psychosom Med. 2015 Sep;77(7):733-42. doi: 10.1097/PSY.0000000000000215.
SeeDB: Efficient Data-Driven Visualization Recommendations to Support Visual Analytics.Publications2015-09-01KnowEnGSeeDB: Efficient Data-Driven Visualization Recommendations to Support Visual Analytics.

Vartak M, Rahman S, Madden S, Parameswaran A, Polyzotis N.

Proceedings VLDB Endowment. 2015 Sep;8(13):2182-2193. pmid: 26779379.
Visualization of Time-Series Sensor Data to Inform the Design of Just-In-Time Adaptive Stress Interventions.Publications2015-09-01MD2KVisualization of Time-Series Sensor Data to Inform the Design of Just-In-Time Adaptive Stress Interventions.

Sharmin M, Raij A, Epstien D, Nahum-Shani I, Beck JG, Vhaduri S, Preston K, Kumar S.

Proc ACM Int Conf Ubiquitous Comput. 2015 Sep;2015:505-516. pmid: 26539566.
CAreDroid: Adaptation Framework for Android Context-Aware Applications.Publications2015-09-01MD2KCAreDroid: Adaptation Framework for Android Context-Aware Applications.

Elmalaki S, Wanner L, Srivastava M.

Proc Annu Int Conf Mob Comput Netw. 2015 Sep;2015:386-399. doi: 10.1145/2789168.2790108.
Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment.Publications2015-09-01BDDSStructural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment.

Moon SW, Dinov ID, Hobel S, Zamanyan A, Choi YC, Shi R, Thompson PM, Toga AW, Alzheimer's Disease Neuroimaging Initiative..

J Neuroimaging. 2015 Sep-Oct;25(5):728-37. doi: 10.1111/jon.12252.
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.Publications2015-09-04BDDSState of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL.

J Proteome Res. 2015 Sep 4;14(9):3461-73. doi: 10.1021/acs.jproteome.5b00500.
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.Publications2015-09-04BDDSMetrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.

J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499.
Atrial natriuretic peptide in cardiovascular biology and disease (NPPA).Publications2015-09-10HeartBD2KAtrial natriuretic peptide in cardiovascular biology and disease (NPPA).

Song W, Wang H, Wu Q.

Gene. 2015 Sep 10;569(1):1-6. doi: 10.1016/j.gene.2015.06.029.
Functions of myosin light chain-2 (MYL2) in cardiac muscle and disease.Publications2015-09-10HeartBD2KFunctions of myosin light chain-2 (MYL2) in cardiac muscle and disease.

Sheikh F, Lyon RC, Chen J.

Gene. 2015 Sep 10;569(1):14-20. doi: 10.1016/j.gene.2015.06.027.
An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin.Publications2015-09-14LINCS-DCICAn Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin.

Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, Mok KW, Heitman NJ, Clavel C, Ma'ayan A, Rendl M.

Dev Cell. 2015 Sep 14;34(5):577-91. doi: 10.1016/j.devcel.2015.06.023.
Similar Subgroups Based on Cognitive Performance Parse Heterogeneity in Adults With ADHD and Healthy Controls.Publications2015-09-14ENIGMASimilar Subgroups Based on Cognitive Performance Parse Heterogeneity in Adults With ADHD and Healthy Controls.

Mostert JC, Hoogman M, Onnink AM, van Rooij D, von Rhein D, van Hulzen KJ, Dammers J, Kan CC, Buitelaar JK, Norris DG, Franke B.

J Atten Disord. 2015 Sep 14;:. doi: 10.1177/1087054715602332.
The KCNE2 K⁺ channel regulatory subunit: Ubiquitous influence, complex pathobiology.Publications2015-09-15HeartBD2KThe KCNE2 K⁺ channel regulatory subunit: Ubiquitous influence, complex pathobiology.

Abbott GW.

Gene. 2015 Sep 15;569(2):162-72. doi: 10.1016/j.gene.2015.06.061.
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.Publications2015-09-15LINCS-DCICGEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A.

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297.
Trans-species learning of cellular signaling systems with bimodal deep belief networks.Publications2015-09-15CCDTrans-species learning of cellular signaling systems with bimodal deep belief networks.

Chen L, Cai C, Chen V, Lu X.

Bioinformatics. 2015 Sep 15;31(18):3008-15. doi: 10.1093/bioinformatics/btv315.
Backward multiple imputation estimation of the conditional lifetime expectancy function with application to censored human longevity data.Publications2015-09-29CPCPBackward multiple imputation estimation of the conditional lifetime expectancy function with application to censored human longevity data.

Kong J, Klein BE, Klein R, Wahba G.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12069-74. doi: 10.1073/pnas.1512237112.
Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis.Publications2015-09-30CCDInterplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis.

Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y.

Nat Commun. 2015 Sep 30;6:8419. doi: 10.1038/ncomms9419.
Perfusion shift from white to gray matter may account for processing speed deficits in schizophrenia.Publications2015-10-01ENIGMAPerfusion shift from white to gray matter may account for processing speed deficits in schizophrenia.

Wright SN, Hong LE, Winkler AM, Chiappelli J, Nugent K, Muellerklein F, Du X, Rowland LM, Wang DJ, Kochunov P.

Hum Brain Mapp. 2015 Oct;36(10):3793-804. doi: 10.1002/hbm.22878.
Carriers of a common variant in the dopamine transporter gene have greater dementia risk, cognitive decline, and faster ventricular expansion.Publications2015-10-01ENIGMACarriers of a common variant in the dopamine transporter gene have greater dementia risk, cognitive decline, and faster ventricular expansion.

Roussotte FF, Gutman BA, Hibar DP, Madsen SK, Narr KL, Thompson PM, Alzheimer's Disease Neuroimaging Initiative (ADNI)..

Alzheimers Dement. 2015 Oct;11(10):1153-62. doi: 10.1016/j.jalz.2014.10.011.
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.Publications2015-10-01LINCS-DCICPublisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.

Rouillard AD, Wang Z, Ma'ayan A.

Comput Biol Chem. 2015 Oct;58:104-19. doi: 10.1016/j.compbiolchem.2015.06.003.
What Is Going on Inside the Arrows? Discovering the Hidden Springs in Causal Models.Publications2015-10-01CCDWhat Is Going on Inside the Arrows? Discovering the Hidden Springs in Causal Models.

Murray-Watters A, Glymour C.

Philos Sci. 2015 Oct;82(4):556-586. doi: 10.1086/682962.
The Matchmaker Exchange: a platform for rare disease gene discovery.Publications2015-10-01BDTGThe Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL.

Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.
Development of the human fetal hippocampal formation during early second trimester.Publications2015-10-01BDDSDevelopment of the human fetal hippocampal formation during early second trimester.

Ge X, Shi Y, Li J, Zhang Z, Lin X, Zhan J, Ge H, Xu J, Yu Q, Leng Y, Teng G, Feng L, Meng H, Tang Y, Zang F, Toga AW, Liu S.

Neuroimage. 2015 Oct 1;119:33-43. doi: 10.1016/j.neuroimage.2015.06.055.
Edge-Centered DTI Connectivity Analysis: Application to Schizophrenia.Publications2015-10-01ENIGMAEdge-Centered DTI Connectivity Analysis: Application to Schizophrenia.

Herskovits EH, Hong LE, Kochunov P, Sampath H, Chen R.

Neuroinformatics. 2015 Oct;13(4):501-9. doi: 10.1007/s12021-015-9273-6.
Developing a utility decision framework to evaluate predictive models in breast cancer risk estimation.Publications2015-10-01CPCPDeveloping a utility decision framework to evaluate predictive models in breast cancer risk estimation.

Wu Y, Abbey CK, Chen X, Liu J, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES.

J Med Imaging (Bellingham). 2015 Oct;2(4):041005. doi: 10.1117/1.JMI.2.4.041005.
Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data.Publications2015-10-01CPCPPrediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data.

Guo W, Li H, Zhu Y, Lan L, Yang S, Drukker K, Morris E, Burnside E, Whitman G, Giger ML, Ji Y, Tcga Breast Phenotype Research Group.

J Med Imaging (Bellingham). 2015 Oct;2(4):041007. doi: 10.1117/1.JMI.2.4.041007.
Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis.Publications2015-10-01LINCS-DCICMorphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis.

Stockton SD Jr, Gomes I, Liu T, Moraje C, Hipólito L, Jones MR, Ma'ayan A, Morón JA, Li H, Devi LA.

Mol Cell Proteomics. 2015 Oct;14(10):2564-76. doi: 10.1074/mcp.M115.047977.
Mapping abnormal subcortical brain morphometry in an elderly HIV+ cohort.Publications2015-10-08ENIGMAMapping abnormal subcortical brain morphometry in an elderly HIV+ cohort.

Wade BS, Valcour VG, Wendelken-Riegelhaupt L, Esmaeili-Firidouni P, Joshi SH, Gutman BA, Thompson PM.

Neuroimage Clin. 2015 Oct 8;9:564-73. doi: 10.1016/j.nicl.2015.10.006.
A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.Publications2015-10-09LINCS-DCICA Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

Liang R, Campreciós G, Kou Y, McGrath K, Nowak R, Catherman S, Bigarella CL, Rimmelé P, Zhang X, Gnanapragasam MN, Bieker JJ, Papatsenko D, Ma'ayan A, Bresnick E, Fowler V, Palis J, Ghaffari S.

PLoS Genet. 2015 Oct 9;11(10):e1005526. doi: 10.1371/journal.pgen.1005526.
A predictive modeling approach for cell line-specific long-range regulatory interactions.Publications2015-10-15CPCPA predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865.
atSNP: transcription factor binding affinity testing for regulatory SNP detection.Publications2015-10-15CPCPatSNP: transcription factor binding affinity testing for regulatory SNP detection.

Zuo C, Shin S, Keleş S.

Bioinformatics. 2015 Oct 15;31(20):3353-5. doi: 10.1093/bioinformatics/btv328.
MinION Analysis and Reference Consortium: Phase 1 data release and analysis.Publications2015-10-15BDTGMinION Analysis and Reference Consortium: Phase 1 data release and analysis.

Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE, MinION Analysis and Reference Consortium..

F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1.
Neurocognitive Deficits in Attention-Deficit/Hyperactivity Disorder With and Without Comorbid Oppositional Defiant Disorder.Publications2015-10-20ENIGMANeurocognitive Deficits in Attention-Deficit/Hyperactivity Disorder With and Without Comorbid Oppositional Defiant Disorder.

Noordermeer SD, Luman M, Buitelaar JK, Hartman CA, Hoekstra PJ, Franke B, Faraone SV, Heslenfeld DJ, Oosterlaan J.

J Atten Disord. 2015 Oct 20;:. doi: 10.1177/1087054715606216.
Structure and function of cardiac troponin C (TNNC1): Implications for heart failure, cardiomyopathies, and troponin modulating drugs.Publications2015-10-25HeartBD2KStructure and function of cardiac troponin C (TNNC1): Implications for heart failure, cardiomyopathies, and troponin modulating drugs.

Li MX, Hwang PM.

Gene. 2015 Oct 25;571(2):153-66. doi: 10.1016/j.gene.2015.07.074.
The NIH BD2K center for big data in translational genomics.Publications2015-11-01BDTGThe NIH BD2K center for big data in translational genomics.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047.
The FHL2 regulation in the transcriptional circuitry of human cancers.Publications2015-11-01HeartBD2KThe FHL2 regulation in the transcriptional circuitry of human cancers.

Cao CY, Mok SW, Cheng VW, Tsui SK.

Gene. 2015 Nov 1;572(1):1-7. doi: 10.1016/j.gene.2015.07.043.
Insight: Semantic Provenance and Analysis Platform for Multi-center Neurology Healthcare Research.Publications2015-11-01Data ProvenanceInsight: Semantic Provenance and Analysis Platform for Multi-center Neurology Healthcare Research.

Ramesh P, Wei A, Welter E, Bamps Y, Stoll S, Bukach A, Sajatovic M, Sahoo SS.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:731-736. doi: 10.1109/BIBM.2015.7359776.
Big biomedical data as the key resource for discovery science.Publications2015-11-01BDDSBig biomedical data as the key resource for discovery science.

Toga AW, Foster I, Kesselman C, Madduri R, Chard K, Deutsch EW, Price ND, Glusman G, Heavner BD, Dinov ID, Ames J, Van Horn J, Kramer R, Hood L.

J Am Med Inform Assoc. 2015 Nov;22(6):1126-31. doi: 10.1093/jamia/ocv077.
The mobilize center: an NIH big data to knowledge center to advance human movement research and improve mobility.Publications2015-11-01MobilizeThe mobilize center: an NIH big data to knowledge center to advance human movement research and improve mobility.

Ku JP, Hicks JL, Hastie T, Leskovec J, Ré C, Delp SL.

J Am Med Inform Assoc. 2015 Nov;22(6):1120-5. doi: 10.1093/jamia/ocv071.
Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching.Publications2015-11-01HeartBD2KPivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching.

Yates JR 3rd.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1804-13. doi: 10.1007/s13361-015-1220-0.
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.Publications2015-11-01HeartBD2KFrom raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.

Lavallée-Adam M, Park SK, Martínez-Bartolomé S, He L, Yates JR 3rd.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1820-6. doi: 10.1007/s13361-015-1161-7.
Surpassing Humans and Computers with JellyBean: Crowd-Vision-Hybrid Counting Algorithms.Publications2015-11-01KnowEnGSurpassing Humans and Computers with JellyBean: Crowd-Vision-Hybrid Counting Algorithms.

Sarma AD, Jain A, Nandi A, Parameswaran A, Widom J.

Proc AAAI Conf Hum Comput Crowdsourc. 2015 Nov;2015:178-187. pmid: 26844304.
Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.Publications2015-11-01LINCS-DCICPrincipal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma'ayan A.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:256-262. doi: 10.1109/BIBM.2015.7359689.
The center for causal discovery of biomedical knowledge from big data.Publications2015-11-01CCDThe center for causal discovery of biomedical knowledge from big data.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team..

J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059.
The center for expanded data annotation and retrieval.Publications2015-11-01CEDARThe center for expanded data annotation and retrieval.

Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA, CEDAR team..

J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi: 10.1093/jamia/ocv048.
Mining Multi-Aspect Reflection of News Events in Twitter: Discovery, Linking and Presentation.Publications2015-11-01KnowEnGMining Multi-Aspect Reflection of News Events in Twitter: Discovery, Linking and Presentation.

Wang J, Tong W, Yu H, Li M, Ma X, Cai H, Hanratty T, Han J.

Proc IEEE Int Conf Data Min. 2015 Nov;2015:429-438. doi: 10.1109/ICDM.2015.112.
KnowSim: A Document Similarity Measure on Structured Heterogeneous Information Networks.Publications2015-11-01KnowEnGKnowSim: A Document Similarity Measure on Structured Heterogeneous Information Networks.

Wang C, Song Y, Li H, Zhang M, Han J.

Proc IEEE Int Conf Data Min. 2015 Nov;2015:1015-1020. doi: 10.1109/ICDM.2015.131.
KnowEnG: a knowledge engine for genomics.Publications2015-11-01KnowEnGKnowEnG: a knowledge engine for genomics.

Sinha S, Song J, Weinshilboum R, Jongeneel V, Han J.

J Am Med Inform Assoc. 2015 Nov;22(6):1115-9. doi: 10.1093/jamia/ocv090.
Titian: Data Provenance Support in Spark.Publications2015-11-01MD2KTitian: Data Provenance Support in Spark.

Interlandi M, Shah K, Tetali SD, Gulzar MA, Yoo S, Kim M, Millstein T, Condie T.

Proceedings VLDB Endowment. 2015 Nov;9(3):216-227. pmid: 26726305.
A Pilot Randomized Trial of Text-Messaging for Symptom Awareness and Diabetes Knowledge in Adolescents With Type 1 Diabetes.Publications2015-11-01MD2KA Pilot Randomized Trial of Text-Messaging for Symptom Awareness and Diabetes Knowledge in Adolescents With Type 1 Diabetes.

Han Y, Faulkner MS, Fritz H, Fadoju D, Muir A, Abowd GD, Head L, Arriaga RI.

J Pediatr Nurs. 2015 Nov-Dec;30(6):850-61. doi: 10.1016/j.pedn.2015.02.002.
Center of excellence for mobile sensor data-to-knowledge (MD2K).Publications2015-11-01MD2KCenter of excellence for mobile sensor data-to-knowledge (MD2K).

Kumar S, Abowd GD, Abraham WT, al'Absi M, Beck JG, Chau DH, Condie T, Conroy DE, Ertin E, Estrin D, Ganesan D, Lam C, Marlin B, Marsh CB, Murphy SA, Nahum-Shani I, Patrick K, Rehg JM, Sharmin M, Shetty V, Sim I, Spring B, Srivastava M, Wetter DW.

J Am Med Inform Assoc. 2015 Nov;22(6):1137-42. doi: 10.1093/jamia/ocv056.
Robust Multi-Network Clustering via Joint Cross-Domain Cluster Alignment.Publications2015-11-01HeartBD2KRobust Multi-Network Clustering via Joint Cross-Domain Cluster Alignment.

Liu R, Cheng W, Tong H, Wang W, Zhang X.

Proc IEEE Int Conf Data Min. 2015 Nov;2015:291-300. doi: 10.1109/ICDM.2015.13.
Optimal mass transport for shape matching and comparison.Publications2015-11-01ENIGMAOptimal mass transport for shape matching and comparison.

Su Z, Wang Y, Shi R, Zeng W, Sun J, Luo F, Gu X.

IEEE Trans Pattern Anal Mach Intell. 2015 Nov;37(11):2246-59. doi: 10.1109/TPAMI.2015.2408346.
Cognitive heterogeneity in adult attention deficit/hyperactivity disorder: A systematic analysis of neuropsychological measurements.Publications2015-11-01ENIGMACognitive heterogeneity in adult attention deficit/hyperactivity disorder: A systematic analysis of neuropsychological measurements.

Mostert JC, Onnink AM, Klein M, Dammers J, Harneit A, Schulten T, van Hulzen KJ, Kan CC, Slaats-Willemse D, Buitelaar JK, Franke B, Hoogman M.

Eur Neuropsychopharmacol. 2015 Nov;25(11):2062-74. doi: 10.1016/j.euroneuro.2015.08.010.
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.Publications2015-11-03HeartBD2KProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.

Xu T, Park SK, Venable JD, Wohlschlegel JA, Diedrich JK, Cociorva D, Lu B, Liao L, Hewel J, Han X, Wong CC, Fonslow B, Delahunty C, Gao Y, Shah H, Yates JR 3rd.

J Proteomics. 2015 Nov 3;129:16-24. doi: 10.1016/j.jprot.2015.07.001.
CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks.Publications2015-11-11LINCS-DCICCyNetworkBMA: a Cytoscape app for inferring gene regulatory networks.

Fronczuk M, Raftery AE, Yeung KY.

Source Code Biol Med. 2015 Nov 11;10:11. doi: 10.1186/s13029-015-0043-5.
Canonical, stable, general mapping using context schemes.Publications2015-11-15BDTGCanonical, stable, general mapping using context schemes.

Novak AM, Rosen Y, Haussler D, Paten B.

Bioinformatics. 2015 Nov 15;31(22):3569-76. doi: 10.1093/bioinformatics/btv435.
Large-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4.Publications2015-11-24LINCS-DCICLarge-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4.

Allen BK, Mehta S, Ember SW, Schonbrunn E, Ayad N, Schürer SC.

Sci Rep. 2015 Nov 24;5:16924. doi: 10.1038/srep16924.
Assessing incremental value of biomarkers with multi-phase nested case-control studies.Publications2015-12-01PIC-SUREAssessing incremental value of biomarkers with multi-phase nested case-control studies.

Zhou QM, Zheng Y, Chibnik LB, Karlson EW, Cai T.

Biometrics. 2015 Dec;71(4):1139-49. doi: 10.1111/biom.12344.
Cerebral Amyloid and Hypertension are Independently Associated with White Matter Lesions in Elderly.Publications2015-12-01ENIGMACerebral Amyloid and Hypertension are Independently Associated with White Matter Lesions in Elderly.

Scott JA, Braskie MN, Tosun D, Thompson PM, Weiner M, DeCarli C, Carmichael OT, Alzheimer’s Disease Neuroimaging Initiative..

Front Aging Neurosci. 2015 Dec 1;7:221. doi: 10.3389/fnagi.2015.00221.
Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width.Publications2015-12-01MobilizeRapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width.

De Sa C, Zhang C, Olukotun K, Ré C.

Adv Neural Inf Process Syst. 2015 Dec;28:3079-3087. pmid: 27279724.
Improved EEG Event Classification Using Differential Energy.Publications2015-12-01Data WranglingImproved EEG Event Classification Using Differential Energy.

Harati A, Golmohammadi M, Lopez S, Obeid I, Picone J.

IEEE Signal Process Med Biol Symp. 2015 Dec;2015:. doi: 10.1109/SPMB.2015.7405421.
On Statistical Analysis of Neuroimages with Imperfect Registration.Publications2015-12-01CPCPOn Statistical Analysis of Neuroimages with Imperfect Registration.

Kim WH, Ravi SN, Johnson SC, Okonkwo OC, Singh V.

Proc IEEE Int Conf Comput Vis. 2015 Dec;2015:666-674. doi: 10.1109/ICCV.2015.83.
Interpolation on the manifold of K component GMMs.Publications2015-12-01CPCPInterpolation on the manifold of K component GMMs.

Kim HJ, Adluru N, Banerjee M, Vemuri BC, Singh V.

Proc IEEE Int Conf Comput Vis. 2015 Dec;2015:2884-2892. doi: 10.1109/ICCV.2015.330.
Rate-Agnostic (Causal) Structure Learning.Publications2015-12-01CCDRate-Agnostic (Causal) Structure Learning.

Plis S, Danks D, Freeman C, Calhoun V.

Adv Neural Inf Process Syst. 2015 Dec;28:3303-3311. pmid: 27182188.
Automated Identification of Abnormal Adult EEGs.Publications2015-12-01Data WranglingAutomated Identification of Abnormal Adult EEGs.

López S, Suarez G, Jungreis D, Obeid I, Picone J.

IEEE Signal Process Med Biol Symp. 2015 Dec;2015:. doi: 10.1109/SPMB.2015.7405423.
ERC analysis: web-based inference of gene function via evolutionary rate covariation.Publications2015-12-01CCDERC analysis: web-based inference of gene function via evolutionary rate covariation.

Wolfe NW, Clark NL.

Bioinformatics. 2015 Dec 1;31(23):3835-7. doi: 10.1093/bioinformatics/btv454.
The cardiac sodium channel gene SCN5A and its gene product NaV1.5: Role in physiology and pathophysiology.Publications2015-12-01HeartBD2KThe cardiac sodium channel gene SCN5A and its gene product NaV1.5: Role in physiology and pathophysiology.

Veerman CC, Wilde AA, Lodder EM.

Gene. 2015 Dec 1;573(2):177-87. doi: 10.1016/j.gene.2015.08.062.
Improved initialisation of model-based clustering using Gaussian hierarchical partitions.Publications2015-12-01LINCS-DCICImproved initialisation of model-based clustering using Gaussian hierarchical partitions.

Scrucca L, Raftery AE.

Adv Data Anal Classif. 2015 Dec;9(4):447-460. doi: 10.1007/s11634-015-0220-z.
Building health behavior models to guide the development of just-in-time adaptive interventions: A pragmatic framework.Publications2015-12-01MD2KBuilding health behavior models to guide the development of just-in-time adaptive interventions: A pragmatic framework.

Nahum-Shani I, Hekler EB, Spruijt-Metz D.

Health Psychol. 2015 Dec;34S:1209-19. doi: 10.1037/hea0000306.
Microrandomized trials: An experimental design for developing just-in-time adaptive interventions.Publications2015-12-01MD2KMicrorandomized trials: An experimental design for developing just-in-time adaptive interventions.

Klasnja P, Hekler EB, Shiffman S, Boruvka A, Almirall D, Tewari A, Murphy SA.

Health Psychol. 2015 Dec;34S:1220-8. doi: 10.1037/hea0000305.
Randomised trials for the Fitbit generation.Publications2015-12-01MD2KRandomised trials for the Fitbit generation.

Dempsey W, Liao P, Klasnja P, Nahum-Shani I, Murphy SA.

Signif (Oxf). 2015 Dec 1;12(6):20-23. doi: 10.1111/j.1740-9713.2015.00863.x.
A Projection free method for Generalized Eigenvalue Problem with a nonsmooth Regularizer.Publications2015-12-01CPCPA Projection free method for Generalized Eigenvalue Problem with a nonsmooth Regularizer.

Hwang SJ, Collins MD, Ravi SN, Ithapu VK, Adluru N, Johnson SC, Singh V.

Proc IEEE Int Conf Comput Vis. 2015 Dec;2015:1841-1849. doi: 10.1109/ICCV.2015.214.
Risk of Type 2 Diabetes Is Lower in US Adults Taking Chromium-Containing Supplements.Publications2015-12-01PIC-SURERisk of Type 2 Diabetes Is Lower in US Adults Taking Chromium-Containing Supplements.

McIver DJ, Grizales AM, Brownstein JS, Goldfine AB.

J Nutr. 2015 Dec;145(12):2675-82. doi: 10.3945/jn.115.214569.
Cannabis use in early adolescence: Evidence of amygdala hypersensitivity to signals of threat.Publications2015-12-01ENIGMACannabis use in early adolescence: Evidence of amygdala hypersensitivity to signals of threat.

Spechler PA, Orr CA, Chaarani B, Kan KJ, Mackey S, Morton A, Snowe MP, Hudson KE, Althoff RR, Higgins ST, Cattrell A, Flor H, Nees F, Banaschewski T, Bokde AL, Whelan R, Büchel C, Bromberg U, Conrod P, Frouin V, Papadopoulos D, Gallinat J, Heinz A, Walter H, Ittermann B, Gowland P, Paus T, Poustka L, Martinot JL, Artiges E, Smolka MN, Schumann G, Garavan H, IMAGEN Consortium..

Dev Cogn Neurosci. 2015 Dec;16:63-70. doi: 10.1016/j.dcn.2015.08.007.
Taming the Wild: A Unified Analysis of Hogwild!-Style Algorithms.Publications2015-12-01MobilizeTaming the Wild: A Unified Analysis of Hogwild!-Style Algorithms.

De Sa C, Zhang C, Olukotun K, Ré C.

Adv Neural Inf Process Syst. 2015 Dec;28:2656-2664. pmid: 27330264.
Adaptability of protein structures to enable functional interactions and evolutionary implications.Publications2015-12-01CCDAdaptability of protein structures to enable functional interactions and evolutionary implications.

Haliloglu T, Bahar I.

Curr Opin Struct Biol. 2015 Dec;35:17-23. doi: 10.1016/j.sbi.2015.07.007.
Deviant white matter structure in adults with attention-deficit/hyperactivity disorder points to aberrant myelination and affects neuropsychological performance.Publications2015-12-03ENIGMADeviant white matter structure in adults with attention-deficit/hyperactivity disorder points to aberrant myelination and affects neuropsychological performance.

Onnink AM, Zwiers MP, Hoogman M, Mostert JC, Dammers J, Kan CC, Vasquez AA, Schene AH, Buitelaar J, Franke B.

Prog Neuropsychopharmacol Biol Psychiatry. 2015 Dec 3;63:14-22. doi: 10.1016/j.pnpbp.2015.04.008.
Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism.Publications2015-12-15CPCPGenome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism.

Papale LA, Zhang Q, Li S, Chen K, Keleş S, Alisch RS.

Hum Mol Genet. 2015 Dec 15;24(24):7121-31. doi: 10.1093/hmg/ddv411.
Cracking the brain's genetic code.Publications2015-12-15ENIGMACracking the brain's genetic code.

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Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15269-70. doi: 10.1073/pnas.1520702112.
Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses.Publications2015-12-15CEDARIntegrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses.

Andres-Terre M, McGuire HM, Pouliot Y, Bongen E, Sweeney TE, Tato CM, Khatri P.

Immunity. 2015 Dec 15;43(6):1199-211. doi: 10.1016/j.immuni.2015.11.003.
Multi-Shell Hybrid Diffusion Imaging (HYDI) at 7 Tesla in TgF344-AD Transgenic Alzheimer Rats.Publications2015-12-18ENIGMAMulti-Shell Hybrid Diffusion Imaging (HYDI) at 7 Tesla in TgF344-AD Transgenic Alzheimer Rats.

Daianu M, Jacobs RE, Weitz TM, Town TC, Thompson PM.

PLoS One. 2015 Dec 18;10(12):e0145205. doi: 10.1371/journal.pone.0145205.
Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures.Publications2015-12-21PIC-SUREGene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures.

Prilutsky D, Kho AT, Palmer NP, Bhakar AL, Smedemark-Margulies N, Kong SW, Margulies DM, Bear MF, Kohane IS.

Mol Autism. 2015 Dec 21;6:66. doi: 10.1186/s13229-015-0061-9.
Classification of follicular lymphoma: the effect of computer aid on pathologists grading.Publications2015-12-30Data CompressionClassification of follicular lymphoma: the effect of computer aid on pathologists grading.

Fauzi MF, Pennell M, Sahiner B, Chen W, Shana'ah A, Hemminger J, Gru A, Kurt H, Losos M, Joehlin-Price A, Kavran C, Smith SM, Nowacki N, Mansor S, Lozanski G, Gurcan MN.

BMC Med Inform Decis Mak. 2015 Dec 30;15:115. doi: 10.1186/s12911-015-0235-6.
Causal Clustering for 1-Factor Measurement Models.Publications2016-01-01CCDCausal Clustering for 1-Factor Measurement Models.

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KDD. 2016;2016:1655-1664. doi: 10.1145/2939672.2939838.
Thalamic alterations in preterm neonates and their relation to ventral striatum disturbances revealed by a combined shape and pose analysis.Publications2016-01-01ENIGMAThalamic alterations in preterm neonates and their relation to ventral striatum disturbances revealed by a combined shape and pose analysis.

Lao Y, Wang Y, Shi J, Ceschin R, Nelson MD, Panigrahy A, Leporé N.

Brain Struct Funct. 2016 Jan;221(1):487-506. doi: 10.1007/s00429-014-0921-7.
Large-scale extraction of gene interactions from full-text literature using DeepDive.Publications2016-01-01MobilizeLarge-scale extraction of gene interactions from full-text literature using DeepDive.

Mallory EK, Zhang C, Ré C, Altman RB.

Bioinformatics. 2016 Jan 1;32(1):106-13. doi: 10.1093/bioinformatics/btv476.
MRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials.Publications2016-01-01BDDS, ENIGMAMRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials.

Hua X, Ching CR, Mezher A, Gutman BA, Hibar DP, Bhatt P, Leow AD, Jack CR Jr, Bernstein MA, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Neurobiol Aging. 2016 Jan;37:26-37. doi: 10.1016/j.neurobiolaging.2015.09.018.
Comprehensive analysis of sequences of a protein switch.Publications2016-01-01LINCS-DCICComprehensive analysis of sequences of a protein switch.

Chen SH, Meller J, Elber R.

Protein Sci. 2016 Jan;25(1):135-46. doi: 10.1002/pro.2723.
Sharing the wealth: Neuroimaging data repositories.Publications2016-01-01BDDSSharing the wealth: Neuroimaging data repositories.

Eickhoff S, Nichols TE, Van Horn JD, Turner JA.

Neuroimage. 2016 Jan 1;124(Pt B):1065-8. doi: 10.1016/j.neuroimage.2015.10.079.
EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY.Publications2016-01-01CEDAREMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY.

Haynes WA, Vallania F, Liu C, Bongen E, Tomczak A, Andres-Terrè M, Lofgren S, Tam A, Deisseroth CA, Li MD, Sweeney TE, Khatri P.

Pac Symp Biocomput. 2016;22:144-153. pmid: 27896970.
DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES.Publications2016-01-01BDTGDATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES.

Yang S, Cline M, Zhang C, Paten B, Lincoln SE.

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The Global Alzheimer's Association Interactive Network.Publications2016-01-01BDDSThe Global Alzheimer's Association Interactive Network.

Toga AW, Neu SC, Bhatt P, Crawford KL, Ashish N.

Alzheimers Dement. 2016 Jan;12(1):49-54. doi: 10.1016/j.jalz.2015.06.1896.
Bisphenol A Disrupts HNF4α-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats.Publications2016-01-01LINCS-DCICBisphenol A Disrupts HNF4α-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats.

Lam HM, Ho SM, Chen J, Medvedovic M, Tam NN.

Endocrinology. 2016 Jan;157(1):207-19. doi: 10.1210/en.2015-1363.
Comparing Mammography Abnormality Features to Genetic Variants in the Prediction of Breast Cancer in Women Recommended for Breast Biopsy.Publications2016-01-01CPCPComparing Mammography Abnormality Features to Genetic Variants in the Prediction of Breast Cancer in Women Recommended for Breast Biopsy.

Burnside ES, Liu J, Wu Y, Onitilo AA, McCarty CA, Page CD, Peissig PL, Trentham-Dietz A, Kitchner T, Fan J, Yuan M.

Acad Radiol. 2016 Jan;23(1):62-9. doi: 10.1016/j.acra.2015.09.007.
PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.Publications2016-01-01KnowEnGPROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.

Wang S, Qu M, Peng J.

Pac Symp Biocomput. 2016;22:27-38. pmid: 27896959.
Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set.Publications2016-01-01CPCPQuantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set.

Li H, Zhu Y, Burnside ES, Huang E, Drukker K, Hoadley KA, Fan C, Conzen SD, Zuley M, Net JM, Sutton E, Whitman GJ, Morris E, Perou CM, Ji Y, Giger ML.

NPJ Breast Cancer. 2016;2:. doi: 10.1038/npjbcancer.2016.12.
Vials: Visualizing Alternative Splicing of Genes.Publications2016-01-01Data VisualizationVials: Visualizing Alternative Splicing of Genes.

Strobelt H, Alsallakh B, Botros J, Peterson B, Borowsky M, Pfister H, Lex A.

IEEE Trans Vis Comput Graph. 2016 Jan;22(1):399-408. doi: 10.1109/TVCG.2015.2467911.
MGH-USC Human Connectome Project datasets with ultra-high b-value diffusion MRI.Publications2016-01-01BDDSMGH-USC Human Connectome Project datasets with ultra-high b-value diffusion MRI.

Fan Q, Witzel T, Nummenmaa A, Van Dijk KR, Van Horn JD, Drews MK, Somerville LH, Sheridan MA, Santillana RM, Snyder J, Hedden T, Shaw EE, Hollinshead MO, Renvall V, Zanzonico R, Keil B, Cauley S, Polimeni JR, Tisdall D, Buckner RL, Wedeen VJ, Wald LL, Toga AW, Rosen BR.

Neuroimage. 2016 Jan 1;124(Pt B):1108-14. doi: 10.1016/j.neuroimage.2015.08.075.
Crowdsourcing in biomedicine: challenges and opportunities.Publications2016-01-01HeartBD2KCrowdsourcing in biomedicine: challenges and opportunities.

Khare R, Good BM, Leaman R, Su AI, Lu Z.

Brief Bioinform. 2016 Jan;17(1):23-32. doi: 10.1093/bib/bbv021.
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.Publications2016-01-01Data WranglingInferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.

Lee E, Ito K, Zhao Y, Schadt EE, Irie HY, Zhu J.

Bioinformatics. 2016 Jan 1;32(1):96-105. doi: 10.1093/bioinformatics/btv531.
Dynamic Model Averaging in Large Model Spaces Using Dynamic Occam's Window.Publications2016-01-01LINCS-DCICDynamic Model Averaging in Large Model Spaces Using Dynamic Occam's Window.

Onorante L, Raftery AE.

Eur Econ Rev. 2016 Jan 1;81:2-14. doi: 10.1016/j.euroecorev.2015.07.013.
Visualizing spatial population structure with estimated effective migration surfaces.Publications2016-01-01Data VisualizationVisualizing spatial population structure with estimated effective migration surfaces.

Petkova D, Novembre J, Stephens M.

Nat Genet. 2016 Jan;48(1):94-100. doi: 10.1038/ng.3464.
Causal discovery and inference: concepts and recent methodological advances.Publications2016-01-01CCDCausal discovery and inference: concepts and recent methodological advances.

Spirtes P, Zhang K.

Appl Inform (Berl). 2016;3:3. doi: 10.1186/s40535-016-0018-x.
Genetic imaging consortium for addiction medicine: From neuroimaging to genes.Publications2016-01-01ENIGMAGenetic imaging consortium for addiction medicine: From neuroimaging to genes.

Mackey S, Kan KJ, Chaarani B, Alia-Klein N, Batalla A, Brooks S, Cousijn J, Dagher A, de Ruiter M, Desrivieres S, Feldstein Ewing SW, Goldstein RZ, Goudriaan AE, Heitzeg MM, Hutchison K, Li CS, London ED, Lorenzetti V, Luijten M, Martin-Santos R, Morales AM, Paulus MP, Paus T, Pearlson G, Schluter R, Momenan R, Schmaal L, Schumann G, Sinha R, Sjoerds Z, Stein DJ, Stein EA, Solowij N, Tapert S, Uhlmann A, Veltman D, van Holst R, Walter H, Wright MJ, Yucel M, Yurgelun-Todd D, Hibar DP, Jahanshad N, Thompson PM, Glahn DC, Garavan H, Conrod P.

Prog Brain Res. 2016;224:203-23. doi: 10.1016/bs.pbr.2015.07.026.
The Image and Data Archive at the Laboratory of Neuro Imaging.Publications2016-01-01BDDSThe Image and Data Archive at the Laboratory of Neuro Imaging.

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Neuroimage. 2016 Jan 1;124(Pt B):1080-3. doi: 10.1016/j.neuroimage.2015.04.067.
Volume and Value of Big Healthcare Data.Publications2016-01-01BDDSVolume and Value of Big Healthcare Data.

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REPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY.Publications2016-01-01PIC-SUREREPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY.

Manrai AK, Wang BL, Patel CJ, Kohane IS.

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Sharing data in the global alzheimer's association interactive network.Publications2016-01-01BDDSSharing data in the global alzheimer's association interactive network.

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Neuroimage. 2016 Jan 1;124(Pt B):1168-74. doi: 10.1016/j.neuroimage.2015.05.082.
The UCSC Genome Browser database: 2016 update.Publications2016-01-04BDTGThe UCSC Genome Browser database: 2016 update.

Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25. doi: 10.1093/nar/gkv1275.
The Reactome pathway Knowledgebase.Publications2016-01-04HeartBD2KThe Reactome pathway Knowledgebase.

Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351.
Head Motion and Inattention/Hyperactivity Share Common Genetic Influences: Implications for fMRI Studies of ADHD.Publications2016-01-08ENIGMAHead Motion and Inattention/Hyperactivity Share Common Genetic Influences: Implications for fMRI Studies of ADHD.

Couvy-Duchesne B, Ebejer JL, Gillespie NA, Duffy DL, Hickie IB, Thompson PM, Martin NG, de Zubicaray GI, McMahon KL, Medland SE, Wright MJ.

PLoS One. 2016 Jan 8;11(1):e0146271. doi: 10.1371/journal.pone.0146271.
Fetal liver hematopoietic stem cell niches associate with portal vessels.Publications2016-01-08LINCS-DCICFetal liver hematopoietic stem cell niches associate with portal vessels.

Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette PS.

Science. 2016 Jan 8;351(6269):176-80. doi: 10.1126/science.aad0084.
Structure and functional roles of Epac2 (Rapgef4).Publications2016-01-10HeartBD2KStructure and functional roles of Epac2 (Rapgef4).

Sugawara K, Shibasaki T, Takahashi H, Seino S.

Gene. 2016 Jan 10;575(2 Pt 3):577-83. doi: 10.1016/j.gene.2015.09.029.
p38 MAP kinases in the heart.Publications2016-01-10HeartBD2Kp38 MAP kinases in the heart.

Yokota T, Wang Y.

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Endothelial nitric oxide synthase: From biochemistry and gene structure to clinical implications of NOS3 polymorphisms.Publications2016-01-10HeartBD2KEndothelial nitric oxide synthase: From biochemistry and gene structure to clinical implications of NOS3 polymorphisms.

Oliveira-Paula GH, Lacchini R, Tanus-Santos JE.

Gene. 2016 Jan 10;575(2 Pt 3):584-99. doi: 10.1016/j.gene.2015.09.061.
A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.Publications2016-01-10BDDSA comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.

Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C.

J Proteomics. 2016 Jan 10;131:122-30. doi: 10.1016/j.jprot.2015.10.019.
The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping.Publications2016-01-13BDDSThe GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping.

Ashish N, Dewan P, Toga AW.

Front Neuroinform. 2016 Jan 13;9:30. doi: 10.3389/fninf.2015.00030.
TNNI1, TNNI2 and TNNI3: Evolution, regulation, and protein structure-function relationships.Publications2016-01-15HeartBD2KTNNI1, TNNI2 and TNNI3: Evolution, regulation, and protein structure-function relationships.

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Gene. 2016 Jan 15;576(1 Pt 3):385-94. doi: 10.1016/j.gene.2015.10.052.
KCNE1 and KCNE3: The yin and yang of voltage-gated K(+) channel regulation.Publications2016-01-15HeartBD2KKCNE1 and KCNE3: The yin and yang of voltage-gated K(+) channel regulation.

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The common genetic influence over processing speed and white matter microstructure: Evidence from the Old Order Amish and Human Connectome Projects.Publications2016-01-15ENIGMAThe common genetic influence over processing speed and white matter microstructure: Evidence from the Old Order Amish and Human Connectome Projects.

Kochunov P, Thompson PM, Winkler A, Morrissey M, Fu M, Coyle TR, Du X, Muellerklein F, Savransky A, Gaudiot C, Sampath H, Eskandar G, Jahanshad N, Patel B, Rowland L, Nichols TE, O'Connell JR, Shuldiner AR, Mitchell BD, Hong LE.

Neuroimage. 2016 Jan 15;125:189-97. doi: 10.1016/j.neuroimage.2015.10.050.
smallWig: parallel compression of RNA-seq WIG files.Publications2016-01-15Data CompressionsmallWig: parallel compression of RNA-seq WIG files.

Wang Z, Weissman T, Milenkovic O.

Bioinformatics. 2016 Jan 15;32(2):173-80. doi: 10.1093/bioinformatics/btv561.
Jagged1 (JAG1): Structure, expression, and disease associations.Publications2016-01-15HeartBD2KJagged1 (JAG1): Structure, expression, and disease associations.

Grochowski CM, Loomes KM, Spinner NB.

Gene. 2016 Jan 15;576(1 Pt 3):381-4. doi: 10.1016/j.gene.2015.10.065.
Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.Publications2016-01-25ENIGMALeveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.

Wang Y, Thompson WK, Schork AJ, Holland D, Chen CH, Bettella F, Desikan RS, Li W, Witoelar A, Zuber V, Devor A, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium., Enhancing Neuro Imaging Genetics through Meta Analysis Consortium., Nöthen MM, Rietschel M, Chen Q, Werge T, Cichon S, Weinberger DR, Djurovic S, O'Donovan M, Visscher PM, Andreassen OA, Dale AM.

PLoS Genet. 2016 Jan 25;12(1):e1005803. doi: 10.1371/journal.pgen.1005803.
The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.Publications2016-02-01BDDSThe Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.

Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E.

Proteomics. 2016 Feb;16(4):634-44. doi: 10.1002/pmic.201500195.
Heritability of complex white matter diffusion traits assessed in a population isolate.Publications2016-02-01ENIGMAHeritability of complex white matter diffusion traits assessed in a population isolate.

Kochunov P, Fu M, Nugent K, Wright SN, Du X, Muellerklein F, Morrissey M, Eskandar G, Shukla DK, Jahanshad N, Thompson PM, Patel B, Postolache TT, Strauss KA, Shuldiner AR, Mitchell BD, Hong LE.

Hum Brain Mapp. 2016 Feb;37(2):525-35. doi: 10.1002/hbm.23047.
Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling.Publications2016-02-01HeartBD2KMatrix metalloproteinases as input and output signals for post-myocardial infarction remodeling.

Lindsey ML, Iyer RP, Jung M, DeLeon-Pennell KY, Ma Y.

J Mol Cell Cardiol. 2016 Feb;91:134-40. doi: 10.1016/j.yjmcc.2015.12.018.
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.Publications2016-02-01Data WranglingFitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

Porebski PJ, Cymborowski M, Pasenkiewicz-Gierula M, Minor W.

Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):266-80. doi: 10.1107/S2059798315024730.
May the fibrosis be with you: Is discoidin domain receptor 2 the receptor we have been looking for?Publications2016-02-01HeartBD2KMay the fibrosis be with you: Is discoidin domain receptor 2 the receptor we have been looking for?

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J Mol Cell Cardiol. 2016 Feb;91:201-3. doi: 10.1016/j.yjmcc.2016.01.006.
Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks.Publications2016-02-01LINCS-DCICModel reduction and parameter estimation of non-linear dynamical biochemical reaction networks.

Sun X, Medvedovic M.

IET Syst Biol. 2016 Feb;10(1):10-6. doi: 10.1049/iet-syb.2015.0034.
Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress.Publications2016-02-01CPCPGenome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress.

Li S, Papale LA, Zhang Q, Madrid A, Chen L, Chopra P, Keleş S, Jin P, Alisch RS.

Neurobiol Dis. 2016 Feb;86:99-108. doi: 10.1016/j.nbd.2015.11.010.
LRP5: A novel anti-inflammatory macrophage marker that positively regulates migration and phagocytosis.Publications2016-02-01HeartBD2KLRP5: A novel anti-inflammatory macrophage marker that positively regulates migration and phagocytosis.

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J Mol Cell Cardiol. 2016 Feb;91:61-2. doi: 10.1016/j.yjmcc.2015.12.027.
The crossroads of inflammation, fibrosis, and arrhythmia following myocardial infarction.Publications2016-02-01HeartBD2KThe crossroads of inflammation, fibrosis, and arrhythmia following myocardial infarction.

Francis Stuart SD, De Jesus NM, Lindsey ML, Ripplinger CM.

J Mol Cell Cardiol. 2016 Feb;91:114-22. doi: 10.1016/j.yjmcc.2015.12.024.
Safeguarding Structural Data Repositories against Bad Apples.Publications2016-02-02Data WranglingSafeguarding Structural Data Repositories against Bad Apples.

Minor W, Dauter Z, Helliwell JR, Jaskolski M, Wlodawer A.

Structure. 2016 Feb 2;24(2):216-20. doi: 10.1016/j.str.2015.12.010.
GenAp: a distributed SQL interface for genomic data.Publications2016-02-04BDTGGenAp: a distributed SQL interface for genomic data.

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BMC Bioinformatics. 2016 Feb 4;17:63. doi: 10.1186/s12859-016-0904-1.
Physiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves.Publications2016-02-05HeartBD2KPhysiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves.

Buffon G, Blasi ÉA, Adamski JM, Ferla NJ, Berger M, Santi L, Lavallée-Adam M, Yates JR 3rd, Beys-da-Silva WO, Sperotto RA.

J Proteome Res. 2016 Feb 5;15(2):431-46. doi: 10.1021/acs.jproteome.5b00729.
Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.Publications2016-02-09Data WranglingInter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.

Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, GTEx Consortium., Zhu J.

Genome Med. 2016 Feb 9;8(1):15. doi: 10.1186/s13073-016-0268-1.
ksRepo: a generalized platform for computational drug repositioning.Publications2016-02-09PIC-SUREksRepo: a generalized platform for computational drug repositioning.

Brown AS, Kong SW, Kohane IS, Patel CJ.

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Protein kinase A catalytic subunit isoform PRKACA; History, function and physiology.Publications2016-02-15HeartBD2KProtein kinase A catalytic subunit isoform PRKACA; History, function and physiology.

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Gene. 2016 Feb 15;577(2):101-8. doi: 10.1016/j.gene.2015.11.052.
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.Publications2016-02-19Data CompressionMetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.

Kim M, Zhang X, Ligo JG, Farnoud F, Veeravalli VV, Milenkovic O.

BMC Bioinformatics. 2016 Feb 19;17:94. doi: 10.1186/s12859-016-0932-x.
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data.Publications2016-02-25BDDSMethodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data.

Dinov ID.

Gigascience. 2016 Feb 25;5:12. doi: 10.1186/s13742-016-0117-6.
The Implicitome: A Resource for Rationalizing Gene-Disease Associations.Publications2016-02-26HeartBD2KThe Implicitome: A Resource for Rationalizing Gene-Disease Associations.

Hettne KM, Thompson M, van Haagen HH, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JF, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen GJ, Roos M, 't Hoen PA, Mons B, Schultes EA.

PLoS One. 2016 Feb 26;11(2):e0149621. doi: 10.1371/journal.pone.0149621.
The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression.Publications2016-02-26CCDThe Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression.

Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA.

J Biol Chem. 2016 Feb 26;291(9):4442-52. doi: 10.1074/jbc.M115.671057.
Discriminatory power of common genetic variants in personalized breast cancer diagnosis.Publications2016-02-27CPCPDiscriminatory power of common genetic variants in personalized breast cancer diagnosis.

Wu Y, Abbey CK, Liu J, Ong I, Peissig P, Onitilo AA, Fan J, Yuan M, Burnside ES.

Proc SPIE Int Soc Opt Eng. 2016 Feb 27;9787:. doi: 10.1117/12.2217030.
A Utility/Cost Analysis of Breast Cancer Risk Prediction Algorithms.Publications2016-02-27CPCPA Utility/Cost Analysis of Breast Cancer Risk Prediction Algorithms.

Abbey CK, Wu Y, Burnside ES, Wunderlich A, Samuelson FW, Boone JM.

Proc SPIE Int Soc Opt Eng. 2016 Feb 27;9787:. doi: 10.1117/12.2217850.
Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.Publications2016-03-01ENIGMAGenetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

Franke B, Stein JL, Ripke S, Anttila V, Hibar DP, van Hulzen KJ, Arias-Vasquez A, Smoller JW, Nichols TE, Neale MC, McIntosh AM, Lee P, McMahon FJ, Meyer-Lindenberg A, Mattheisen M, Andreassen OA, Gruber O, Sachdev PS, Roiz-Santiañez R, Saykin AJ, Ehrlich S, Mather KA, Turner JA, Schwarz E, Thalamuthu A, Yao Y, Ho YY, Martin NG, Wright MJ, Schizophrenia Working Group of the Psychiatric Genomics Consortium., Psychosis Endophenotypes International Consortium., Wellcome Trust Case Control Consortium 2., Enigma Consortium., O'Donovan MC, Thompson PM, Neale BM, Medland SE, Sullivan PF.

Nat Neurosci. 2016 Mar;19(3):420-31. doi: 10.1038/nn.4228.
In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands.Publications2016-03-01LINCS-DCICIn utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands.

Govindarajah V, Leung YK, Ying J, Gear R, Bornschein RL, Medvedovic M, Ho SM.

J Nutr Biochem. 2016 Mar;29:73-82. doi: 10.1016/j.jnutbio.2015.11.003.
Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.Publications2016-03-01Data WranglingCrystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.

Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W.

Mol Immunol. 2016 Mar;71:143-51. doi: 10.1016/j.molimm.2016.02.003.
Using computer-extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage.Publications2016-03-01CPCPUsing computer-extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage.

Burnside ES, Drukker K, Li H, Bonaccio E, Zuley M, Ganott M, Net JM, Sutton EJ, Brandt KR, Whitman GJ, Conzen SD, Lan L, Ji Y, Zhu Y, Jaffe CC, Huang EP, Freymann JB, Kirby JS, Morris EA, Giger ML.

Cancer. 2016 Mar 1;122(5):748-57. doi: 10.1002/cncr.29791.
Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running.Publications2016-03-01MobilizeStretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running.

Uchida TK, Hicks JL, Dembia CL, Delp SL.

PLoS One. 2016 Mar 1;11(3):e0150378. doi: 10.1371/journal.pone.0150378.
Protein purification and crystallization artifacts: The tale usually not told.Publications2016-03-01Data WranglingProtein purification and crystallization artifacts: The tale usually not told.

Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W.

Protein Sci. 2016 Mar;25(3):720-33. doi: 10.1002/pro.2861.
Markov Boundary Discovery with Ridge Regularized Linear Models.Publications2016-03-01CCDMarkov Boundary Discovery with Ridge Regularized Linear Models.

Strobl EV, Visweswaran S.

J Causal Inference. 2016 Mar;4(1):31-48. doi: 10.1515/jci-2015-0011.
The impact of structural genomics: the first quindecennial.Publications2016-03-01Data WranglingThe impact of structural genomics: the first quindecennial.

Grabowski M, Niedzialkowska E, Zimmerman MD, Minor W.

J Struct Funct Genomics. 2016 Mar;17(1):1-16. doi: 10.1007/s10969-016-9201-5.
Disrupted rich club network in behavioral variant frontotemporal dementia and early-onset Alzheimer's disease.Publications2016-03-01ENIGMADisrupted rich club network in behavioral variant frontotemporal dementia and early-onset Alzheimer's disease.

Daianu M, Mezher A, Mendez MF, Jahanshad N, Jimenez EE, Thompson PM.

Hum Brain Mapp. 2016 Mar;37(3):868-83. doi: 10.1002/hbm.23069.
A history of breast cancer and older age allow risk stratification of mammographic BI-RADS 3 ratings in the diagnostic setting.Publications2016-03-01CPCPA history of breast cancer and older age allow risk stratification of mammographic BI-RADS 3 ratings in the diagnostic setting.

Benndorf M, Wu Y, Burnside ES.

Clin Imaging. 2016 Mar-Apr;40(2):200-4. doi: 10.1016/j.clinimag.2015.10.011.
Heritability and reliability of automatically segmented human hippocampal formation subregions.Publications2016-03-01ENIGMAHeritability and reliability of automatically segmented human hippocampal formation subregions.

Whelan CD, Hibar DP, van Velzen LS, Zannas AS, Carrillo-Roa T, McMahon K, Prasad G, Kelly S, Faskowitz J, deZubiracay G, Iglesias JE, van Erp TG, Frodl T, Martin NG, Wright MJ, Jahanshad N, Schmaal L, Sämann PG, Thompson PM, Alzheimer's Disease Neuroimaging Initiative..

Neuroimage. 2016 Mar;128:125-37. doi: 10.1016/j.neuroimage.2015.12.039.
Electrophysiological Endophenotypes for Schizophrenia.Publications2016-03-01ENIGMAElectrophysiological Endophenotypes for Schizophrenia.

Owens EM, Bachman P, Glahn DC, Bearden CE.

Harv Rev Psychiatry. 2016 Mar-Apr;24(2):129-47. doi: 10.1097/HRP.0000000000000110.
PROX: Approximated Summarization of Data Provenance.Publications2016-03-01Data ProvenancePROX: Approximated Summarization of Data Provenance.

Ainy E, Bourhis P, Davidson SB, Deutch D, Milo T.

Adv Database Technol. 2016 Mar;2016:620-623. pmid: 27570843.
Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis.Publications2016-03-01CEDARGenome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis.

Sweeney TE, Braviak L, Tato CM, Khatri P.

Lancet Respir Med. 2016 Mar;4(3):213-24. doi: 10.1016/S2213-2600(16)00048-5.
Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.Publications2016-03-04ENIGMAAccounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

Sul JH, Bilow M, Yang WY, Kostem E, Furlotte N, He D, Eskin E.

PLoS Genet. 2016 Mar 4;12(3):e1005849. doi: 10.1371/journal.pgen.1005849.
Integrated analysis of gray and white matter alterations in attention-deficit/hyperactivity disorder.Publications2016-03-04ENIGMAIntegrated analysis of gray and white matter alterations in attention-deficit/hyperactivity disorder.

Francx W, Llera A, Mennes M, Zwiers MP, Faraone SV, Oosterlaan J, Heslenfeld D, Hoekstra PJ, Hartman CA, Franke B, Buitelaar JK, Beckmann CF.

Neuroimage Clin. 2016 Mar 4;11:357-67. doi: 10.1016/j.nicl.2016.03.005.
New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer.Publications2016-03-04Data WranglingNew Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer.

Petralia F, Song WM, Tu Z, Wang P.

J Proteome Res. 2016 Mar 4;15(3):743-54. doi: 10.1021/acs.jproteome.5b00925.
Data publication with the structural biology data grid supports live analysis.Publications2016-03-07BDDSData publication with the structural biology data grid supports live analysis.

Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P.

Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882.
Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution.Publications2016-03-07CPCPFurther support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution.

Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z.

Elife. 2016 Mar 7;5:e14409. doi: 10.7554/eLife.14409.
Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma.Publications2016-03-08LINCS-DCICIntegrative radiogenomic analysis for multicentric radiophenotype in glioblastoma.

Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH.

Oncotarget. 2016 Mar 8;7(10):11526-38. doi: 10.18632/oncotarget.7115.
Effect of lossy compression of quality scores on variant calling.Publications2016-03-10Data CompressionEffect of lossy compression of quality scores on variant calling.

Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E.

Brief Bioinform. 2016 Mar 10;:. doi: 10.1093/bib/bbw011.
A large dataset of protein dynamics in the mammalian heart proteome.Publications2016-03-15HeartBD2KA large dataset of protein dynamics in the mammalian heart proteome.

Lau E, Cao Q, Ng DC, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem DA, Lam MP, Ge J, Ping P.

Sci Data. 2016 Mar 15;3:160015. doi: 10.1038/sdata.2016.15.
Wikidata as a semantic framework for the Gene Wiki initiative.Publications2016-03-17HeartBD2KWikidata as a semantic framework for the Gene Wiki initiative.

Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI.

Database (Oxford). 2016;2016:. doi: 10.1093/database/baw015.
Sparse regression models for unraveling group and individual associations in eQTL mapping.Publications2016-03-22Data WranglingSparse regression models for unraveling group and individual associations in eQTL mapping.

Cheng W, Shi Y, Zhang X, Wang W.

BMC Bioinformatics. 2016 Mar 22;17:136. doi: 10.1186/s12859-016-0986-9.
Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics.Publications2016-03-24HeartBD2KUsing PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics.

Lavallée-Adam M, Yates JR 3rd.

Curr Protoc Bioinformatics. 2016 Mar 24;53:13.28.1-16. doi: 10.1002/0471250953.bi1328s53.
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.Publications2016-03-28HeartBD2KCentralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

Putman TE, Burgstaller-Muehlbacher S, Waagmeester A, Wu C, Su AI, Good BM.

Database (Oxford). 2016;2016:. doi: 10.1093/database/baw028.
Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.Publications2016-03-29LINCS-DCICSignaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.

Rezza A, Wang Z, Sennett R, Qiao W, Wang D, Heitman N, Mok KW, Clavel C, Yi R, Zandstra P, Ma'ayan A, Rendl M.

Cell Rep. 2016 Mar 29;14(12):3001-18. doi: 10.1016/j.celrep.2016.02.078.
Brainhack: a collaborative workshop for the open neuroscience community.Publications2016-03-31BDDS, ENIGMABrainhack: a collaborative workshop for the open neuroscience community.

Cameron Craddock R, S Margulies D, Bellec P, Nolan Nichols B, Alcauter S, A Barrios F, Burnod Y, J Cannistraci C, Cohen-Adad J, De Leener B, Dery S, Downar J, Dunlop K, R Franco A, Seligman Froehlich C, J Gerber A, S Ghosh S, J Grabowski T, Hill S, Sólon Heinsfeld A, Matthew Hutchison R, Kundu P, R Laird A, Liew SL, J Lurie D, G McLaren D, Meneguzzi F, Mennes M, Mesmoudi S, O'Connor D, H Pasaye E, Peltier S, Poline JB, Prasad G, Fraga Pereira R, Quirion PO, Rokem A, S Saad Z, Shi Y, C Strother S, Toro R, Q Uddin L, D Van Horn J, W Van Meter J, C Welsh R, Xu T.

Gigascience. 2016 Mar 31;5:16. doi: 10.1186/s13742-016-0121-x.
Comment on: 'ERGC: an efficient referential genome compression algorithm'.Publications2016-04-01Data CompressionComment on: 'ERGC: an efficient referential genome compression algorithm'.

Deorowicz S, Grabowski S, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2016 Apr 1;32(7):1115-7. doi: 10.1093/bioinformatics/btv704.
APPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE.Publications2016-04-01ENIGMAAPPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE.

Zhang J, Stonnington C, Li Q, Shi J, Bauer RJ 3rd, Gutman BA, Chen K, Reiman EM, Thompson PM, Ye J, Wang Y.

Proc IEEE Int Symp Biomed Imaging. 2016 Apr;2016:646-650. doi: 10.1109/ISBI.2016.7493350.
MORPHOMETRIC ANALYSIS OF HIPPOCAMPUS AND LATERAL VENTRICLE REVEALS REGIONAL DIFFERENCE BETWEEN COGNITIVELY STABLE AND DECLINING PERSONS.Publications2016-04-01ENIGMAMORPHOMETRIC ANALYSIS OF HIPPOCAMPUS AND LATERAL VENTRICLE REVEALS REGIONAL DIFFERENCE BETWEEN COGNITIVELY STABLE AND DECLINING PERSONS.

Zhang W, Shi J, Stonnington C, Bauer RJ 3rd, Gutman BA, Chen K, Thompson PM, Reiman EM, Caselli RJ, Wang Y.

Proc IEEE Int Symp Biomed Imaging. 2016 Apr;2016:14-18. doi: 10.1109/ISBI.2016.7493200.
Global Data Sharing in Alzheimer Disease Research.Publications2016-04-01BDDSGlobal Data Sharing in Alzheimer Disease Research.

Ashish N, Bhatt P, Toga AW.

Alzheimer Dis Assoc Disord. 2016 Apr-Jun;30(2):160-8. doi: 10.1097/WAD.0000000000000121.
Subcortical brain volume abnormalities in 2028 individuals with schizophrenia and 2540 healthy controls via the ENIGMA consortium.Publications2016-04-01ENIGMASubcortical brain volume abnormalities in 2028 individuals with schizophrenia and 2540 healthy controls via the ENIGMA consortium.

van Erp TG, Hibar DP, Rasmussen JM, Glahn DC, Pearlson GD, Andreassen OA, Agartz I, Westlye LT, Haukvik UK, Dale AM, Melle I, Hartberg CB, Gruber O, Kraemer B, Zilles D, Donohoe G, Kelly S, McDonald C, Morris DW, Cannon DM, Corvin A, Machielsen MW, Koenders L, de Haan L, Veltman DJ, Satterthwaite TD, Wolf DH, Gur RC, Gur RE, Potkin SG, Mathalon DH, Mueller BA, Preda A, Macciardi F, Ehrlich S, Walton E, Hass J, Calhoun VD, Bockholt HJ, Sponheim SR, Shoemaker JM, van Haren NE, Hulshoff Pol HE, Ophoff RA, Kahn RS, Roiz-Santiañez R, Crespo-Facorro B, Wang L, Alpert KI, Jönsson EG, Dimitrova R, Bois C, Whalley HC, McIntosh AM, Lawrie SM, Hashimoto R, Thompson PM, Turner JA.

Mol Psychiatry. 2016 Apr;21(4):547-53. doi: 10.1038/mp.2015.63.
Growing Wikipedia Across Languages via Recommendation.Publications2016-04-01MobilizeGrowing Wikipedia Across Languages via Recommendation.

Wulczyn E, West R, Zia L, Leskovec J.

Proc Int World Wide Web Conf. 2016 Apr;2016:975-985. pmid: 27819073.
The effect of increased genetic risk for Alzheimer's disease on hippocampal and amygdala volume.Publications2016-04-01ENIGMAThe effect of increased genetic risk for Alzheimer's disease on hippocampal and amygdala volume.

Lupton MK, Strike L, Hansell NK, Wen W, Mather KA, Armstrong NJ, Thalamuthu A, McMahon KL, de Zubicaray GI, Assareh AA, Simmons A, Proitsi P, Powell JF, Montgomery GW, Hibar DP, Westman E, Tsolaki M, Kloszewska I, Soininen H, Mecocci P, Velas B, Lovestone S, Alzheimer's Disease Neuroimaging Initiative., Brodaty H, Ames D, Trollor JN, Martin NG, Thompson PM, Sachdev PS, Wright MJ.

Neurobiol Aging. 2016 Apr;40:68-77. doi: 10.1016/j.neurobiolaging.2015.12.023.
Long-read sequence assembly of the gorilla genome.Publications2016-04-01BDTGLong-read sequence assembly of the gorilla genome.

Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE.

Science. 2016 Apr 1;352(6281):aae0344. doi: 10.1126/science.aae0344.
CVXPY: A Python-Embedded Modeling Language for Convex Optimization.Publications2016-04-01MobilizeCVXPY: A Python-Embedded Modeling Language for Convex Optimization.

Diamond S, Boyd S.

J Mach Learn Res. 2016 Apr;17:. pmid: 27375369.
Age exacerbates HIV-associated white matter abnormalities.Publications2016-04-01ENIGMAAge exacerbates HIV-associated white matter abnormalities.

Seider TR, Gongvatana A, Woods AJ, Chen H, Porges EC, Cummings T, Correia S, Tashima K, Cohen RA.

J Neurovirol. 2016 Apr;22(2):201-12. doi: 10.1007/s13365-015-0386-3.
Multiple testing correction in linear mixed models.Publications2016-04-01ENIGMAMultiple testing correction in linear mixed models.

Joo JW, Hormozdiari F, Han B, Eskin E.

Genome Biol. 2016 Apr 1;17:62. doi: 10.1186/s13059-016-0903-6.
Neural basis of reward anticipation and its genetic determinants.Publications2016-04-05ENIGMANeural basis of reward anticipation and its genetic determinants.

Jia T, Macare C, Desrivières S, Gonzalez DA, Tao C, Ji X, Ruggeri B, Nees F, Banaschewski T, Barker GJ, Bokde AL, Bromberg U, Büchel C, Conrod PJ, Dove R, Frouin V, Gallinat J, Garavan H, Gowland PA, Heinz A, Ittermann B, Lathrop M, Lemaitre H, Martinot JL, Paus T, Pausova Z, Poline JB, Rietschel M, Robbins T, Smolka MN, Müller CP, Feng J, Rothenfluh A, Flor H, Schumann G, IMAGEN Consortium..

Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):3879-84. doi: 10.1073/pnas.1503252113.
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.Publications2016-04-05Data WranglingOutcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-8. doi: 10.1016/j.str.2016.02.017.
GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.Publications2016-04-05LINCS-DCICGUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

Hung LH, Kristiyanto D, Lee SB, Yeung KY.

PLoS One. 2016 Apr 5;11(4):e0152686. doi: 10.1371/journal.pone.0152686.
Design and computational analysis of single-cell RNA-sequencing experiments.Publications2016-04-07CPCPDesign and computational analysis of single-cell RNA-sequencing experiments.

Bacher R, Kendziorski C.

Genome Biol. 2016 Apr 7;17:63. doi: 10.1186/s13059-016-0927-y.
Systematic correlation of environmental exposure and physiological and self-reported behaviour factors with leukocyte telomere length.Publications2016-04-08PIC-SURESystematic correlation of environmental exposure and physiological and self-reported behaviour factors with leukocyte telomere length.

Patel CJ, Manrai AK, Corona E, Kohane IS.

Int J Epidemiol. 2016 Apr 8;:. doi: 10.1093/ije/dyw043.
Influence of APOE Genotype on Hippocampal Atrophy over Time - An N=1925 Surface-Based ADNI Study.Publications2016-04-11ENIGMAInfluence of APOE Genotype on Hippocampal Atrophy over Time - An N=1925 Surface-Based ADNI Study.

Li B, Shi J, Gutman BA, Baxter LC, Thompson PM, Caselli RJ, Wang Y, Alzheimer’s Disease Neuroimaging Initiative..

PLoS One. 2016 Apr 11;11(4):e0152901. doi: 10.1371/journal.pone.0152901.
A crowdsourcing workflow for extracting chemical-induced disease relations from free text.Publications2016-04-17HeartBD2KA crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Li TS, Bravo À, Furlong LI, Good BM, Su AI.

Database (Oxford). 2016;2016:. doi: 10.1093/database/baw051.
BigDebug: Debugging Primitives for Interactive Big Data Processing in Spark.Publications2016-05-01MD2KBigDebug: Debugging Primitives for Interactive Big Data Processing in Spark.

Gulzar MA, Interlandi M, Yoo S, Tetali SD, Condie T, Millstein T, Kim M.

Proc Int Conf Softw Eng. 2016 May;2016:784-795. doi: 10.1145/2884781.2884813.
Utilizing uncoded consultation notes from electronic medical records for predictive modeling of colorectal cancer.Publications2016-05-01PIC-SUREUtilizing uncoded consultation notes from electronic medical records for predictive modeling of colorectal cancer.

Hoogendoorn M, Szolovits P, Moons LM, Numans ME.

Artif Intell Med. 2016 May;69:53-61. doi: 10.1016/j.artmed.2016.03.003.
Mapping Brain Anatomical Connectivity Using Diffusion Magnetic Resonance Imaging: Structural connectivity of the human brain.Publications2016-05-01BDDSMapping Brain Anatomical Connectivity Using Diffusion Magnetic Resonance Imaging: Structural connectivity of the human brain.

Li J, Shi Y, Toga AW.

IEEE Signal Process Mag. 2016 May;33(3):36-51. doi: 10.1109/MSP.2015.2510024.
A role for the bacterial GATC methylome in antibiotic stress survival.Publications2016-05-01KnowEnGA role for the bacterial GATC methylome in antibiotic stress survival.

Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ.

Nat Genet. 2016 May;48(5):581-6. doi: 10.1038/ng.3530.
The Use of Behavior Change Techniques and Theory in Technologies for Cardiovascular Disease Prevention and Treatment in Adults: A Comprehensive Review.Publications2016-05-01MobilizeThe Use of Behavior Change Techniques and Theory in Technologies for Cardiovascular Disease Prevention and Treatment in Adults: A Comprehensive Review.

Winter SJ, Sheats JL, King AC.

Prog Cardiovasc Dis. 2016 May-Jun;58(6):605-12. doi: 10.1016/j.pcad.2016.02.005.
Finding Significant Stress Episodes in a Discontinuous Time Series of Rapidly Varying Mobile Sensor Data.Publications2016-05-01MD2KFinding Significant Stress Episodes in a Discontinuous Time Series of Rapidly Varying Mobile Sensor Data.

Sarker H, Tyburski M, Rahman MM, Hovsepian K, Sharmin M, Epstein DH, Preston KL, Furr-Holden CD, Milam A, Nahum-Shani I, al'Absi M, Kumar S.

Proc SIGCHI Conf Hum Factor Comput Syst. 2016 May;2016:4489-4501. doi: 10.1145/2858036.2858218.
Entorhinal Cortex Thickness across the Human Lifespan.Publications2016-05-01ENIGMAEntorhinal Cortex Thickness across the Human Lifespan.

Hasan KM, Mwangi B, Cao B, Keser Z, Tustison NJ, Kochunov P, Frye RE, Savatic M, Soares J.

J Neuroimaging. 2016 May;26(3):278-82. doi: 10.1111/jon.12297.
Temporal neutrophil polarization following myocardial infarction.Publications2016-05-01HeartBD2KTemporal neutrophil polarization following myocardial infarction.

Ma Y, Yabluchanskiy A, Iyer RP, Cannon PL, Flynn ER, Jung M, Henry J, Cates CA, Deleon-Pennell KY, Lindsey ML.

Cardiovasc Res. 2016 May 1;110(1):51-61. doi: 10.1093/cvr/cvw024.
Guidelines for the functional annotation of microRNAs using the Gene Ontology.Publications2016-05-01HeartBD2KGuidelines for the functional annotation of microRNAs using the Gene Ontology.

Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.

RNA. 2016 May;22(5):667-76. doi: 10.1261/rna.055301.115.
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.Publications2016-05-01CPCPOEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.

Bioinformatics. 2016 May 1;32(9):1408-10. doi: 10.1093/bioinformatics/btw004.
An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem.Publications2016-05-04CCDAn exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem.

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Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9.
Whole-Genome Sequencing of a Healthy Aging Cohort.Publications2016-05-05HeartBD2KWhole-Genome Sequencing of a Healthy Aging Cohort.

Erikson GA, Bodian DL, Rueda M, Molparia B, Scott ER, Scott-Van Zeeland AA, Topol SE, Wineinger NE, Niederhuber JE, Topol EJ, Torkamani A.

Cell. 2016 May 5;165(4):1002-11. doi: 10.1016/j.cell.2016.03.022.
High-performance web services for querying gene and variant annotation.Publications2016-05-06HeartBD2K, Data WranglingHigh-performance web services for querying gene and variant annotation.

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C.

Genome Biol. 2016 May 6;17(1):91. doi: 10.1186/s13059-016-0953-9.
TNNT1, TNNT2, and TNNT3: Isoform genes, regulation, and structure-function relationships.Publications2016-05-10HeartBD2KTNNT1, TNNT2, and TNNT3: Isoform genes, regulation, and structure-function relationships.

Wei B, Jin JP.

Gene. 2016 May 10;582(1):1-13. doi: 10.1016/j.gene.2016.01.006.
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.Publications2016-05-13Data CompressionFast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.

Wiedenhoeft J, Brugel E, Schliep A.

PLoS Comput Biol. 2016 May 13;12(5):e1004871. doi: 10.1371/journal.pcbi.1004871.
Leveraging Citizen Science and Information Technology for Population Physical Activity Promotion.Publications2016-05-15MobilizeLeveraging Citizen Science and Information Technology for Population Physical Activity Promotion.

King AC, Winter SJ, Sheats JL, Rosas LG, Buman MP, Salvo D, Rodriguez NM, Seguin RA, Moran M, Garber R, Broderick B, Zieff SG, Sarmiento OL, Gonzalez SA, Banchoff A, Dommarco JR.

Transl J Am Coll Sports Med. 2016 May 15;1(4):30-44. pmid: 27525309.
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.Publications2016-05-26LINCS-DCICGlucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.

Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW.

Sci Rep. 2016 May 26;6:26419. doi: 10.1038/srep26419.
A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions.Publications2016-05-27CPCPA multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions.

Fotuhi Siahpirani A, Ay F, Roy S.

Genome Biol. 2016 May 27;17(1):114. doi: 10.1186/s13059-016-0962-8.
Sample size calculations for micro-randomized trials in mHealth.Publications2016-05-30MD2KSample size calculations for micro-randomized trials in mHealth.

Liao P, Klasnja P, Tewari A, Murphy SA.

Stat Med. 2016 May 30;35(12):1944-71. doi: 10.1002/sim.6847.
MET network in PubMed: a text-mined network visualization and curation system.Publications2016-05-30HeartBD2KMET network in PubMed: a text-mined network visualization and curation system.

Dai HJ, Su CH, Lai PT, Huang MS, Jonnagaddala J, Rose Jue T, Rao S, Chou HJ, Milacic M, Singh O, Syed-Abdul S, Hsu WL.

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A Review of Social Media Technologies Across the Global HIV Care Continuum.Publications2016-06-01Data WranglingA Review of Social Media Technologies Across the Global HIV Care Continuum.

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Curr Opin Psychol. 2016 Jun 1;9:56-66. doi: 10.1016/j.copsyc.2015.10.024.
Coupled Harmonic Bases for Longitudinal Characterization of Brain Networks.Publications2016-06-01CPCPCoupled Harmonic Bases for Longitudinal Characterization of Brain Networks.

Hwang SJ, Adluru N, Collins MD, Ravi SN, Bendlin BB, Johnson SC, Singh V.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2016 Jun-Jul;2016:2517-2525. pmid: 27812274.
Heritability and genetic correlation between the cerebral cortex and associated white matter connections.Publications2016-06-01ENIGMAHeritability and genetic correlation between the cerebral cortex and associated white matter connections.

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Hum Brain Mapp. 2016 Jun;37(6):2331-47. doi: 10.1002/hbm.23177.
Subcortical brain alterations in major depressive disorder: findings from the ENIGMA Major Depressive Disorder working group.Publications2016-06-01BDDSSubcortical brain alterations in major depressive disorder: findings from the ENIGMA Major Depressive Disorder working group.

Schmaal L, Veltman DJ, van Erp TG, Sämann PG, Frodl T, Jahanshad N, Loehrer E, Tiemeier H, Hofman A, Niessen WJ, Vernooij MW, Ikram MA, Wittfeld K, Grabe HJ, Block A, Hegenscheid K, Völzke H, Hoehn D, Czisch M, Lagopoulos J, Hatton SN, Hickie IB, Goya-Maldonado R, Krämer B, Gruber O, Couvy-Duchesne B, Rentería ME, Strike LT, Mills NT, de Zubicaray GI, McMahon KL, Medland SE, Martin NG, Gillespie NA, Wright MJ, Hall GB, MacQueen GM, Frey EM, Carballedo A, van Velzen LS, van Tol MJ, van der Wee NJ, Veer IM, Walter H, Schnell K, Schramm E, Normann C, Schoepf D, Konrad C, Zurowski B, Nickson T, McIntosh AM, Papmeyer M, Whalley HC, Sussmann JE, Godlewska BR, Cowen PJ, Fischer FH, Rose M, Penninx BW, Thompson PM, Hibar DP.

Mol Psychiatry. 2016 Jun;21(6):806-12. doi: 10.1038/mp.2015.69.
Pathfinder: Visual Analysis of Paths in Graphs.Publications2016-06-01Data VisualizationPathfinder: Visual Analysis of Paths in Graphs.

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Comput Graph Forum. 2016 Jun;35(3):71-80. doi: 10.1111/cgf.12883.
From Visual Exploration to Storytelling and Back Again.Publications2016-06-01Data VisualizationFrom Visual Exploration to Storytelling and Back Again.

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Childhood abuse and deprivation are associated with distinct sex-dependent differences in brain morphology.Publications2016-06-01ENIGMAChildhood abuse and deprivation are associated with distinct sex-dependent differences in brain morphology.

Everaerd D, Klumpers F, Zwiers M, Guadalupe T, Franke B, van Oostrom I, Schene A, Fernández G, Tendolkar I.

Neuropsychopharmacology. 2016 Jun;41(7):1716-23. doi: 10.1038/npp.2015.344.
EmptyHeaded: A Relational Engine for Graph Processing.Publications2016-06-01MobilizeEmptyHeaded: A Relational Engine for Graph Processing.

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Proc ACM SIGMOD Int Conf Manag Data. 2016 Jun-Jul;2016:431-446. doi: 10.1145/2882903.2915213.
Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions.Publications2016-06-01BDDSProbability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions.

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Response to Dr Fried & Dr Kievit, and Dr Malhi et al.Publications2016-06-01ENIGMAResponse to Dr Fried & Dr Kievit, and Dr Malhi et al.

Schmaal L, Veltman DJ, van Erp TG, Sämann PG, Frodl T, Jahanshad N, Loehrer E, Vernooij MW, Niessen WJ, Ikram MA, Wittfeld K, Grabe HJ, Block A, Hegenscheid K, Hoehn D, Czisch M, Lagopoulos J, Hatton SN, Hickie IB, Goya-Maldonado R, Krämer B, Gruber O, Couvy-Duchesne B, Rentería ME, Strike LT, Wright MJ, de Zubicaray GI, McMahon KL, Medland SE, Gillespie NA, Hall GB, van Velzen LS, van Tol MJ, van der Wee NJ, Veer IM, Walter H, Schramm E, Normann C, Schoepf D, Konrad C, Zurowski B, McIntosh AM, Whalley HC, Sussmann JE, Godlewska BR, Fischer FH, Penninx BW, Thompson PM, Hibar DP.

Mol Psychiatry. 2016 Jun;21(6):726-8. doi: 10.1038/mp.2016.9.
Voxel-based morphometry analysis reveals frontal brain differences in participants with ADHD and their unaffected siblings.Publications2016-06-01ENIGMAVoxel-based morphometry analysis reveals frontal brain differences in participants with ADHD and their unaffected siblings.

Bralten J, Greven CU, Franke B, Mennes M, Zwiers MP, Rommelse NN, Hartman C, van der Meer D, O'Dwyer L, Oosterlaan J, Hoekstra PJ, Heslenfeld D, Arias-Vasquez A, Buitelaar JK.

J Psychiatry Neurosci. 2016 Jun;41(4):272-9. pmid: 26679925.
Characterising resting-state functional connectivity in a large sample of adults with ADHD.Publications2016-06-03ENIGMACharacterising resting-state functional connectivity in a large sample of adults with ADHD.

Mostert JC, Shumskaya E, Mennes M, Onnink AM, Hoogman M, Kan CC, Arias Vasquez A, Buitelaar J, Franke B, Norris DG.

Prog Neuropsychopharmacol Biol Psychiatry. 2016 Jun 3;67:82-91. doi: 10.1016/j.pnpbp.2016.01.011.
Learning mixed graphical models with separate sparsity parameters and stability-based model selection.Publications2016-06-06CCDLearning mixed graphical models with separate sparsity parameters and stability-based model selection.

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BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:175. doi: 10.1186/s12859-016-1039-0.
Using genomic annotations increases statistical power to detect eGenes.Publications2016-06-15ENIGMAUsing genomic annotations increases statistical power to detect eGenes.

Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E.

Bioinformatics. 2016 Jun 15;32(12):i156-i163. doi: 10.1093/bioinformatics/btw272.
Comparing the Consumption of CPU Hours with Scientific Output for the Extreme Science and Engineering Discovery Environment (XSEDE).Publications2016-06-16Data VisualizationComparing the Consumption of CPU Hours with Scientific Output for the Extreme Science and Engineering Discovery Environment (XSEDE).

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PLoS One. 2016 Jun 16;11(6):e0157628. doi: 10.1371/journal.pone.0157628.
Targeting MTHFD2 in acute myeloid leukemia.Publications2016-06-27LINCS-TGTargeting MTHFD2 in acute myeloid leukemia.

Pikman Y, Puissant A, Alexe G, Furman A, Chen LM, Frumm SM, Ross L, Fenouille N, Bassil CF, Lewis CA, Ramos A, Gould J, Stone RM, DeAngelo DJ, Galinsky I, Clish CB, Kung AL, Hemann MT, Vander Heiden MG, Banerji V, Stegmaier K.

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Effects of Three Motivationally Targeted Mobile Device Applications on Initial Physical Activity and Sedentary Behavior Change in Midlife and Older Adults: A Randomized Trial.Publications2016-06-28MobilizeEffects of Three Motivationally Targeted Mobile Device Applications on Initial Physical Activity and Sedentary Behavior Change in Midlife and Older Adults: A Randomized Trial.

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MMP-9 signaling in the left ventricle following myocardial infarction.Publications2016-07-01HeartBD2KMMP-9 signaling in the left ventricle following myocardial infarction.

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Am J Physiol Heart Circ Physiol. 2016 Jul 1;311(1):H190-8. doi: 10.1152/ajpheart.00243.2016.
Calponin isoforms CNN1, CNN2 and CNN3: Regulators for actin cytoskeleton functions in smooth muscle and non-muscle cells.Publications2016-07-01HeartBD2KCalponin isoforms CNN1, CNN2 and CNN3: Regulators for actin cytoskeleton functions in smooth muscle and non-muscle cells.

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Attention-Deficit/Hyperactivity Disorder symptoms coincide with altered striatal connectivity.Publications2016-07-01ENIGMAAttention-Deficit/Hyperactivity Disorder symptoms coincide with altered striatal connectivity.

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Biol Psychiatry Cogn Neurosci Neuroimaging. 2016 Jul;1(4):353-363. doi: 10.1016/j.bpsc.2016.03.008.
Quantifying patterns of brain activity: Distinguishing unaffected siblings from participants with ADHD and healthy individuals.Publications2016-07-02ENIGMAQuantifying patterns of brain activity: Distinguishing unaffected siblings from participants with ADHD and healthy individuals.

Wolfers T, van Rooij D, Oosterlaan J, Heslenfeld D, Hartman CA, Hoekstra PJ, Beckmann CF, Franke B, Buitelaar JK, Marquand AF.

Neuroimage Clin. 2016 Jul 2;12:227-33. doi: 10.1016/j.nicl.2016.06.020.
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.Publications2016-07-03LINCS-DCICThe harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.

Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A.

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Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR.Publications2016-07-05BDTGEvaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR.

Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP.

Genome Biol. 2016 Jul 5;17(1):148. doi: 10.1186/s13059-016-1012-2.
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.Publications2016-07-05LINCS-DCICAn open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

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Imputing Phenotypes for Genome-wide Association Studies.Publications2016-07-07ENIGMAImputing Phenotypes for Genome-wide Association Studies.

Hormozdiari F, Kang EY, Bilow M, Ben-David E, Vulpe C, McLachlan S, Lusis AJ, Han B, Eskin E.

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Higher-order organization of complex networks.Publications2016-07-08MobilizeHigher-order organization of complex networks.

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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.Publications2016-07-08LINCS-DCICEnrichr: a comprehensive gene set enrichment analysis web server 2016 update.

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A.

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Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.Publications2016-07-15KnowEnGCharacterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.

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Inferring the Interactions of Risk Factors from EHRs.Publications2016-07-19Data WranglingInferring the Interactions of Risk Factors from EHRs.

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Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records.Publications2016-07-19PIC-SUREEfficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records.

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Biomed Inform Insights. 2016 Jul 19;8:29-38. doi: 10.4137/BII.S38916.
Comparative Evaluation for Brain Structural Connectivity Approaches: Towards Integrative Neuroinformatics Tool for Epilepsy Clinical Research.Publications2016-07-20Data ProvenanceComparative Evaluation for Brain Structural Connectivity Approaches: Towards Integrative Neuroinformatics Tool for Epilepsy Clinical Research.

Yang S, Tatsuoka C, Ghosh K, Lacuey-Lecumberri N, Lhatoo SD, Sahoo SS.

AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:446-54. pmid: 27570685.
Correction: Effects of Three Motivationally Targeted Mobile Device Applications on Initial Physical Activity and Sedentary Behavior Change in Midlife and Older Adults: A Randomized Trial.Publications2016-07-21MobilizeCorrection: Effects of Three Motivationally Targeted Mobile Device Applications on Initial Physical Activity and Sedentary Behavior Change in Midlife and Older Adults: A Randomized Trial.

PLOS ONE Staff..

PLoS One. 2016 Jul 21;11(7):e0160113. doi: 10.1371/journal.pone.0160113.
Environment-Wide Association Study of Blood Pressure in the National Health and Nutrition Examination Survey (1999-2012).Publications2016-07-26PIC-SUREEnvironment-Wide Association Study of Blood Pressure in the National Health and Nutrition Examination Survey (1999-2012).

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Sci Rep. 2016 Jul 26;6:30373. doi: 10.1038/srep30373.
Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.Publications2016-07-27CPCPAnalysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.

Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R.

Dev Biol. 2016 Jul 27;:. doi: 10.1016/j.ydbio.2016.05.024.
Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.Publications2016-08-01CPCPIntegrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.

Liu P, Sanalkumar R, Bresnick EH, Keleş S, Dewey CN.

Genome Res. 2016 Aug;26(8):1124-33. doi: 10.1101/gr.199174.115.
Drug-induced adverse events prediction with the LINCS L1000 data.Publications2016-08-01LINCS-DCICDrug-induced adverse events prediction with the LINCS L1000 data.

Wang Z, Clark NR, Ma'ayan A.

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Using automatically extracted information from mammography reports for decision-support.Publications2016-08-01CPCPUsing automatically extracted information from mammography reports for decision-support.

Bozkurt S, Gimenez F, Burnside ES, Gulkesen KH, Rubin DL.

J Biomed Inform. 2016 Aug;62:224-31. doi: 10.1016/j.jbi.2016.07.001.
mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models.Publications2016-08-01LINCS-DCICmclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models.

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Interpretable Decision Sets: A Joint Framework for Description and Prediction.Publications2016-08-01MobilizeInterpretable Decision Sets: A Joint Framework for Description and Prediction.

Lakkaraju H, Bach SH, Jure L.

KDD. 2016 Aug;2016:1675-1684. doi: 10.1145/2939672.2939874.
node2vec: Scalable Feature Learning for Networks.Publications2016-08-01Mobilizenode2vec: Scalable Feature Learning for Networks.

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Enlarged striatal volume in adults with ADHD carrying the 9-6 haplotype of the dopamine transporter gene DAT1.Publications2016-08-01ENIGMAEnlarged striatal volume in adults with ADHD carrying the 9-6 haplotype of the dopamine transporter gene DAT1.

Onnink AM, Franke B, van Hulzen K, Zwiers MP, Mostert JC, Schene AH, Heslenfeld DJ, Oosterlaan J, Hoekstra PJ, Hartman CA, Vasquez AA, Kan CC, Buitelaar J, Hoogman M.

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Connecting the Dots: From Big Data to Healthy Heart.Publications2016-08-02HeartBD2KConnecting the Dots: From Big Data to Healthy Heart.

Lau E, Watson KE, Ping P.

Circulation. 2016 Aug 2;134(5):362-4. doi: 10.1161/CIRCULATIONAHA.116.021892.
Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations.Publications2016-08-05BDDSPredictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations.

Dinov ID, Heavner B, Tang M, Glusman G, Chard K, Darcy M, Madduri R, Pa J, Spino C, Kesselman C, Foster I, Deutsch EW, Price ND, Van Horn JD, Ames J, Clark K, Hood L, Hampstead BM, Dauer W, Toga AW.

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A comprehensive and scalable database search system for metaproteomics.Publications2016-08-16HeartBD2KA comprehensive and scalable database search system for metaproteomics.

Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR 3rd, Su AI, Wolan DW.

BMC Genomics. 2016 Aug 16;17(1):642. doi: 10.1186/s12864-016-2855-3.
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.Publications2016-08-17CPCPSingle-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.

Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA.

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mCrave: Continuous Estimation of Craving During Smoking Cessation.Publications2016-09-01MD2KmCrave: Continuous Estimation of Craving During Smoking Cessation.

Chatterjee S, Hovsepian K, Sarker H, Saleheen N, al'Absi M, Atluri G, Ertin E, Lam C, Lemieux A, Nakajima M, Spring B, Wetter DW, Kumar S.

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Making the cut: improved ranking and selection for large-scale inference.Publications2016-09-01CPCPMaking the cut: improved ranking and selection for large-scale inference.

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GTRAC: fast retrieval from compressed collections of genomic variants.Publications2016-09-01Data CompressionGTRAC: fast retrieval from compressed collections of genomic variants.

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mSieve: Differential Behavioral Privacy in Time Series of Mobile Sensor Data.Publications2016-09-01MD2KmSieve: Differential Behavioral Privacy in Time Series of Mobile Sensor Data.

Saleheen N, Chakraborty S, Ali N, Mahbubur Rahman M, Hossain SM, Bari R, Buder E, Srivastava M, Kumar S.

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Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach.Publications2016-09-01ENIGMAPathway analysis in attention deficit hyperactivity disorder: An ensemble approach.

Mooney MA, McWeeney SK, Faraone SV, Hinney A, Hebebrand J, IMAGE2 Consortium., German ADHD GWAS Group., Nigg JT, Wilmot B.

Am J Med Genet B Neuropsychiatr Genet. 2016 Sep;171(6):815-26. doi: 10.1002/ajmg.b.32446.
A predictive enrichment procedure to identify potential responders to a new therapy for randomized, comparative controlled clinical studies.Publications2016-09-01PIC-SUREA predictive enrichment procedure to identify potential responders to a new therapy for randomized, comparative controlled clinical studies.

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Biometrics. 2016 Sep;72(3):877-87. doi: 10.1111/biom.12461.
Disease-specific classification using deconvoluted whole blood gene expression.Publications2016-09-06Data WranglingDisease-specific classification using deconvoluted whole blood gene expression.

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Quantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy.Publications2016-09-08ENIGMAQuantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy.

Alhusaini S, Whelan CD, Sisodiya SM, Thompson PM.

Neuroimage Clin. 2016 Sep 8;12:526-534. doi: 10.1016/j.nicl.2016.09.005.
Subclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates.Publications2016-09-08CPCPSubclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates.

Sievers CK, Zou LS, Pickhardt PJ, Matkowskyj KA, Albrecht DM, Clipson L, Bacher JW, Pooler BD, Moawad FJ, Cash BD, Reichelderfer M, Vo TN, Newton MA, Larget BR, Halberg RB.

Gut. 2016 Sep 8;:. doi: 10.1136/gutjnl-2016-312232.
Distinct Subcortical Volume Alterations in Pediatric and Adult OCD: A Worldwide Meta- and Mega-Analysis.Publications2016-09-09ENIGMADistinct Subcortical Volume Alterations in Pediatric and Adult OCD: A Worldwide Meta- and Mega-Analysis.

Boedhoe PS, Schmaal L, Abe Y, Ameis SH, Arnold PD, Batistuzzo MC, Benedetti F, Beucke JC, Bollettini I, Bose A, Brem S, Calvo A, Cheng Y, Cho KI, Dallaspezia S, Denys D, Fitzgerald KD, Fouche JP, Giménez M, Gruner P, Hanna GL, Hibar DP, Hoexter MQ, Hu H, Huyser C, Ikari K, Jahanshad N, Kathmann N, Kaufmann C, Koch K, Kwon JS, Lazaro L, Liu Y, Lochner C, Marsh R, Martínez-Zalacaín I, Mataix-Cols D, Menchón JM, Minuzzi L, Nakamae T, Nakao T, Narayanaswamy JC, Piras F, Piras F, Pittenger C, Reddy YC, Sato JR, Simpson HB, Soreni N, Soriano-Mas C, Spalletta G, Stevens MC, Szeszko PR, Tolin DF, Venkatasubramanian G, Walitza S, Wang Z, van Wingen GA, Xu J, Xu X, Yun JY, Zhao Q, ENIGMA OCD Working Group., Thompson PM, Stein DJ, van den Heuvel OA.

Am J Psychiatry. 2016 Sep 9;:appiajp201616020201. doi: 10.1176/appi.ajp.2016.16020201.
Perspective: Beyond the genome.Publications2016-09-15PIC-SUREPerspective: Beyond the genome.

Leppert J, Patel C.

Nature. 2016 Sep 15;537(7620):S105. doi: 10.1038/537S105a.
PRKCE gene encoding protein kinase C-epsilon-Dual roles at sarcomeres and mitochondria in cardiomyocytes.Publications2016-09-15HeartBD2KPRKCE gene encoding protein kinase C-epsilon-Dual roles at sarcomeres and mitochondria in cardiomyocytes.

Scruggs SB, Wang D, Ping P.

Gene. 2016 Sep 15;590(1):90-6. doi: 10.1016/j.gene.2016.06.016.
Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction.Publications2016-09-15HeartBD2KAdapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction.

Lindsey ML, Hall ME, Harmancey R, Ma Y.

Clin Proteomics. 2016 Sep 15;13:19. doi: 10.1186/s12014-016-9120-2.
Simulating Ideal Assistive Devices to Reduce the Metabolic Cost of Running.Publications2016-09-22MobilizeSimulating Ideal Assistive Devices to Reduce the Metabolic Cost of Running.

Uchida TK, Seth A, Pouya S, Dembia CL, Hicks JL, Delp SL.

PLoS One. 2016 Sep 22;11(9):e0163417. doi: 10.1371/journal.pone.0163417.
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.Publications2016-09-26LINCS-DCICExtraction and analysis of signatures from the Gene Expression Omnibus by the crowd.

Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FM, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A.

Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.
MeSHDD: Literature-based drug-drug similarity for drug repositioning.Publications2016-09-27PIC-SUREMeSHDD: Literature-based drug-drug similarity for drug repositioning.

Brown AS, Patel CJ.

J Am Med Inform Assoc. 2016 Sep 27;:. doi: 10.1093/jamia/ocw142.
A comprehensive tractography study of patients with bipolar disorder and their unaffected siblings.Publications2016-10-01ENIGMAA comprehensive tractography study of patients with bipolar disorder and their unaffected siblings.

Sprooten E, Barrett J, McKay DR, Knowles EE, Mathias SR, Winkler AM, Brumbaugh MS, Landau S, Cyr L, Kochunov P, Glahn DC.

Hum Brain Mapp. 2016 Oct;37(10):3474-85. doi: 10.1002/hbm.23253.
Transformation Invariant Control of Voxel-Wise False Discovery Rate.Publications2016-10-01BDDSTransformation Invariant Control of Voxel-Wise False Discovery Rate.

Li J, Shi Y, Toga AW.

IEEE Trans Med Imaging. 2016 Oct;35(10):2243-2257. doi: 10.1109/TMI.2016.2554554.
Abnormal asymmetries in subcortical brain volume in schizophrenia.Publications2016-10-01ENIGMAAbnormal asymmetries in subcortical brain volume in schizophrenia.

Okada N, Fukunaga M, Yamashita F, Koshiyama D, Yamamori H, Ohi K, Yasuda Y, Fujimoto M, Watanabe Y, Yahata N, Nemoto K, Hibar DP, van Erp TG, Fujino H, Isobe M, Isomura S, Natsubori T, Narita H, Hashimoto N, Miyata J, Koike S, Takahashi T, Yamasue H, Matsuo K, Onitsuka T, Iidaka T, Kawasaki Y, Yoshimura R, Watanabe Y, Suzuki M, Turner JA, Takeda M, Thompson PM, Ozaki N, Kasai K, Hashimoto R.

Mol Psychiatry. 2016 Oct;21(10):1460-6. doi: 10.1038/mp.2015.209.
Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.Publications2016-10-01LINCS-DCICPolycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.

von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A.

Nat Neurosci. 2016 Oct;19(10):1321-30. doi: 10.1038/nn.4360.
Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.Publications2016-10-01Data ProvenanceInsight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

Sahoo SS, Ramesh P, Welter E, Bukach A, Valdez J, Tatsuoka C, Bamps Y, Stoll S, Jobst BC, Sajatovic M.

Int J Med Inform. 2016 Oct;94:21-30. doi: 10.1016/j.ijmedinf.2016.06.009.
Hyperbolic Space Sparse Coding with Its Application on Prediction of Alzheimer's Disease in Mild Cognitive Impairment.Publications2016-10-01ENIGMAHyperbolic Space Sparse Coding with Its Application on Prediction of Alzheimer's Disease in Mild Cognitive Impairment.

Zhang J, Shi J, Stonnington C, Li Q, Gutman BA, Chen K, Reiman EM, Caselli RJ, Thompson PM, Ye J, Wang Y.

Med Image Comput Comput Assist Interv. 2016 Oct;9900:326-334. doi: 10.1007/978-3-319-46720-7_38.
A Comparison of Methamphetamine Users to a Matched NHANES Cohort: Propensity Score Analyses for Oral Health Care and Dental Service Need.Publications2016-10-01MD2KA Comparison of Methamphetamine Users to a Matched NHANES Cohort: Propensity Score Analyses for Oral Health Care and Dental Service Need.

Murphy DA, Harrell L, Fintzy R, Belin TR, Gutierrez A, Vitero SJ, Shetty V.

J Behav Health Serv Res. 2016 Oct;43(4):676-690. doi: 10.1007/s11414-014-9449-0.
Adaptive Signal Recovery on Graphs via Harmonic Analysis for Experimental Design in Neuroimaging.Publications2016-10-01CPCPAdaptive Signal Recovery on Graphs via Harmonic Analysis for Experimental Design in Neuroimaging.

Kim WH, Hwang SJ, Adluru N, Johnson SC, Singh V.

Comput Vis ECCV. 2016 Oct;9910:188-205. doi: 10.1007/978-3-319-46466-4_12.
Abundant Inverse Regression using Sufficient Reduction and its Applications.Publications2016-10-01CPCPAbundant Inverse Regression using Sufficient Reduction and its Applications.

Kim HJ, Smith BM, Adluru N, Dyer CR, Johnson SC, Singh V.

Comput Vis ECCV. 2016 Oct;9907:570-584. doi: 10.1007/978-3-319-46487-9_35.
Brain structural changes following adaptive cognitive training assessed by Tensor-Based Morphometry (TBM).Publications2016-10-01ENIGMABrain structural changes following adaptive cognitive training assessed by Tensor-Based Morphometry (TBM).

Colom R, Hua X, Martínez K, Burgaleta M, Román FJ, Gunter JL, Carmona S, Jaeggi SM, Thompson PM.

Neuropsychologia. 2016 Oct;91:77-85. doi: 10.1016/j.neuropsychologia.2016.07.034.
A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways.Publications2016-10-04CCDA regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways.

Huang T, Alvarez AA, Pangeni RP, M Horbinski C, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY.

Nat Commun. 2016 Oct 4;7:12885. doi: 10.1038/ncomms12885.
Discovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data.Publications2016-10-07ENIGMADiscovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data.

Kang EY, Martin L, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E.

Genetics. 2016 Oct 7;:. doi: 10.1534/genetics.115.177246.
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.Publications2016-10-25CPCPA statistical approach for identifying differential distributions in single-cell RNA-seq experiments.

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C.

Genome Biol. 2016 Oct 25;17(1):222. doi: 10.1186/s13059-016-1077-y.
A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey.Publications2016-10-25PIC-SUREA database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey.

Patel CJ, Pho N, McDuffie M, Easton-Marks J, Kothari C, Kohane IS, Avillach P.

Sci Data. 2016 Oct 25;3:160096. doi: 10.1038/sdata.2016.96.
Phenome-wide association study of autoantibodies to citrullinated and non-citrullinated epitopes in rheumatoid arthritis.Publications2016-10-28PIC-SUREPhenome-wide association study of autoantibodies to citrullinated and non-citrullinated epitopes in rheumatoid arthritis.

Liao KP, Sparks JA, Hejblum BP, Kuo IH, Cui J, Lahey LJ, Cagan A, Gainer VS, Liu W, Cai TT, Sokolove J, Cai T.

Arthritis Rheumatol. 2016 Oct 28;:. doi: 10.1002/art.39974.
MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays.Publications2016-11-01CPCPMR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays.

Li H, Zhu Y, Burnside ES, Drukker K, Hoadley KA, Fan C, Conzen SD, Whitman GJ, Sutton EJ, Net JM, Ganott M, Huang E, Morris EA, Perou CM, Ji Y, Giger ML.

Radiology. 2016 Nov;281(2):382-391. doi: 10.1148/radiol.2016152110.
A public database of macromolecular diffraction experiments.Publications2016-11-01Data WranglingA public database of macromolecular diffraction experiments.

Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W.

Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1181-1193. doi: 10.1107/S2059798316014716.
Computational discovery of transcription factors associated with drug response.Publications2016-11-01KnowEnGComputational discovery of transcription factors associated with drug response.

Hanson C, Cairns J, Wang L, Sinha S.

Pharmacogenomics J. 2016 Nov;16(6):573-582. doi: 10.1038/tpj.2015.74.
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.Publications2016-11-04HeartBD2KData-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.

Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P.

J Proteome Res. 2016 Nov 4;15(11):4126-4134. doi: 10.1021/acs.jproteome.6b00095.
Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.Publications2016-11-04BDDSMetrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW.

J Proteome Res. 2016 Nov 4;15(11):3951-3960. doi: 10.1021/acs.jproteome.6b00511.
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.Publications2016-11-04BDDSHuman Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3961-3970. doi: 10.1021/acs.jproteome.6b00392.
Somatic cancer variant curation and harmonization through consensus minimum variant level data.Publications2016-11-04Data WranglingSomatic cancer variant curation and harmonization through consensus minimum variant level data.

Ritter DI, Roychowdhury S, Roy A, Rao S, Landrum MJ, Sonkin D, Shekar M, Davis CF, Hart RK, Micheel C, Weaver M, Van Allen EM, Parsons DW, McLeod HL, Watson MS, Plon SE, Kulkarni S, Madhavan S, ClinGen Somatic Cancer Working Group..

Genome Med. 2016 Nov 4;8(1):117. doi: 10.1186/s13073-016-0367-z.
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.Publications2016-11-04BDDSTiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. doi: 10.1021/acs.jproteome.6b00445.
A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes.Publications2016-11-14KnowEnGA network-based phenotype mapping approach to identify genes that modulate drug response phenotypes.

Cairns J, Ung CY, da Rocha EL, Zhang C, Correia C, Weinshilboum R, Wang L, Li H.

Sci Rep. 2016 Nov 14;6:37003. doi: 10.1038/srep37003.
GEN3VA: aggregation and analysis of gene expression signatures from related studies.Publications2016-11-15LINCS-DCICGEN3VA: aggregation and analysis of gene expression signatures from related studies.

Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A.

BMC Bioinformatics. 2016 Nov 15;17(1):461. doi: 10.1186/s12859-016-1321-1.
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.Publications2016-11-25BDTGThe Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.

Jain M, Olsen HE, Paten B, Akeson M.

Genome Biol. 2016 Nov 25;17(1):239. doi: 10.1186/s13059-016-1103-0.
Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers.Publications2016-11-29CCDPointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers.

Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC.

J Pathol Inform. 2016 Nov 29;7:47. doi: 10.4103/2153-3539.194839.
KCNE4 and KCNE5: K(+) channel regulation and cardiac arrhythmogenesis.Publications2016-11-30HeartBD2KKCNE4 and KCNE5: K(+) channel regulation and cardiac arrhythmogenesis.

Abbott GW.

Gene. 2016 Nov 30;593(2):249-60. doi: 10.1016/j.gene.2016.07.069.
Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations.Publications2016-12-01CCDSignal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations.

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X.

Cancer Res. 2016 Dec 1;76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740.
Knowledge gaps to understanding cardiac macrophage polarization following myocardial infarction.Publications2016-12-01HeartBD2KKnowledge gaps to understanding cardiac macrophage polarization following myocardial infarction.

Lindsey ML, Saucerman JJ, DeLeon-Pennell KY.

Biochim Biophys Acta. 2016 Dec;1862(12):2288-2292. doi: 10.1016/j.bbadis.2016.05.013.
Subcortical volumetric abnormalities in bipolar disorder.Publications2016-12-01ENIGMASubcortical volumetric abnormalities in bipolar disorder.

Hibar DP, Westlye LT, van Erp TG, Rasmussen J, Leonardo CD, Faskowitz J, Haukvik UK, Hartberg CB, Doan NT, Agartz I, Dale AM, Gruber O, Krämer B, Trost S, Liberg B, Abé C, Ekman CJ, Ingvar M, Landén M, Fears SC, Freimer NB, Bearden CE, Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes., Sprooten E, Glahn DC, Pearlson GD, Emsell L, Kenney J, Scanlon C, McDonald C, Cannon DM, Almeida J, Versace A, Caseras X, Lawrence NS, Phillips ML, Dima D, Delvecchio G, Frangou S, Satterthwaite TD, Wolf D, Houenou J, Henry C, Malt UF, Bøen E, Elvsåshagen T, Young AH, Lloyd AJ, Goodwin GM, Mackay CE, Bourne C, Bilderbeck A, Abramovic L, Boks MP, van Haren NE, Ophoff RA, Kahn RS, Bauer M, Pfennig A, Alda M, Hajek T, Mwangi B, Soares JC, Nickson T, Dimitrova R, Sussmann JE, Hagenaars S, Whalley HC, McIntosh AM, Thompson PM, Andreassen OA.

Mol Psychiatry. 2016 Dec;21(12):1710-1716. doi: 10.1038/mp.2015.227.
Novel genetic loci underlying human intracranial volume identified through genome-wide association.Publications2016-12-01ENIGMANovel genetic loci underlying human intracranial volume identified through genome-wide association.

Adams HH, Hibar DP, Chouraki V, Stein JL, Nyquist PA, Rentería ME, Trompet S, Arias-Vasquez A, Seshadri S, Desrivières S, Beecham AH, Jahanshad N, Wittfeld K, Van der Lee SJ, Abramovic L, Alhusaini S, Amin N, Andersson M, Arfanakis K, Aribisala BS, Armstrong NJ, Athanasiu L, Axelsson T, Beiser A, Bernard M, Bis JC, Blanken LM, Blanton SH, Bohlken MM, Boks MP, Bralten J, Brickman AM, Carmichael O, Chakravarty MM, Chauhan G, Chen Q, Ching CR, Cuellar-Partida G, Braber AD, Doan NT, Ehrlich S, Filippi I, Ge T, Giddaluru S, Goldman AL, Gottesman RF, Greven CU, Grimm O, Griswold ME, Guadalupe T, Hass J, Haukvik UK, Hilal S, Hofer E, Hoehn D, Holmes AJ, Hoogman M, Janowitz D, Jia T, Kasperaviciute D, Kim S, Klein M, Kraemer B, Lee PH, Liao J, Liewald DC, Lopez LM, Luciano M, Macare C, Marquand A, Matarin M, Mather KA, Mattheisen M, Mazoyer B, McKay DR, McWhirter R, Milaneschi Y, Mirza-Schreiber N, Muetzel RL, Maniega SM, Nho K, Nugent AC, Loohuis LM, Oosterlaan J, Papmeyer M, Pappa I, Pirpamer L, Pudas S, Pütz B, Rajan KB, Ramasamy A, Richards JS, Risacher SL, Roiz-Santiañez R, Rommelse N, Rose EJ, Royle NA, Rundek T, Sämann PG, Satizabal CL, Schmaal L, Schork AJ, Shen L, Shin J, Shumskaya E, Smith AV, Sprooten E, Strike LT, Teumer A, Thomson R, Tordesillas-Gutierrez D, Toro R, Trabzuni D, Vaidya D, Van der Grond J, Van der Meer D, Van Donkelaar MM, Van Eijk KR, Van Erp TG, Van Rooij D, Walton E, Westlye LT, Whelan CD, Windham BG, Winkler AM, Woldehawariat G, Wolf C, Wolfers T, Xu B, Yanek LR, Yang J, Zijdenbos A, Zwiers MP, Agartz I, Aggarwal NT, Almasy L, Ames D, Amouyel P, Andreassen OA, Arepalli S, Assareh AA, Barral S, Bastin ME, Becker DM, Becker JT, Bennett DA, Blangero J, van Bokhoven H, Boomsma DI, Brodaty H, Brouwer RM, Brunner HG, Buckner RL, Buitelaar JK, Bulayeva KB, Cahn W, Calhoun VD, Cannon DM, Cavalleri GL, Chen C, Cheng CY, Cichon S, Cookson MR, Corvin A, Crespo-Facorro B, Curran JE, Czisch M, Dale AM, Davies GE, De Geus EJ, De Jager PL, de Zubicaray GI, Delanty N, Depondt C, DeStefano AL, Dillman A, Djurovic S, Donohoe G, Drevets WC, Duggirala R, Dyer TD, Erk S, Espeseth T, Evans DA, Fedko IO, Fernández G, Ferrucci L, Fisher SE, Fleischman DA, Ford I, Foroud TM, Fox PT, Francks C, Fukunaga M, Gibbs JR, Glahn DC, Gollub RL, Göring HH, Grabe HJ, Green RC, Gruber O, Gudnason V, Guelfi S, Hansell NK, Hardy J, Hartman CA, Hashimoto R, Hegenscheid K, Heinz A, Le Hellard S, Hernandez DG, Heslenfeld DJ, Ho BC, Hoekstra PJ, Hoffmann W, Hofman A, Holsboer F, Homuth G, Hosten N, Hottenga JJ, Pol HE, Ikeda M, Ikram MK, Jack CR Jr, Jenkinson M, Johnson R, Jönsson EG, Jukema JW, Kahn RS, Kanai R, Kloszewska I, Knopman DS, Kochunov P, Kwok JB, Lawrie SM, Lemaître H, Liu X, Longo DL, Longstreth WT Jr, Lopez OL, Lovestone S, Martinez O, Martinot JL, Mattay VS, McDonald C, McIntosh AM, McMahon KL, McMahon FJ, Mecocci P, Melle I, Meyer-Lindenberg A, Mohnke S, Montgomery GW, Morris DW, Mosley TH, Mühleisen TW, Müller-Myhsok B, Nalls MA, Nauck M, Nichols TE, Niessen WJ, Nöthen MM, Nyberg L, Ohi K, Olvera RL, Ophoff RA, Pandolfo M, Paus T, Pausova Z, Penninx BW, Pike GB, Potkin SG, Psaty BM, Reppermund S, Rietschel M, Roffman JL, Romanczuk-Seiferth N, Rotter JI, Ryten M, Sacco RL, Sachdev PS, Saykin AJ, Schmidt R, Schofield PR, Sigurdsson S, Simmons A, Singleton A, Sisodiya SM, Smith C, Smoller JW, Soininen H, Srikanth V, Steen VM, Stott DJ, Sussmann JE, Thalamuthu A, Tiemeier H, Toga AW, Traynor BJ, Troncoso J, Turner JA, Tzourio C, Uitterlinden AG, Hernández MC, Van der Brug M, Van der Lugt A, Van der Wee NJ, Van Duijn CM, Van Haren NE, Van T Ent D, Van Tol MJ, Vardarajan BN, Veltman DJ, Vernooij MW, Völzke H, Walter H, Wardlaw JM, Wassink TH, Weale ME, Weinberger DR, Weiner MW, Wen W, Westman E, White T, Wong TY, Wright CB, Zielke HR, Zonderman AB, Deary IJ, DeCarli C, Schmidt H, Martin NG, De Craen AJ, Wright MJ, Launer LJ, Schumann G, Fornage M, Franke B, Debette S, Medland SE, Ikram MA, Thompson PM.

Nat Neurosci. 2016 Dec;19(12):1569-1582. doi: 10.1038/nn.4398.
ApoE ε4 Is Associated With Cognition, Brain Integrity, and Atrophy in HIV Over Age 60.Publications2016-12-01ENIGMAApoE ε4 Is Associated With Cognition, Brain Integrity, and Atrophy in HIV Over Age 60.

Wendelken LA, Jahanshad N, Rosen HJ, Busovaca E, Allen I, Coppola G, Adams C, Rankin KP, Milanini B, Clifford K, Wojta K, Nir TM, Gutman BA, Thompson PM, Valcour V.

J Acquir Immune Defic Syndr. 2016 Dec 1;73(4):426-432. doi: 10.1097/QAI.0000000000001091.
Heterochronicity of white matter development and aging explains regional patient control differences in schizophrenia.Publications2016-12-01ENIGMAHeterochronicity of white matter development and aging explains regional patient control differences in schizophrenia.

Kochunov P, Ganjgahi H, Winkler A, Kelly S, Shukla DK, Du X, Jahanshad N, Rowland L, Sampath H, Patel B, O'Donnell P, Xie Z, Paciga SA, Schubert CR, Chen J, Zhang G, Thompson PM, Nichols TE, Hong LE.

Hum Brain Mapp. 2016 Dec;37(12):4673-4688. doi: 10.1002/hbm.23336.
Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress.Publications2016-12-01CPCPSex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress.

Papale LA, Li S, Madrid A, Zhang Q, Chen L, Chopra P, Jin P, Keleş S, Alisch RS.

Neurobiol Dis. 2016 Dec;96:54-66. doi: 10.1016/j.nbd.2016.08.014.
Partitioning heritability analysis reveals a shared genetic basis of brain anatomy and schizophrenia.Publications2016-12-01ENIGMAPartitioning heritability analysis reveals a shared genetic basis of brain anatomy and schizophrenia.

Lee PH, Baker JT, Holmes AJ, Jahanshad N, Ge T, Jung JY, Cruz Y, Manoach DS, Hibar DP, Faskowitz J, McMahon KL, de Zubicaray GI, Martin NH, Wright MJ, Öngür D, Buckner R, Roffman J, Thompson PM, Smoller JW.

Mol Psychiatry. 2016 Dec;21(12):1680-1689. doi: 10.1038/mp.2016.164.
An advanced white matter tract analysis in frontotemporal dementia and early-onset Alzheimer's disease.Publications2016-12-01ENIGMAAn advanced white matter tract analysis in frontotemporal dementia and early-onset Alzheimer's disease.

Daianu M, Mendez MF, Baboyan VG, Jin Y, Melrose RJ, Jimenez EE, Thompson PM.

Brain Imaging Behav. 2016 Dec;10(4):1038-1053. doi: 10.1007/s11682-015-9458-5.
Development of a dynamic computational model of social cognitive theory.Publications2016-12-01MobilizeDevelopment of a dynamic computational model of social cognitive theory.

Riley WT, Martin CA, Rivera DE, Hekler EB, Adams MA, Buman MP, Pavel M, King AC.

Transl Behav Med. 2016 Dec;6(4):483-495. doi: 10.1007/s13142-015-0356-6.
Correcting the record of structural publications requires joint effort of the community and journal editors.Publications2016-12-01Data WranglingCorrecting the record of structural publications requires joint effort of the community and journal editors.

Rupp B, Wlodawer A, Minor W, Helliwell JR, Jaskolski M.

FEBS J. 2016 Dec;283(24):4452-4457. doi: 10.1111/febs.13765.
Colocalization of GWAS and eQTL Signals Detects Target Genes.Publications2016-12-01ENIGMAColocalization of GWAS and eQTL Signals Detects Target Genes.

Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JW, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E.

Am J Hum Genet. 2016 Dec 1;99(6):1245-1260. doi: 10.1016/j.ajhg.2016.10.003.
Cardiovascular proteomics in the era of big data: experimental and computational advances.Publications2016-12-05HeartBD2KCardiovascular proteomics in the era of big data: experimental and computational advances.

Lam MP, Lau E, Ng DC, Wang D, Ping P.

Clin Proteomics. 2016 Dec 5;13:23. doi: 10.1186/s12014-016-9124-y.
Screening Breast MRI Outcomes in Routine Clinical Practice: Comparison to BI-RADS Benchmarks.Publications2016-12-13CPCPScreening Breast MRI Outcomes in Routine Clinical Practice: Comparison to BI-RADS Benchmarks.

Strigel RM, Rollenhagen J, Burnside ES, Elezaby M, Fowler AM, Kelcz F, Salkowski L, DeMartini WB.

Acad Radiol. 2016 Dec 13;:. doi: 10.1016/j.acra.2016.10.014.
Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.Publications2016-12-20LINCS-DCICEstimating uncertainty in respondent-driven sampling using a tree bootstrap method.

Baraff AJ, McCormick TH, Raftery AE.

Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14668-14673. doi: 10.1073/pnas.1617258113.
Proteomics Research in Cardiovascular Medicine and Biomarker Discovery.Publications2016-12-27HeartBD2KProteomics Research in Cardiovascular Medicine and Biomarker Discovery.

Lam MP, Ping P, Murphy E.

J Am Coll Cardiol. 2016 Dec 27;68(25):2819-2830. doi: 10.1016/j.jacc.2016.10.031.
Conformal invariants for multiply connected surfaces: Application to landmark curve-based brain morphometry analysis.Publications2017-01-01ENIGMAConformal invariants for multiply connected surfaces: Application to landmark curve-based brain morphometry analysis.

Shi J, Zhang W, Tang M, Caselli RJ, Wang Y.

Med Image Anal. 2017 Jan;35:517-529. doi: 10.1016/j.media.2016.09.001.
Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers.Publications2017-01-01LINCS-DCICKrüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers.

Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma'ayan A, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC.

J Am Soc Nephrol. 2017 Jan;28(1):166-184. doi: 10.1681/ASN.2015060672.
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations.Publications2017-01-01PIC-SUREBridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations.

Luo Y, Uzuner Ö, Szolovits P.

Brief Bioinform. 2017 Jan;18(1):160-178. doi: 10.1093/bib/bbw001.
Multimodal neuroimaging of male and female brain structure in health and disease across the life span.Publications2017-01-02ENIGMAMultimodal neuroimaging of male and female brain structure in health and disease across the life span.

Jahanshad N, Thompson PM.

J Neurosci Res. 2017 Jan 2;95(1-2):371-379. doi: 10.1002/jnr.23919.
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.Publications2017-01-04BDDSThe ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936.
Drug Response Prediction as a Link Prediction Problem.Publications2017-01-09Data CompressionDrug Response Prediction as a Link Prediction Problem.

Stanfield Z, Coşkun M, Koyutürk M.

Sci Rep. 2017 Jan 9;7:40321. doi: 10.1038/srep40321.
ENIGMA and the individual: Predicting factors that affect the brain in 35 countries worldwide.Publications2017-01-15ENIGMAENIGMA and the individual: Predicting factors that affect the brain in 35 countries worldwide.

Thompson PM, Andreassen OA, Arias-Vasquez A, Bearden CE, Boedhoe PS, Brouwer RM, Buckner RL, Buitelaar JK, Bulayeva KB, Cannon DM, Cohen RA, Conrod PJ, Dale AM, Deary IJ, Dennis EL, de Reus MA, Desrivieres S, Dima D, Donohoe G, Fisher SE, Fouche JP, Francks C, Frangou S, Franke B, Ganjgahi H, Garavan H, Glahn DC, Grabe HJ, Guadalupe T, Gutman BA, Hashimoto R, Hibar DP, Holland D, Hoogman M, Pol HE, Hosten N, Jahanshad N, Kelly S, Kochunov P, Kremen WS, Lee PH, Mackey S, Martin NG, Mazoyer B, McDonald C, Medland SE, Morey RA, Nichols TE, Paus T, Pausova Z, Schmaal L, Schumann G, Shen L, Sisodiya SM, Smit DJ, Smoller JW, Stein DJ, Stein JL, Toro R, Turner JA, van den Heuvel MP, van den Heuvel OL, van Erp TG, van Rooij D, Veltman DJ, Walter H, Wang Y, Wardlaw JM, Whelan CD, Wright MJ, Ye J, ENIGMA Consortium..

Neuroimage. 2017 Jan 15;145(Pt B):389-408. doi: 10.1016/j.neuroimage.2015.11.057.
Toward Automating HIV Identification: Machine Learning for Rapid Identification of HIV-Related Social Media Data.Publications2017-02-01Data WranglingToward Automating HIV Identification: Machine Learning for Rapid Identification of HIV-Related Social Media Data.

Young SD, Yu W, Wang W.

J Acquir Immune Defic Syndr. 2017 Feb 1;74 Suppl 2:S128-S131. doi: 10.1097/QAI.0000000000001240.
BioGPSTools2016-05-31HeartBD2KA free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function. Learn more here.
Mark2CureTools2016-05-31HeartBD2KThe ability to read remains a uniquely human skill. Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery. You can help them by identifying key pieces of information in scientific text to discover cures faster.
MyGene.infoTools2016-05-31HeartBD2KMyGene.info provides simple-to-use REST web services to query/retrieve gene annotation data.
ProteinInferenceTools2016-05-31HeartBD2KA proteomics tool developed to calculate protein FDR for both individual experiments and large-scale proteomics projects that combine multiple sample fractions or experiments.
Guten TagTools2016-05-31HeartBD2KGutenTag is software to identify peptides by the sequence tagging technique. SEQUEST searches a sequence database by mass, but GutenTag searches with short sequences derived directly from the spectrum.
ColanderTools2016-05-31HeartBD2KColander is a MS/MS data pre-processing program for selecting CID MS/MS spectra generated from phosphopeptides.
DeBunkerTools2016-05-31HeartBD2KDeBunker is a phosphorylation validation program
GeneWikiTools2016-05-31HeartBD2K
CPMTools2016-05-31HeartBD2KThe Charge Prediction Machine (CPM) is a tool for Inferring Precursor Charge States of Low Resolution Electron Transfer Dissociation Tandem Mass Spectra.
UnitemareTools2016-05-31HeartBD2KA tool developed for migrating existing SEQUEST results to the new unified file format. To learn more, visit here.
PatternLab for ProteomicsTools2016-05-31HeartBD2KPatternLab provides tools for analyzing shotgun proteomic data quantitated by spectral counting (with DTASelect) or labeling (with Census). The modules provide means to point differentialy expressed proteins / peptides (ACFold / TFold modules), find proteins with simmilar expression profiles in time-course experiments (TrendQuest module), find unique proteins to a state (Area proportional venn diagram module) and help interpreting results according to the Gene Ontology (Gene Ontology Explorer module).
YADATools2016-05-31HeartBD2KYADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.
MyVariant.infoTools2016-05-31HeartBD2KMyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources. It’s designed with simplicity and performance emphasized. You can use use it to annotate discovered variants with the up-to-date variant annotation; or query for specific known variants using a combination of your query criteria, especially across multiple data resources (e.g. to get all variants on gene CDK2, having polyphen2 score > 0.99, and also found in cosmic database using this query). MyVariant.info can also be used to power a web application which requires querying or retrieving variant annotations, without the need of maintaining your own local database backend.
Knowledge.bioTools2016-05-31HeartBD2KKnowledge.Bio is an open access web-based “rich client desktop” computer application that provides value-added access to the network of interconnected knowledge mined in the scientific literature from more than 20,000,000 PubMed abstracts.
RawExtractorTools2016-05-31HeartBD2KRawExtractor is a program to extract MS and MS/MS spectra from RAW files generated by Thermo mass spectrometers, such as LTQ, LTQ-Orbitrap, LCQ, and stores the spectra in ms1, ms2 or mzXML file format. The spectra files generated by RawExtractor program are used as input for protein identification programs SEQUEST, ProLuCID and quantitatation program Census.
CensusTools2016-05-31HeartBD2KQuantitative Analysis Tool for both labeling and labeling free analysis. To learn more, click here.
ProLuCIDTools2016-05-31HeartBD2KProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed in the Yates laboratory at The Scripps Research Institute.
SEQUESTTools2016-05-31HeartBD2KSEQUEST performs automated peptide/protein sequencing via database searching of MS/MS spectra without the need for any manual sequence interepretation.
DTASelectTools2016-05-31HeartBD2KDTASelect organizes and filters SEQUEST identifications, reducing the time required to interpret the results for each sample.
PINTTools2016-05-31HeartBD2KPINT, the Proteomics INTegrator, is an online experiment repository for final results comming from different qualitative and/or quantitative proteomics assays.
PSEA-QuantTools2016-05-31HeartBD2KPSEA-Quant is a protein set enrichment analysis algorithm for label-free and label-based mass spectrometry-based quantitative proteomics. It identifies protein sets from the Gene Ontology and Molecular Signature databases that are statistically significantly enriched with abundant proteins, which are measured with high reproducibility across a set of replicates.
IP2Tools2016-05-31HeartBD2KThe Integrated Proteomics Pipeline (IP2) is a proteomics data analysis platform.
BD2KPubMedTools2016-05-31HeartBD2KBD2KPubMed is a software tool that employs publicly available data to analyze scientific trends and research directions in a particular field of interest.
ProturnTools2016-05-31HeartBD2KCalculation of protein turnover rates from heavy water labeling mass spectrometry experiments. To learn more, click here.
BranchTools2016-05-31HeartBD2KExplores biomedical data using decision trees: Rules can encapsulate hypotheses that can be tested with data. They can also be used to make predictions.
OncoRepTools2016-05-31HeartBD2KOncoRep is a fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene fusion events, identification of clinical actionable mutations (in coding regions) and identification of treatable target structures. Furthermore, OncoRep reports suitable drugs based on identified actionable targets, which can be considered in the treatment decision making process.
Omics PipeTools2016-05-31HeartBD2KThe goals of Omics Pipe are to provide researchers with an open-source computational solution to implement ‘best practice’ pipelines with minimal development overhead and providing visual outputs to aid the researcher in biological interpretation. Currently Omics Pipe automates and provides summary reports for two RNA sequencing (RNA-seq) pipelines, variant calling from whole exome sequencing (WES) and whole genome sequencing (WGS) based on the Genome Analysis Toolkit (GATK), two ChIP-seq pipelines and a custom RNA-seq pipeline for personalized cancer genomic medicine reporting.
PRIDETools2016-05-31HeartBD2KThe PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.
ProteomeXchangeTools2016-05-31HeartBD2KThe ProteomeXchange consortium has been set up to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination.
Sage SynapseTools2016-05-31HeartBD2KSage Bionetworks has developed Synapse as an informatics platform dedicated to supporting the large-scale pooling of data, knowledge, and expertise across institutional boundaries to solve some of the most challenge problems in biomedical research.
Expression AtlasTools2016-05-31HeartBD2KThe Expression Atlas provides information on gene expression patterns under different biological conditions.
Gene Expression AtlasTools2016-05-31HeartBD2K
PSICQUICTools2016-05-31HeartBD2K
MetaboLightsTools2016-05-31HeartBD2KMetaboLights is a database for Metabolomics experiments and derived information.
BeagleTools2016-05-19BDDS, University of ChicagoBeagle, a 150 teraflops, 18,000-core Cray XE6 supercomputer that will support computation, simulation and data analysis for the biomedical research community.
HarmonizomeTools2016-05-19DCIC, Icahn School of Medicine at Mount SinaiHarmonizome is the Biological Knowledge Engine. Built on top of information about genes and proteins from 114 datasets, the Harmonizome is a knowledge engine for a diverse set of integrated resources.
EnrichrTools2016-05-19Icahn School of Medicine at Mount SinaiEnrichr is the Search Engine for Gene Lists and Signatures. An easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists.
GEO2EnrichrTools2016-05-19Icahn School of Medicine at Mount SinaiGEO2Enrichr is the Differential Expression Analysis Tool. A browser extension and web application to extract gene sets from GEO and analyze these lists for common biological functions.
LINCS Data PortalTools2016-05-19LINCSLINCS Data Portal is to access LINCS Data and Signatures. Features for searching and exploring LINCS dataset packages and reagents.
piLINCSTools2016-05-19LINCSpiLINCS is the interface to panoramaweb.org. A seamless user interface and intermediate API for accessing LINCS proteomics datasets (P100, GCP, etc.) on Panorama.
LINCS Information Framework (LIFE)Tools2016-05-19The University of Miami LINCS CenterLIFE is the LINCS Information System. Integrates all LINCS content leveraging a semantic knowledge model and common LINCS metadata standards.
iLINCSTools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiA computational biology project aimed at developing statistical methods and computational tools for integrative analysis of the data produced by the Library of Integrated Network-based Cellular Signatures (LINCS) program. Read more here.
LINCS Canvas BrowserTools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiThe LINCS Canvas Browser is an interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.
Drug/Cell-line BrowserTools2016-05-19LINCS, Icahn School of Medicine at Mount Sinai< href="http://www.maayanlab.net/LINCS/DCB/">Drug/Cell-line Browser is an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies.
Network2CanvasTools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiNetwork2Canvas is a web application that provides an alternative way to view networks and visualizes them by placing nodes on a square toroidal canvas.
Docent ITools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiDocent I is the overview guide into LINCS data. Docent provides a quantified, interactive view of the biological entities such as cell lines, small molecules, and assays within LINCS data.
Docent IITools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiDocent II is an overview of the LINCS Data Signature Generation Centers (DSGCs) Data Release Milestones. Docent II provides an interactive plot of available and upcoming data from the LINCS DSGCs.
Docent IIITools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiDocent III is an overview of the LINCS Consortium's datasets by assay and cell type. Docent III provides an interactive matrix of the most studied cell lines by assay.
Docent IVTools2016-05-19LINCS, Icahn School of Medicine at Mount SinaiDocent IV is the searchable overview of the LINCS Consortium's datasets. Docent IV provides two interfaces for searching LINCS data by assay, perturbagen, cell, and readout.
TransProteomics Pipeline (TPP)Tools2016-05-19BDDSAnalyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).
Big Data DashboardTools2016-05-19BDDS
2016 Innovation LabEvents2016-03-29BD2K Training Coordination CenterThe BD2K Training Coordination Center is organizing an Innovation Lab on Interdisciplinary Approaches to Biomedical Data Science Challenges of Wearable and/or Ambient Sensors on June 15-19 2016 at the UCLA Lake Arrowhead conference Center. The deadline to submit applications is 11:59pm, EST on April 4, 2016. To learn more or to register, click here.
Precision Behavioral Interventions Key to Population HealthEvents2016-03-28MobilizeAt the MD2K and Mobilize hosted mHealthConnect workshop at Stanford, scientists and researchers gathered to develop solutions for the challenges of digital health. For a first-hand account of the action, check out the Forbes article by David Shaywitz.
MD2K Webinar SeriesEvents2016-03-02MD2KDr. Karen Hovsepian and Hillol Sarker: cStress and Just-in-Time Stress Interventions. To watch the webinar, click here.
A Hackathon Using the Cancer Genomics CloudEvents2016-02-26BD2KHacking Cancer, a hackathon in collaboration with the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative and Seven Bridges, will be happening April 1st to 3rd in Cambridge, MA. Take a look at the event's agenda here.
2016 mHealth Training InstituteEvents2016-02-04MD2KThis week-long immersion program provides 30 selected participants with a core educational grounding in mHealth perspectives and methodologies and helps foster the intrapersonal and interpersonal skills and attitudes necessary for transdisciplinary collaborations. Applications are open and are due on February 28th. For more information, click here.
BD2K-LINCS DCIC: 1st Annual Systems Biology Data Science SymposiumEvents2016-02-01LINCS-DCICOn January 19-20, 2016, the first annual Systems Biology Data Science Symposium (SBDSS 2016) at the University of Miami brought together the BD2K-LINCS Data Coordination and Integration Center, local researchers, and outside experts who apply or develop computational systems biology resources. In presentations, a poster reception and several working sessions, the DCIC showcased tools/resources and scientific projects, connected developers with users, and initiated new collaborations. Congratulations to all attendees and the BD2K-LINCS DCIC on the success of the symposium! For more information about the SBDSS 2016, click here.
2nd BD2K/4th Network of BioThings HackathonEvents2015-11-23BD2KOn November 18th-20th, the CEDAR center and HeartBD2K center hosted a “Network of BioThings” Hackathon at Stanford University. The 3-day event brought together over 25 participants from various BD2K programs. Within 3 days, participants of varying backgrounds in data-science engaged in vibrant discussions to tackle some of the issues in biomedical research and created potential solutions by the end of the event. Check out the projects that were made at the Hackathon here.
Women in Data ScienceEvents2015-11-16MobilizeNovember 2, 2015, The Mobilize Center for Mobility Data Integration to Insight co-sponsored the Inaugural Women in Data Science Conference to inspire, educate and support women in industry, academia, government and NGOs. The one-day technical conference shared the latest data science-related research, taught how leading-edge companies are leveraging data science for success, brainstormed ways to better support women in data science, and allowed attendees to connect with potential mentors, collaborators, and funders. To learn more about the successful conference, click here.
2017 CCD Summer Short CourseEvents2017-03-28CCDThe Center for Causal Discovery will hold its third annual Summer Short Course in Causal Discovery from Biomedical Data at Carnegie Mellon University, Pittsburgh, PA on June 12-15, 2017.
BD2K-LINCS DCIC Systems Biology Data Science SymposiumEvents2015-10-13LINCS-DCICThe BD2K-LINCS Data Coordination and Integration Center will host the two-day Systems Biology Data Science Symposium (SBDSS) on January 19-20, 2016 at the University of Miami.
BD2K-LINCS-DCIC Summer Research Training Program in Biomedical Big Data ScienceEvents2015-10-13LINCS-DCICProgram Dates: June 6, 2016 - August 12, 2016 The BD2K-LINCS DCIC is currently accepting applications for the summer 2016 session! The BD2K-LINCS DCIC Summer Research Training Program in Biomedical Big Data Science is a research intensive ten-week training program for undergraduate and graduate students interested in participating in cutting edge research projects aimed at solving data-intensive biomedical problems.
BD2K-LINCS DCIC New Resource > > Harmonizome Mobile AppTools2015-10-13LINCS-DCICTo create the Harmonizome mobile app, members of the Ma’ayan Laboratory at the Icahn School of Medicine at Mount Sinai assembled, extracted, and organized knowledge from over 60 online resources, including novel databases. The Harmonizome serves this accumulated knowledge in an easy to access interface where users can enter their gene of interest to discover properties of genes. The knowledge spans many bioinformatics systems biology resources from expression in cells, tissues and diseases; regulation by transcription factors, chromatin marks and microRNAs; functional membership in protein complexes, pathways and ontologies; genomic associations with disease, and differential expression upon treatment of human cells with drugs; as well as structural and other genomic features
BD2K All Hands Grantee MeetingEvents2015-10-13BD2KNational Institutes of Health Big Data to Knowledge (BD2K) All Hands Grantee Meeting When: November 12 - 13, 2015 Where: Natcher Center (BLDG 45), NIH Main Campus, Bethesda, MD The BD2K 2015 All Hands Meeting will bring together researchers, educators, developers, and trainees from all of the BD2K initiative grants.
California Big Data Biomedical WorkshopEvents2015-10-09BDDSCalifornia has been the beneficiary of a number of the NIH's BD2K grants – from U54 centers of excellence, coordinating centers, to training project grants. Given that the NIH expects us all to cultivate “consortium activities,” we felt that a get together to share ideas and plan for such interactivities would be in order.
HUPO 2015 Bioinformatics HubEvents2015-09-27BD2KThe Bioinformatics Hub at HUPO 2015 in Vancouver begins today!

The objective of this hands-on meeting is to develop and execute original bioinformatics analyses on the publicly available human proteomics data during the conference, facilitated by several leading proteomics informatics groups, and completely open for participation by any and all interested conference attendees.
2nd BD2K 4th Network of BioThings HackathonEvents2015-09-14CEDAR, HeartBD2K, bioCADDIEWhat: 2nd BD2K / 4th Network of BioThings Hackathon (#hackBD2K)

This Hackathon will feature:

networking and mentoring with leading researchers and experts
hacking on exciting projects
prizes for the best contributions!
delicious food during the hackathon
When: November 18-20, 2015
AztecTools2015-07-01HeartBD2KBD2K Aztec is a global biomedical resource discovery index that allows users to simultaneously search a diverse array of tools. The resources indexed include web services, standalone software, publications, and large libraries composed of many interrelated functions. Aztec will ensure that software tools remain findable in the long term by issuing persistent DOIs and routinely updating metadata for the entire index. Aztec's established ontologies and robust API support the programmatic query of its entire database, as well as the construction of indexes for specialized subdomains. Aztec fosters an environment of sustainable resource support and discovery, empowering researchers to overcome the challenges of information science in the 21st century.
ReactomeTools2015-01-01HeartBD2KReactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.
MMap: Fast Billion-Scale Graph Computation on a PC via Memory Mapping.Publications, Tools2014-10-01MD2KMMap: Fast Billion-Scale Graph Computation on a PC via Memory Mapping.

Lin Z, Kahng M, Sabrin KM, Chau DH, Lee H, Kang U.

Proc IEEE Int Conf Big Data. 2014 Oct;2014:159-164. doi: 10.1109/BigData.2014.7004226.
COPaKBTools2011-05-12HeartBD2KCOPaKB is a centralized platform of cardiac proteomic data, relevant cardiocascular phenotypes and proteomic bioinformatics tools. COPaKB includes Mass Spec data as well as curated protein molecular and biomedical phenotype properties, which are organized into a relational database, MySQL ver. 5.6. COPaKb is also interfaced to a website -www.hearproteome.org- for public data retrieval and analysis.
EnigmaVisTools2011ENIGMAEnigmaVis is a tool for generating interactive plots that you can use to visualize and navigate datasets from ENIGMA. To get begin, make a query using the fields below. Hit submit to generate your plot. Additional documentation of features will be displayed below the plot, after it is generated.

Link: enigma.ini.usc.edu/enigma-vis
OpenSimTools2016MobilizeOpenSim is software for biomechanical modeling and simulation, which will serve as a common standard for integrating and analyzing mobility big data, including robust optimization methods for general use in biomedical big data analytics.

Link: opensim.stanford.edu
DeepDiveTools2016MobilizeOpenSim is software for developing, testing, and understanding trained systems that integrate diverse data and model types through logic rules.

Link: deepdive.stanford.edu
SNAPTools2016MobilizeSNAP (Stanford Network Analysis Project) is software for modeling and probing behavioral dynamics and decision making, as well as the dynamics of large social networks.

Link: snap.stanford.edu
Causal WebTools2016CCDOur user-friendly web application for performing causal discovery analysis on big data using large memory servers at the Pittsburgh Supercomputing Center. Use this software if you want to quickly try out a causal discovery algorithm or if you have big data that cannot be analyzed on your local hardware.

Link: ccd2.vm.bridges.psc.edu/ccd/
Causal CommandTools2016CCDA Java library and command line implementation of algorithms for performing causal discovery on big data. Use this software if you are interested incorporating analysis via a shell script or in a Java-based program.

Link: internal.rods.pitt.edu/datadepot
Py CausalTools2016CCDA python module that wraps algorithms for performing causal discovery on big data.

Link: github.com/bd2kccd/py-causal
R CausalTools2016CCDAn R module that wraps algorithms for performing causal discovery on big data.

Link: github.com/bd2kccd/r-causal
TETRADTools2016-05-19CCDTETRAD is a desktop java application that can connect to outside super computing resources if neccesary which creates, simulates data from, estimates, tests, predicts with, and searches for causal and statistical models. The aim of the program is to provide sophisticated methods in a friendly interface requiring very little statistical sophistication of the user and no programming knowledge.

Link: github.com/cmu-phil/tetrad
PIC-SURE RESTful APITools2016PIC-SUREHarvard University Medical School (HMS) Patient-Centered Informatics Common: Standardized Unification of Research Elements (PIC-SURE) is developing an open-source infrastructure that will foster the incorporation of multiple heterogeneous patient level clinical, omics and environment datasets. This system embraces the idea of decentralized datasets of varying types, and the protocols used to access them while still providing a simple communication layer that can handle querying, joining, and computing on. The BD2K PIC-SURE RESTful API implementation is called Inter Resource Communication Tool (IRCT). Link: bd2k-picsure.hms.harvard.edu
ExAC REST APITools2016PIC-SUREThe Exome Aggregation Consortium (ExAC) Browser is a product created at the Broad Institue. It contains genomic information ono ver 60,000 individuals who were sequenced through a variety of projects. You can learn more about this project at the ExAC web site (exac.broadinstitute.org). As part of the NIH BD2K PIC-SURE Center of Excellence the HMS Department of Biomedical informatics extended the ExAC application by providing a REST service. These services enable a user to integrate ExAC services into their own tools, querying the variant information and returning the data in an easy to use JSON format. Link: exac.hms.harvard.edu
NHANES Dataset ExplorerTools2016PIC-SURENHANES patient level public data with 41K patients. Link: nhanes.hms.harvard.edu
LincscloudTools2016LINCS-TGThe LINCS L1000 dataset is a catalog of gene-expression data collected from human cells treated with chemical compounds and genetic reagents. Computational methods to reduce the number of necessary genomic measurements, along with streamlined methodologies, have enabled us to significantly increase the size of the dataset and, along with it, our potential to connect human diseases with the genes that underlie them and the drugs that treat them.

Our goal is to make the L1000 data -- which currently comprises over 1.4M gene-expression profiles -- analyzable by all members of the biomedical research community. The best way to achieve that, we believe, is via an elastic and scalable cloud-based environment with an integrated suite of data, compute services, and tools. Such a system would have several modes of access -- user-friendly web applications, command-line UNIX interfaces, and data APIs -- thus eliminating the need for users to have to download large files. We are working to develop and broadly release such an environment: lincscloud.org.
ConnectivityMapTools2016LINCS-TGCMap is a resource that uses gene expression signatures to probe relationships between diseases, cell physiology, and therapeutics. The patterns of gene expression (a "signature") that arise from a disease, genetic perturbation (knockdown or overexpression of a gene) or treatment with a small molecule compound are compared for similarity to all perturbational signatures in the database. Perturbagens that give rise to highly similar (or opposing) expression signatures are "connected" and thus may have related effects on the cell. Our goal is to use these connections to uncover novel treatments for a variety of diseases, including cancers, neurological diseases, and infectious diseases. Link: clue.io
DERVIATools2016BDDSDERVIA is a suite of tools and services that are designed to significantly reduce the overhead and complexity of creating and managing complex, big datasets. DERVIA provide a digital asset management system for scientific data to streamlines the acquisition, modeling, management and sharing of complex, big data, and provides interfaces so that these data can be delivered to diverse external tools for big-data analysis and analytic tools. http://bd2k.ini.usc.edu/tools/dervia/
Big Data Repository (BDR)Tools2016BDDSTThe BDDS Data Repository (BDR) is a set of data services built to support the publication and discovery of biomedical data. BDR can be used to store and publish biomedical data from many domains, including neuroimaging, proteomics, and genomics. The production-ready data publication service offers a scalable repository where researchers can publish, preserve, and share even the largest biomedical research data. Data deposited in the BDR is associated with a persistent identifier that can be uniquely referenced in publications. Researchers themselves manage access to published data, including options to share data publically or with specific groups of users. Published data can be described with a variety of standard, customized and domain-specific metadata, all of which is indexed in the BDR discovery service and may be searched by other users. http://bd2k.ini.usc.edu/tools/big-data-repository/
GEMTools2016BDDSThe GAAIN Entity Mapper (GEM) is a software system for automated matching or mapping of data elements. The application context is that of matching corresponding data elements in the process of harmonization of disparate, independently created datasets or databases in the biomedical domain. The current process of manually mapping datasets is very resource and time intensive and we built the GEM system as an intelligent software assistant to aid data analysts with the data mapping process by providing suggestions for element matches. http://bd2k.ini.usc.edu/tools/gem/
BDDS GalaxyTools2016BDDSGenetic association is when one or more genotypes co-occur with a phenotype more often than random. In biomedical research, it often refers to the association of genetic polymorphism, such as SNPs, with a phenotype, usually a disease. Tools in this category are designed to assess such associations. BDDS Galaxy genetic association tools, NeuroimagingPheWAS toolbox and the well established PLINK will be integrated in the pipeline. http://bd2k.ini.usc.edu/tools/association-studies/
Neuroimaging PhewasTools2016BDDSNeuroimaging based phenome-wide association study (PheWAS), with a genotype-to-phenotype strategy, explores the associations of a SNP (or SNPs) of interest with diverse brain phenotypes, such as cortical thickness, surface area, cortical volume and etc. at each brain point, extracted from neuroimaging data. This method has the power to detect potential novel genotype-to-phenotype associations and consequently would provide a comprehensive view for the mechanism of how the SNP of interest influences the brain. http://bd2k.ini.usc.edu/tools/neuroimaging-phewas/
Panther Overrepresentation TestTools2016BDDSThe PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 104 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. http://bd2k.ini.usc.edu/tools/panther/
MINIDTools2016BDDSThe BDDS Minimal Viable Identifier (minid) pilot enables unambiguous naming and identification of research data products. Minids are designed to be lightweight, enabling simple creation and use, and requiring only minimal metadata to be specified about the object. Due to their lightweight nature minids can be associated with any data product and at any stage of the research lifecycle including raw, derived, and final data products. Association of minids with all biomedical data will enable researchers to unambiguously refer to data, track relationships between data, exchange references (rather than files) between researchers and applications, and verify the integrity of referenced data. http://bd2k.ini.usc.edu/tools/minid/
BDBAGTools2016BDDSThe BD Bag Software software allows researchers to address a significant Big Data challenge of assembling, identifying, and providing access to subsets of data in a large and complex data collection workflow such as from a catalog search to an analysis pipeline and to a publication service. This collection of utilities work with BagIt packages that conform to the BDDS Baggit and BDDS Bagit/RO (link to https://github.com/ResearchObject/bagit-ro) profiles. A unique aspect of this work is that the data that is aggregated need not be collocated: instead, data collections can be uniquely identified where large elements may be located in cloud or enterprise storage. This is critical for big data elements where the cost of transfer of the data can be prohibitive. Another important feature is the use of JSON-LD to provide a standard way for linking metadata with existing ontologies and vocabularies. As the first example use of JSON-LD metadata, a model has been developed for representing ontology-based file types. http://bd2k.ini.usc.edu/tools/bdbag/
Big Data Quality Control (BDQC)Tools2016BDDSBDDS is developing a fully automated tool for performing quality controls on big data. BDQC identifies anomalous files among large collections of files that are a priori assumed to be equivalent in structure and content. It was motivated by the realization that when running complex pipelines on large data sets, errors creep in for a variety of reasons, mostly related to the (unpredictable) runtime environment. BDQC is intended to 1) validate primary input data to pipelines; 2) validate output (or intermediate stages of) data processing pipelines; 3) discover potentially "interesting" outliers. Although it was developed in the context of genomics research, it is expressly not tied to a specific knowledge domain. It can be customized (via the plugin mechanism) for specific domain needs. http://bd2k.ini.usc.edu/tools/big-data-quality-control/
BRCA ExchangeTools2016BDTGThe goals of the BRCA Exchange are to aggregate, curate and share BRCA variation data, which generally exists in disparate silos. https://github.com/BD2KGenomics/brca-exchange
DCC DashboardTools2016BDTGhttps://github.com/BD2KGenomics/dcc-dashboard
CGGloudTools2016BDTGCGCloud lets you automate the creation, management and provisioning of VMs and clusters of VMs in Amazon EC2. While allowing for easy programmatic customization of VMs in developement, it also provides rock-solid reproducability in production. https://github.com/BD2KGenomics/cgcloud
ToilTools2016BDTGToil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the principles of functional programming. Full documentation for the latest stable release can be found at http://toil.readthedocs.io/en/releases-3.5.x/
CGL Docker LibTools2016BDTGhttps://github.com/BD2KGenomics/cgl-docker-lib
ProTECTTools2016BDTGProTECT uses sequencing information from a patient to predict the neo-epitopes produced in their tumors that can be used in T-cell based, or peptide vaccine based therapies. https://github.com/BD2KGenomics/protect
ClusterEngTools2016KnowEnGhttp://www.knoweng.org/education/clustereng/
ClusTypeTools2015KnowEnGhttp://shanzhenren.github.io/ClusType/
SegPhraseTools2015KnowEnGhttps://github.com/shangjingbo1226/SegPhrase
AutoPhraseTools2017KnowEnGhttps://github.com/shangjingbo1226/AutoPhrase
SaulTools2016KnowEnGSaul is a modeling language implemented as a domain specific language (DSL) in Scala. The main goal of Saul is to facilitate designing machine learning models with arbitrary configurations for the application programmer. https://github.com/IllinoisCogComp/saul
ZenvisageTools2015KnowEnGZenvisage is a visual exploration system that can automatically identify and recommend interesting visualizations. The user can specify at a high level what they are looking for, and the system will do the rest. http://zenvisage.github.io/
DataSpreadTools2015KnowEnGSpreadsheets have found ubiquitous use by scientists, business and financial analysts, researchers, and lay users. However, spreadsheets cannot express complex operations (e.g., joins), cannot handle large datasets, do not support collaboration, and foster errors, redundancy, and stale data. On the other hand, relational databases are well-known to be powerful and scalable, but are not flexible, intuitive, and interactive.

DataSpread addresses these limitations by holistically unifying spread-sheets with databases: preserving spreadsheets as the front-end, and databases as the back-end. http://dataspread.github.io/
CEDAR WorkbenchTools2016CEDARThe CEDAR Workbench, as we refer to the suite of CEDAR tools, makes it easy to collect and use metadata. Eventually our tools will cover the entire lifecycle of metadata, from before the first metadata record is created to its eventual processing, and even enhancement, by users and analysts. But for now, CEDAR tools help you create forms to collect metadata, make those available to users, and download the information that users have provided.
http://cedar.metadatacenter.net/
EBSeqHMMTools2015CPCPEBSeqHMM is an R package that implements an auto-regressive hidden Markov model for identifying genes and isoforms that have expression changes in ordered RNA-seq experiments, and clustering the identified genes into paths showing similar changes. EBSeqHMM is suitable for any ordered RNA-seq experiment including time courses and spatially ordered experiments. https://www.bioconductor.org/packages/release/bioc/html/EBSeqHMM.html
OscopeTools2015CPCPOscope is a statistical pipeline for identifying oscillatory genes and characterizing one cycle of their oscillation, referred to as a base-cycle, in unsynchronized snapshot single cell RNA-seq experiments. The Oscope pipeline includes three modules: a paired-sine model module to identify candidate oscillator pairs; a clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to estimate the base-cycle oscillation within each group.

http://www.bioconductor.org/packages/devel/bioc/html/Oscope.html
OEFinderTools2015CPCPOEFinder is an R package that allows an investigator to identify genes having the so-called ordering effect in single-cell RNA-seq data generated by the Fluidigm C1 platform. This effect (Leng et al., Nature Methods, 2015) refers to significantly increased gene expression in cells captured from sites with small or large plate output IDs. https://github.com/lengning/OEFinder

RolemodelTools2015CPCPThe role model is a probability model used in the context of gene set analysis to describe the functional content of a user-supplied gene list, such as one derived from a genome-wide experiment. It integrates the list with gene sets from a knowledge base (e.g. Gene Ontology) and aims to summarize gene functions that are represented at an unusually high rate on the list. Compared to other gene-set enrichment analysis schemes, role model calculations contend better with the complexity of the knowledge base, including redundancies caused by overlapping sets and the effects of set-size variation.

https://github.com/wiscstatman/rolemodel
GADGETTools2016CPCPGADGET is a web tool for finding and ranking genes and metabolites that are associated with a given query in the biomedical literature. It's like a version of PubMed that returns genes and metabolites instead of articles. http://gadget.biostat.wisc.edu/
rvaluesTools2015CPCPrvalues is an R package for computing "r-values" from various kinds of user input such as a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units. https://cran.r-project.org/web/packages/rvalues/
atSNPTools2016CPCPatSNP (Affinity Test for regulatory SNP detection) is an R package for computing and testing large-scale motif-SNP interactions. It provides three main functions: (1) Computing the binding affinity scores for both the reference and the SNP alleles based on position weight matrices; (2) Computing the p-values of the affinity scores for each allele; (3) Computing the p-values of the affinity score changes between the reference and the SNP alleles. https://github.com/chandlerzuo/atSNP
MBASICTools2015CPCPMBASIC (Matrix Based Analysis for State-space Inference and Clustering) is a statistical framework for integrative analysis of many related experiments where observations are collected over a set of units. The MBASIC framework allows for simultaneous projection of the observations onto a discrete state space and clustering the units based on their state-space profiles. MBASIC is applicable to many high throughput sequencing datasets. For example, it enables analysis of large collections of ChIP-seq datasets by simultaneously identifying genomic loci with peaks and similar peak patterns across multiple conditions. https://github.com/keleslab/mbasic
ConciergeTools2016LINCS-DCICConcierge provides multiple points of entry to the LINCS tools and databases. http://lincs-dcic.org/#/getting-started/concierge
L1000CDS2 (API)Tools2016LINCS-DCICL1000CDS2 queries gene expression signatures against the LINCS L1000 to identify and prioritize small molecules that can reverse or mimic the observed input expression pattern. http://amp.pharm.mssm.edu/L1000CDS2/
Gen3vaTools2016LINCS-DCICGen3va aggregates and analyzes gene expression signatures extracted from GEO by the crowd using GEO2Enrichr. http://amp.pharm.mssm.edu/gen3va
CREEDSTools2016LINCS-DCICCollections of processed gene, drug and disease signatures from GEO. http://amp.pharm.mssm.edu/CREEDS/
SEP L1000Tools2016LINCS-DCICSEP L1000 is a web portal to share predicted ADRs. http://maayanlab.net/SEP-L1000/
SlicrTools2016LINCS-DCICSlicr is a metadata search engine that searches for LINCS L1000 gene expression profiles and signatures matching user's input parameters. http://amp.pharm.mssm.edu/Slicr
PAEATools2016LINCS-DCICPAEA is a new R/Shiny gene set enrichment web application with over 70 gene set libraries available for enrichment analysis. http://amp.pharm.mssm.edu/PAEA/
GUIdockTools2016LINCS-DCICA method for deploying containers with a graphical user interface. https://github.com/WebDataScience/GUIdock
MD2K PlatformTools2016MD2KThe MD2K platform is designed from the ground up as a high-frequency data stream processing toolchain that provides flexible data types and custom object storage. It can collect and analyze data from tens of wearable sensors via a wide array of wireless radios (ANT, Bluetooth, Bluetooth LE, etc.). It also provides native support for triggering notifications, self-report prompts, and interventions based on real-time values of digital biomarkers derived from sensor data. http://docs.md2k.org/
CVXTools2014MobilizeCVX is matlab software for convex optimization: http://stanford.edu/~boyd/cvx/
CVXPYTools2015MobilizeCVXPY is a convex optimization modeling layer for Python: CVXPY, a convex optimization modeling layer for Python

DCCPTools2016MobilizeDCCP is a CVXPY extension for difference of convex programming: https://github.com/cvxgrp/dccp
GLRMTools2016MobilizeGLRM, generalized low rank models: https://github.com/madeleineudell/LowRankModels.jl
ECOSTools2014MobilizeECOS, an SOCP solver suitable for embedded applications:https://github.com/embotech/ecos
SCSTools2016MobilizeSCS, first-order primal-dual cone solver for large problems: https://github.com/cvxgrp/scs
CVXGENTools2014MobilizeCVXGEN, a code generator for convex optimization
POGSTools2015MobilizeProximal Graph Solver (POGS) is a solver for convex optimization problems in graph form using Alternating Direction Method of Multipliers (ADMM).
https://github.com/foges/pogs
GamselTools2015MobilizeGamsel fits a regularization path for generalized additive models with many variables. It uses an overlapped group lasso penalty to create sticking points at constant, linear and non-linear terms.
Glinternet2017MobilizeGlinternet fits a regularization path to include main effects and interactions in linear and logistic regression models. Can deal with quantitative and factor predictors. Glinternet uses the overlap group-lasso to enforce strict hierarchy, which also encourages interactions among variables with strong main effects. The code is efficient, and can handle problems with many thousands of variables.

GlmnetTools2016MobilizeGlmnet fits the entire regularition path for an elastic-net regularized glm. The models included are Gaussian, binomial, multinomial, Poisson, and the Cox model.
softImputeTools2015MobilizeSoftImpute fits a low-rank matrix approximation to a matrix with missing values via nuclear-norm regularization. The algorithm works like EM, filling in the missing values with the current guess, and then solving the optimization problem on the complete matrix using a soft-thresholded SVD. Special sparse-matrix classes available for very large matrices.
SparsenetTools2014Mobilize
Sparsenet: fit a linear model regularized by the nonconvex MC+ sparsity penalty
Sparsenet uses coordinate descent on the MC+ nonconvex penalty family, and fits a surface of solutions over the two-dimensional parameter space. This penalty family is indexed by an overall strength paramter λ (like lasso), and a convexity parameter γ, with γ=∞ corresponding to the lasso, and γ=1 best subset selection.
SvmPathTools2014MobilizeThe software, written in the S language for R, computes the entire solution path for the two-class SVM model. The solution is calculated for every value of the cost parameter C, essentially with the same computing cost of a single SVM solution.
glmpath2014MobilizeThis algorithm uses predictor-corrector method to compute the entire regularization path for generalized linear models with L1 penalty. Somewhat superceded by the package glmnet above, but not entirely. Glmpath is able to estimate the knots or entry points for each variable as it enters the path.
LARSTools2014MobilizeThe software, written in the S language, computes the entire LAR, Lasso, or (epsilon) forward stagewise coefficient path in the same order of computations as a single least-squares fit.
gamTools2016Mobilize
gam
R routines for fitting generalized additive models. This package corresponds to the gam models described in Chapter 7 of the "white" book Statistical Models in S Wadsworth (1992) Chambers and Hastie (eds).
Formulas s() and lo() allow for smoothing splines and local regression smoothers. Any family is accommodated, using the same family functions as glm(). Generic functions for plotting, anova, summary, predict etc. Recent (2013) improvements to the function step.gam()
mdaTools2016MobilizeR routines for Flexible Discriminant Analysis, Penalized Discriminant Analysis and Nonparametric Mixture Discriminant Analysis models. These tools are enhancements on the lda function in R, and allow linear, polynomial, and nonparametric versions of discriminant analysis and mixture models. There are easy to use predict methods. These methods are described in Elements of Statistical Learning (chapter 12), as well as the original references.
imputeTools2014MobilizeImputation of missing data, intended for microarray and expression arrays. Impute uses knn to impute the missing values for a gene, by using the average values from the k-nearest neighbors in the space of the non-missing elements. The algorithm is fortran-based, and uses an adaptive combination of recursive 2-means clustering and nearest neighbors.
Squish: Near-Optimal Compression for Archival of Relational Datasets.Publications2016-08BDDSSquish: Near-Optimal Compression for Archival of Relational Datasets.

Gao Y, Parameswaran A

KDD pmid: 28180028 doi: 10.1145/2939672.2939867
Squish: Near-Optimal Compression for Archival of Relational Datasets.Publications2016-08KnowengSquish: Near-Optimal Compression for Archival of Relational Datasets.

Gao Y, Parameswaran A

KDD pmid: 28180028 doi: 10.1145/2939672.2939867
Decibel: The Relational Dataset Branching System.Publications2016-05BDDSDecibel: The Relational Dataset Branching System.

Maddox M, Goehring D, Elmore AJ, Madden S, Parameswaran A, Deshpande A

Proceedings VLDB Endowment pmid: 28149668 doi: 10.14778/2947618.2947619
Decibel: The Relational Dataset Branching System.Publications2016-05KnowengDecibel: The Relational Dataset Branching System.

Maddox M, Goehring D, Elmore AJ, Madden S, Parameswaran A, Deshpande A

Proceedings VLDB Endowment pmid: 28149668 doi: 10.14778/2947618.2947619
Topological false discovery rates for brain mapping based on signal height.Publications2016-11-09BDDSTopological false discovery rates for brain mapping based on signal height.

Li J, Gahm JK, Shi Y, Toga AW

Neuroimage pmid: 27838286 doi: 10.1016/j.neuroimage.2016.09.045
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.Publications2017-01-04BDDSPANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD

Nucleic Acids Res. pmid: 27899595 doi: 10.1093/nar/gkw1138
Comparison of genomic data via statistical distribution.Publications2016-10-21BDDSComparison of genomic data via statistical distribution.

Amiri S, Dinov ID

J. Theor. Biol. pmid: 27460589 doi: 10.1016/j.jtbi.2016.07.032
Modeling Gene-Wise Dependencies Improves the Identification of Drug Response Biomarkers in Cancer Studies.Publications2017-01-12BDTGModeling Gene-Wise Dependencies Improves the Identification of Drug Response Biomarkers in Cancer Studies.

Nikolova O, Moser R, Kemp C, Gonen M, Margolin AA

Bioinformatics pmid: 28082455 doi: 10.1093/bioinformatics/btw836
The UCSC Genome Browser database: 2017 update.Publications2017-01-04BDTGThe UCSC Genome Browser database: 2017 update.

Tyner C, Kent WJ, et. al.

Nucleic Acids Res. pmid: 27899642 doi: 10.1093/nar/gkw1134
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.Publications2016-09-29BDTGRepresenting and decomposing genomic structural variants as balanced integer flows on sequence graphs.

Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D

BMC Bioinformatics pmid: 27687569 doi: 10.1186/s12859-016-1258-4
Computational pan-genomics: status, promises and challenges.Publications2016-10-21BDTGComputational pan-genomics: status, promises and challenges.



Brief. Bioinformatics pmid: 27769991 doi: 10.1093/bib/bbw089
Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.Publications2016-07-12BDTGIntegrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.

Salomonis N, Lutzko C, et. al.

Stem Cell Reports pmid: 27293150 doi: 10.1016/j.stemcr.2016.05.006
A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.Publications2016-06-28BDTGA Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.

Noren DP, Qutub AA, et. al.

PLoS Comput. Biol. pmid: 27351836 doi: 10.1371/journal.pcbi.1004890
Crowdsourcing biomedical research: leveraging communities as innovation engines.Publications2016-07-15BDTGCrowdsourcing biomedical research: leveraging communities as innovation engines.

Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G

Nat. Rev. Genet. pmid: 27418159 doi: 10.1038/nrg.2016.69
Facilitating a culture of responsible and effective sharing of cancer genome data.Publications2016-05-05BDTGFacilitating a culture of responsible and effective sharing of cancer genome data.

Siu LL, Voest EE, et. al.

Nat. Med. pmid: 27149219 doi: 10.1038/nm.4089
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.Publications2016-03BDTGChromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE

Genome Res. pmid: 26848124 doi: 10.1101/gr.193474.115
Inferring causal molecular networks: empirical assessment through a community-based effort.Publications2016-04BDTGInferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Mukherjee S, et. al.

Nat. Methods pmid: 26901648 doi: 10.1038/nmeth.3773
UCSC Data Integrator and Variant Annotation Integrator.Publications2016-05-01BDTGUCSC Data Integrator and Variant Annotation Integrator.

Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ

Bioinformatics pmid: 26740527 doi: 10.1093/bioinformatics/btv766
Durable Disease Control with MEK Inhibition in a Patient with NRAS-mutated Atypical Chronic Myeloid Leukemia.Publications2015-12-17BDTGDurable Disease Control with MEK Inhibition in a Patient with NRAS-mutated Atypical Chronic Myeloid Leukemia.

Khanna V, Pierce ST, Dao KH, Tognon CE, Hunt DE, Junio B, Tyner JW, Druker BJ

Cureus pmid: 26870618 doi: 10.7759/cureus.414
Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.Publications2016-01-28BDTGMolecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

Ceccarelli M, Verhaak RG, et. al.

Cell pmid: 26824661 doi: 10.1016/j.cell.2015.12.028
App-enabled trial participation: Tectonic shift or tepid rumble?Publications2015-07-22BDTGApp-enabled trial participation: Tectonic shift or tepid rumble?

Friend SH

Sci Transl Med pmid: 26203077 doi: 10.1126/scitranslmed.aab1206
Therapeutically Targetable ALK Mutations in Leukemia.Publications2015-06-01BDTGTherapeutically Targetable ALK Mutations in Leukemia.

Maxson JE, Davare MA, Luty SB, Eide CA, Chang BH, Loriaux MM, Tognon CE, Bottomly D, Wilmot B, McWeeney SK, Druker BJ, Tyner JW

Cancer Res. pmid: 26032424 doi: 10.1158/0008-5472.CAN-14-1576
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.Publications2015-06-25BDTGComprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.



N. Engl. J. Med. pmid: 26061751 doi: 10.1056/NEJMoa1402121
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.Publications2015-07BDTGCombining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Ewing AD, Boutros PC, et. al.

Nat. Methods pmid: 25984700 doi: 10.1038/nmeth.3407
Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.Publications2015-03-23BDTGPitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.

Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF

Dev. Cell pmid: 25805138 doi: 10.1016/j.devcel.2015.01.013
Integrative analysis of 111 reference human epigenomes.Publications2015-02-19BDTGIntegrative analysis of 111 reference human epigenomes.

Kundaje A, Kellis M, et. al.

Nature pmid: 25693563 doi: 10.1038/nature14248
The Genome 10K Project: a way forward.Publications2015BDTGThe Genome 10K Project: a way forward.

Koepfli KP

Annu Rev Anim Biosci pmid: 25689317 doi: 10.1146/annurev-animal-090414-014900
Detecting and targetting oncogenic fusion proteins in the genomic era.Publications2015-05BDTGDetecting and targetting oncogenic fusion proteins in the genomic era.

Davare MA

Biol. Cell pmid: 25631473 doi: 10.1111/boc.201400096
Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors.Publications2015BDTGStepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors.

Jang IS

Pac Symp Biocomput pmid: 25592566
Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.Publications2015-01-08BDTGSingle-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ

Cell Stem Cell pmid: 25575081 doi: 10.1016/j.stem.2014.11.005
The UCSC Genome Browser database: 2015 update.Publications2015-01BDTGThe UCSC Genome Browser database: 2015 update.

Rosenbloom KR, Kent WJ, et. al.

Nucleic Acids Res. pmid: 25428374 doi: 10.1093/nar/gku1177
Building a pan-genome reference for a population.Publications2015-05BDTGBuilding a pan-genome reference for a population.

Nguyen N

J. Comput. Biol. pmid: 25565268 doi: 10.1089/cmb.2014.0146
Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.Publications2015-02BDTGDatabase of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.

Dienstmann R, Jang IS, Bot B, Friend S, Guinney J

Cancer Discov pmid: 25656898 doi: 10.1158/2159-8290.CD-14-1118
The UCSC Cancer Genomics Browser: update 2015.Publications2015-01BDTGThe UCSC Cancer Genomics Browser: update 2015.

Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J

Nucleic Acids Res. pmid: 25392408 doi: 10.1093/nar/gku1073
RADIA: RNA and DNA integrated analysis for somatic mutation detection.Publications2014-11-18BDTGRADIA: RNA and DNA integrated analysis for somatic mutation detection.

Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D

PLoS ONE pmid: 25405470 doi: 10.1371/journal.pone.0111516
Navigating protected genomics data with UCSC Genome Browser in a Box.Publications2015-03-01BDTGNavigating protected genomics data with UCSC Genome Browser in a Box.

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ

Bioinformatics pmid: 25348212 doi: 10.1093/bioinformatics/btu712
Toward better benchmarking: challenge-based methods assessment in cancer genomics.Publications2014-09-17BDTGToward better benchmarking: challenge-based methods assessment in cancer genomics.



Genome Biol. pmid: 25314947 doi: 10.1186/s13059-014-0462-7
Simulation studies as designed experiments: the comparison of penalized regression models in the ""large p, small n"" setting.Publications2014-10-07BDTGSimulation studies as designed experiments: the comparison of penalized regression models in the ""large p, small n"" setting.

Chaibub Neto E, Bare JC, Margolin AA

PLoS ONE pmid: 25289666 doi: 10.1371/journal.pone.0107957
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.Publications2014-12-11BDTGAn evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D

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IntOGen-mutations identifies cancer drivers across tumor types.Publications2013-11BDTGIntOGen-mutations identifies cancer drivers across tumor types.

Gonzalez-Perez A

Nat. Methods pmid: 24037244 doi: 10.1038/nmeth.2642
Alignathon: a competitive assessment of whole-genome alignment methods.Publications2014-12BDTGAlignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Paten B, et. al.

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The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.Publications2014-09-29BDTGThe Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.

Wilks C, Maltbie D, et. al.

Database (Oxford) pmid: 25267794 doi: 10.1093/database/bau093
Potential for bias in studies on efficacy of prophylactic surgery for BRCA1 and BRCA2 mutation.Publications2003-07-02BDTGPotential for bias in studies on efficacy of prophylactic surgery for BRCA1 and BRCA2 mutation.

Klaren HM

J. Natl. Cancer Inst. pmid: 12837830
A Hybrid Causal Search Algorithm for Latent Variable Models.Publications2016-08CCDA Hybrid Causal Search Algorithm for Latent Variable Models.

Ogarrio JM, Spirtes P, Ramsey J

JMLR Workshop Conf Proc pmid: 28239434
Domain Adaptation with Conditional Transferable Components.Publications2016-06CCDDomain Adaptation with Conditional Transferable Components.

Gong M, Zhang K, Liu T, Tao D, Glymour C, Scholkopf B

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Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis.Publications2017-02CCDRegulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis.

Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y

EBioMedicine pmid: 28040451 doi: 10.1016/j.ebiom.2016.12.014
Estimating Causal Effects with Ancestral Graph Markov Models.Publications2016-08CCDEstimating Causal Effects with Ancestral Graph Markov Models.

Malinsky D, Spirtes P

JMLR Workshop Conf Proc pmid: 28217244
Causal Discovery from Subsampled Time Series Data by Constraint Optimization.Publications2016-08CCDCausal Discovery from Subsampled Time Series Data by Constraint Optimization.

Hyttinen A, Plis S, Jarvisalo M, Eberhardt F, Danks D

JMLR Workshop Conf Proc pmid: 28203316
Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.Publications2016-09CCDHundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

Chikina M, Robinson JD, Clark NL

Mol. Biol. Evol. pmid: 27329977 doi: 10.1093/molbev/msw112
Latent Variable Graphical Model Selection using Harmonic Analysis: Applications to the Human Connectome Project (HCP).Publications2016-06CPCPLatent Variable Graphical Model Selection using Harmonic Analysis: Applications to the Human Connectome Project (HCP).

Kim WH, Kim HJ, Adluru N, Singh V

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit pmid: 28255221 doi: 10.1109/CVPR.2016.268
Data-Driven Contextual Valence Shifter Quantification for Multi-Theme Sentiment Analysis.Publications2016-10KnowengData-Driven Contextual Valence Shifter Quantification for Multi-Theme Sentiment Analysis.

Yu H, Shang J, Hsu M, Castellanos M, Han J

Proc ACM Int Conf Inf Knowl Manag pmid: 28232874 doi: 10.1145/2983323.2983793
Representing Documents via Latent Keyphrase Inference.Publications2016-04KnowengRepresenting Documents via Latent Keyphrase Inference.

Liu J, Ren X, Shang J, Cassidy T, Voss CR, Han J

Proc Int World Wide Web Conf pmid: 28229132 doi: 10.1145/2872427.2883088
FacetGist: Collective Extraction of Document Facets in Large Technical Corpora.Publications2016-10KnowengFacetGist: Collective Extraction of Document Facets in Large Technical Corpora.

Siddiqui T, Ren X, Parameswaran A, Han J

Proc ACM Int Conf Inf Knowl Manag pmid: 28210517 doi: 10.1145/2983323.2983828
Mining Discriminative Patterns to Predict Health Status for Cardiopulmonary Patients.Publications2016-10KnowengMining Discriminative Patterns to Predict Health Status for Cardiopulmonary Patients.

Cheng Q, Shang J, Juen J, Han J, Schatz B

ACM BCB pmid: 28174760 doi: 10.1145/2975167.2975171
MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.Publications2016-05KnowengMACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.

Shang J, Peng J, Han J

Proc SIAM Int Conf Data Min pmid: 28174677 doi: 10.1137/1.9781611974348.63
Dynamics of Large Multi-View Social Networks: Synergy, Cannibalization and Cross-View Interplay.Publications2016-08KnowengDynamics of Large Multi-View Social Networks: Synergy, Cannibalization and Cross-View Interplay.

Shi Y, Kim M, Chatterjee S, Tiwari M, Ghosh S, Rosales R

KDD pmid: 28203486 doi: 10.1145/2939672.2939814
Interactive Data Exploration with Smart Drill-Down.Publications2016-05KnowengInteractive Data Exploration with Smart Drill-Down.

Joglekar M, Garcia-Molina H, Parameswaran A

Proc Int Conf Data Eng pmid: 28210096 doi: 10.1109/ICDE.2016.7498300
DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework.Publications2016-05KnowengDPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework.

Shang J, Tong W, Peng J, Han J

Proc SIAM Int Conf Data Min pmid: 28163983 doi: 10.1137/1.9781611974348.64
GMove: Group-Level Mobility Modeling Using Geo-Tagged Social Media.Publications2016-08KnowengGMove: Group-Level Mobility Modeling Using Geo-Tagged Social Media.

Zhang C, Zhang K, Yuan Q, Zhang L, Hanratty T, Han J

KDD pmid: 28163978 doi: 10.1145/2939672.2939793
Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting.Publications2016-06KnowengTowards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting.

Das Sarma A, Parameswaran A, Widom J

Proc ACM SIGMOD Int Conf Manag Data pmid: 28149000 doi: 10.1145/2882903.2882953
Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information.Publications2017-01-12MobilizeDigital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information.

Li X, Dunn J, Salins D, Zhou G, Zhou W, Schussler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP

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Reactome pathway analysis: a high-performance in-memory approach.Publications2017-03-02HeartBD2KReactome pathway analysis: a high-performance in-memory approach.

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H

BMC Bioinformatics pmid: 28249561 doi: 10.1186/s12859-017-1559-2
Chemoproteomic profiling and discovery of protein electrophiles in human cells.Publications2017-03HeartBD2KChemoproteomic profiling and discovery of protein electrophiles in human cells.

Matthews ML, He L, Horning BD, Olson EJ, Correia BE, Yates JR 3rd, Dawson PE, Cravatt BF

Nat Chem pmid: 28221344 doi: 10.1038/nchem.2645
Early matrix metalloproteinase-9 inhibition post-myocardial infarction worsens cardiac dysfunction by delaying inflammation resolution.Publications2016-11HeartBD2KEarly matrix metalloproteinase-9 inhibition post-myocardial infarction worsens cardiac dysfunction by delaying inflammation resolution.

Iyer RP, de Castro Bras LE, Patterson NL, Bhowmick M, Flynn ER, Asher M, Cannon PL, Deleon-Pennell KY, Fields GB, Lindsey ML

J. Mol. Cell. Cardiol. pmid: 27746126 doi: 10.1016/j.yjmcc.2016.10.005
HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.Publications2012-03HeartBD2KHUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.

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Proteomics pmid: 22539426 doi: 10.1002/pmic.201270015
Analytic Complexity and Challenges in Identifying Mixtures of Exposures Associated with Phenotypes in the Exposome Era.Publications2017PIC-SUREAnalytic Complexity and Challenges in Identifying Mixtures of Exposures Associated with Phenotypes in the Exposome Era.

Patel CJ

Curr Epidemiol Rep pmid: 28251040 doi: 10.1007/s40471-017-0100-5
The Exposome Research Paradigm: an Opportunity to Understand the Environmental Basis for Human Health and Disease.Publications2017-03PIC-SUREThe Exposome Research Paradigm: an Opportunity to Understand the Environmental Basis for Human Health and Disease.

Buck Louis GM, Smarr MM, Patel CJ

Curr Environ Health Rep pmid: 28194614 doi: 10.1007/s40572-017-0126-3
Structured Matrix Completion with Applications to Genomic Data Integration.Publications2016PIC-SUREStructured Matrix Completion with Applications to Genomic Data Integration.

Cai T, Cai TT, Zhang A

J Am Stat Assoc pmid: 28042188 doi: 10.1080/01621459.2015.1021005
Evaluating surrogate marker information using censored data.Publications2017-01-15PIC-SUREEvaluating surrogate marker information using censored data.

Parast L, Cai T, Tian L

Stat Med pmid: 28088843 doi: 10.1002/sim.7220
Predictive Modeling of Physician-Patient Dynamics That Influence Sleep Medication Prescriptions and Clinical Decision-Making.Publications2017-02-09PIC-SUREPredictive Modeling of Physician-Patient Dynamics That Influence Sleep Medication Prescriptions and Clinical Decision-Making.

Beam AL, Kartoun U, Pai JK, Chatterjee AK, Fitzgerald TP, Shaw SY, Kohane IS

Sci Rep pmid: 28181568 doi: 10.1038/srep42282
Large-scale identification of patients with cerebral aneurysms using natural language processing.Publications2017-01-10PIC-SURELarge-scale identification of patients with cerebral aneurysms using natural language processing.

Castro VM, Dligach D, Finan S, Yu S, Can A, Abd-El-Barr M, Gainer V, Shadick NA, Murphy S, Cai T, Savova G, Weiss ST, Du R

Neurology pmid: 27927935 doi: 10.1212/WNL.0000000000003490
A review of validation strategies for computational drug repositioning.Publications2016-11-22PIC-SUREA review of validation strategies for computational drug repositioning.



Brief. Bioinformatics pmid: 27881429 doi: 10.1093/bib/bbw110
Surrogate-assisted feature extraction for high-throughput phenotyping.Publications2016-09-15PIC-SURESurrogate-assisted feature extraction for high-throughput phenotyping.

Yu S, Chakrabortty A, Liao KP, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T

J Am Med Inform Assoc pmid: 27632993 doi: 10.1093/jamia/ocw135
On longitudinal prediction with time-to-event outcome: Comparison of modeling options.Publications2016-07-20PIC-SUREOn longitudinal prediction with time-to-event outcome: Comparison of modeling options.

Maziarz M, Heagerty P, Cai T, Zheng Y

Biometrics pmid: 27438160 doi: 10.1111/biom.12562
Prioritizing individual genetic variants after kernel machine testing using variable selection.Publications2016-12PIC-SUREPrioritizing individual genetic variants after kernel machine testing using variable selection.

He Q, Cai T, Liu Y, Zhao N, Harmon QE, Almli LM, Binder EB, Engel SM, Ressler KJ, Conneely KN, Lin X, Wu MC

Genet. Epidemiol. pmid: 27488097 doi: 10.1002/gepi.21993
Identifying predictive markers for personalized treatment selection.Publications2016-12PIC-SUREIdentifying predictive markers for personalized treatment selection.

Shen Y, Cai T

Biometrics pmid: 26999054 doi: 10.1111/biom.12511
Estimation and testing for multiple regulation of multivariate mixed outcomes.Publications2016-12PIC-SUREEstimation and testing for multiple regulation of multivariate mixed outcomes.

Agniel D, Liao KP, Cai T

Biometrics pmid: 26910481 doi: 10.1111/biom.12495
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain.Publications2016-02-19LINCS-DCICRegulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain.

Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB

Elife pmid: 26894958 doi: 10.7554/eLife.10421
Towards a Holistic Cortical Thickness Descriptor: Heat Kernel-Based Grey Matter Morphology Signatures.Publications2017-02-15ENIGMATowards a Holistic Cortical Thickness Descriptor: Heat Kernel-Based Grey Matter Morphology Signatures.

Wang G, Wang Y

Neuroimage pmid: 28033566 doi: 10.1016/j.neuroimage.2016.12.014
Reproducibility of tract-based white matter microstructural measures using the ENIGMA-DTI protocol.Publications2017-01-14ENIGMAReproducibility of tract-based white matter microstructural measures using the ENIGMA-DTI protocol.

Acheson A, Wijtenburg SA, Rowland LM, Winkler A, Mathias CW, Hong LE, Jahanshad N, Patel B, Thompson PM, McGuire SA, Sherman PM, Kochunov P, Dougherty DM

Brain Behav pmid: 28239525 doi: 10.1002/brb3.615
Allostatic load and reduced cortical thickness in schizophrenia.Publications2017-03ENIGMAAllostatic load and reduced cortical thickness in schizophrenia.

Chiappelli J, Kochunov P, Savransky A, Fisseha F, Wisner K, Du X, Rowland LM, Hong LE

Psychoneuroendocrinology pmid: 28027496 doi: 10.1016/j.psyneuen.2016.11.021
Diffusion-weighted imaging uncovers likely sources of processing-speed deficits in schizophrenia.Publications2016-11-22ENIGMADiffusion-weighted imaging uncovers likely sources of processing-speed deficits in schizophrenia.

Kochunov P, Rowland LM, Fieremans E, Veraart J, Jahanshad N, Eskandar G, Du X, Muellerklein F, Savransky A, Shukla D, Sampath H, Thompson PM, Hong LE

Proc. Natl. Acad. Sci. U.S.A. pmid: 27834215 doi: 10.1073/pnas.1608246113
Exome chip analyses in adult attention deficit hyperactivity disorder.Publications2016-10-18ENIGMAExome chip analyses in adult attention deficit hyperactivity disorder.

Zayats T, Johansson S, et. al.

Transl Psychiatry pmid: 27754487 doi: 10.1038/tp.2016.196
3D tract-specific local and global analysis of white matter integrity in Alzheimer's disease.Publications2017-03ENIGMA3D tract-specific local and global analysis of white matter integrity in Alzheimer's disease.

Jin Y, Huang C, Daianu M, Zhan L, Dennis EL, Reid RI, Jack CR Jr, Zhu H, Thompson PM

Hum Brain Mapp pmid: 27883250 doi: 10.1002/hbm.23448
Structural asymmetries of the human cerebellum in relation to cerebral cortical asymmetries and handedness.Publications2016-08-26ENIGMAStructural asymmetries of the human cerebellum in relation to cerebral cortical asymmetries and handedness.

Kavaklioglu T, Guadalupe T, Zwiers M, Marquand AF, Onnink M, Shumskaya E, Brunner H, Fernandez G, Fisher SE, Francks C

Brain Struct Funct pmid: 27566607 doi: 10.1007/s00429-016-1295-9
Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment.Publications2016-06-23ENIGMAIdentification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment.

Le Hellard S, Witoelar A, Zuber V, Bettella F, Hugdahl K, Espeseth T, Steen VM, Melle I, Desikan R, Schork AJ, Thompson WK, Dale AM, Djurovic S, Andreassen OA

Schizophr Bull pmid: 27338279 doi: 10.1093/schbul/sbw085
Distinct Subcortical Volume Alterations in Pediatric and Adult OCD: A Worldwide Meta- and Mega-Analysis.Publications2016-09-09ENIGMADistinct Subcortical Volume Alterations in Pediatric and Adult OCD: A Worldwide Meta- and Mega-Analysis.

Boedhoe PS, van den Heuvel OA, et. al.

Am J Psychiatry pmid: 27609241
Cognitive profiles and heritability estimates in the Old Order Amish.Publications2016-08ENIGMACognitive profiles and heritability estimates in the Old Order Amish.

Kuehner RM

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Hierarchical Span-Based Conditional Random Fields for Labeling and Segmenting Events in Wearable Sensor Data Streams.Publications2016-06MD2KHierarchical Span-Based Conditional Random Fields for Labeling and Segmenting Events in Wearable Sensor Data Streams.

Adams RJ, Saleheen N, Thomaz E, Parate A, Kumar S, Marlin BM

Proc Int Conf Mach Learn pmid: 28090606
Barriers and Negative Nudges: Exploring Challenges in Food Journaling.Publications2015-04MD2KBarriers and Negative Nudges: Exploring Challenges in Food Journaling.

Cordeiro F, Epstein DA, Thomaz E, Bales E, Jagannathan AK, Abowd GD, Fogarty J

Proc SIGCHI Conf Hum Factor Comput Syst pmid: 26894233
Domain Adaptation Methods for Improving Lab-to-field Generalization of Cocaine Detection using Wearable ECG.Publications2016-09MD2KDomain Adaptation Methods for Improving Lab-to-field Generalization of Cocaine Detection using Wearable ECG.

Natarajan A, Angarita G, Gaiser E, Malison R, Ganesan D, Marlin BM

Proc ACM Int Conf Ubiquitous Comput pmid: 28090605 doi: 10.1145/2971648.2971666
Measurement Error and Causal Discovery.Publications2016-06CCDMeasurement Error and Causal Discovery.

Scheines R, Ramsey J

CEUR Workshop Proc pmid: 28280453
Biologically Relevant Heterogeneity: Metrics and Practical Insights.Publications2017-03CCDBiologically Relevant Heterogeneity: Metrics and Practical Insights.

Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL

SLAS Discov pmid: 28231035 doi: 10.1177/2472555216682725
Modeling the Temporal Evolution of Postoperative Complications.Publications2017-02-10CPCPModeling the Temporal Evolution of Postoperative Complications.

Feld SI, Cobian AG, Tevis SE, Kennedy GD, Craven MW

AMIA Annu Symp Proc pmid: 28269851
RNA-Binding Protein IGF2BP1 in Cutaneous Squamous Cell Carcinoma.Publications2017-03CPCPRNA-Binding Protein IGF2BP1 in Cutaneous Squamous Cell Carcinoma.

Kim T, Havighurst T, Kim K, Hebbring SJ, Ye Z, Aylward J, Keles S, Xu YG, Spiegelman VS

J. Invest. Dermatol. pmid: 27856289 doi: 10.1016/j.jid.2016.10.042
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.Publications2016-11-11CPCPA MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.

Zuo C, Chen K, Keles S

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Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions.Publications2015-07CPCPRecombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions.

Lee K, Kolb AW, Sverchkov Y, Cuellar JA, Craven M, Brandt CR

J. Virol. pmid: 25926637 doi: 10.1128/JVI.00880-15
Subcortical brain volume differences in participants with attention deficit hyperactivity disorder in children and adults: a cross-sectional mega-analysis.Publications2017-02-16ENIGMASubcortical brain volume differences in participants with attention deficit hyperactivity disorder in children and adults: a cross-sectional mega-analysis.

Hoogman M, Franke B, et. al.

Lancet Psychiatry pmid: 28219628 doi: 10.1016/S2215-0366(17)30049-4
Simultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies.Publications2017-03ENIGMASimultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies.

Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S

Genetics pmid: 28132020 doi: 10.1534/genetics.116.198473
The impact of aging on cardiac extracellular matrix.Publications2017-02HeartBD2KThe impact of aging on cardiac extracellular matrix.

Meschiari CA, Ero OK, Pan H, Finkel T, Lindsey ML

Geroscience pmid: 28299638 doi: 10.1007/s11357-017-9959-9
Genetic Dissection of Cardiac Remodeling in an Isoproterenol-Induced Heart Failure Mouse Model.Publications2016-07-06HeartBD2KGenetic Dissection of Cardiac Remodeling in an Isoproterenol-Induced Heart Failure Mouse Model.

Wang JJ, Rau C, Avetisyan R, Ren S, Romay MC, Stolin G, Gong KW, Wang Y, Lusis AJ

PLoS Genet. pmid: 27385019 doi: 10.1371/journal.pgen.1006038
Reactome from a WikiPathways Perspective.Publications2016-05-20HeartBD2KReactome from a WikiPathways Perspective.

Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT

PLoS Comput. Biol. pmid: 27203685 doi: 10.1371/journal.pcbi.1004941
Laissez-Faire : Fully Asymmetric Backscatter Communication.Publications2015-08MD2KLaissez-Faire : Fully Asymmetric Backscatter Communication.

Hu P, Zhang P, Ganesan D

Proc ACM SIGCOMM Conf pmid: 28286885 doi: 10.1145/2829988.2787477
Physical performance analysis: A new approach to assessing free-living physical activity in musculoskeletal pain and mobility-limited populations.Publications2017-02-24MobilizePhysical performance analysis: A new approach to assessing free-living physical activity in musculoskeletal pain and mobility-limited populations.

Smuck M, Tomkins-Lane C, Ith MA, Jarosz R, Kao MJ

PLoS ONE pmid: 28235039 doi: 10.1371/journal.pone.0172804
Objective measurement of free-living physical activity (performance) in lumbar spinal stenosis: are physical activity guidelines being met?Publications2017-01MobilizeObjective measurement of free-living physical activity (performance) in lumbar spinal stenosis: are physical activity guidelines being met?

Norden J, Smuck M, Sinha A, Hu R, Tomkins-Lane C

Spine J pmid: 27793759 doi: 10.1016/j.spinee.2016.10.016
Making a meaningful impact: modelling simultaneous frictional collisions in spatial multibody systems.Publications2015-05-08MobilizeMaking a meaningful impact: modelling simultaneous frictional collisions in spatial multibody systems.

Uchida TK, Sherman MA, Delp SL

Proc. Math. Phys. Eng. Sci. pmid: 27547093 doi: 10.1098/rspa.2014.0859
HSPA5 Gene encoding Hsp70 chaperone BiP in the endoplasmic reticulum.Publications2017-3-7HeartBD2KWang J, Lee J, Liem D, Ping P. HSPA5 Gene encoding Hsp70 chaperone BiP in the
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Proteomics Research in Cardiovascular Medicine and Biomarker Discovery.Publications2016-12-27HeartBD2KLam MP, Ping P, Murphy E. Proteomics Research in Cardiovascular Medicine and
Biomarker Discovery. J Am Coll Cardiol. 2016 Dec 27;68(25):2819-2830. doi:
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Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome.Publications2016-12-20HeartBD2KGarlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P. Equipping Physiologists
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Towards an efficient compression of 3D coordinates of macromolecular structures.Publications2017-03-31Data CompressionValasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW (2017) Towards an efficient compression of 3D coordinates of macromolecular structures. PLOS ONE 12(3): e0174846. doi: 10.1371/journal.pone.01748464
Web-based molecular graphics for large complexes. In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16).Publications2016-07-22Data CompressionRose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW (2016) Web-based molecular graphics for large complexes. In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16). ACM, New York, NY, USA, 185-186. doi: 10.1145/2945292.2945324
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. Publications2017-01-04Data CompressionRose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017 Jan 4;45(D1):D271-D281. doi: 10.1093/nar/gkw1000
MacroMolecular TransmIssion Format (MMTF)Tools2017Data CompressionThe Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis. APIs to use MMTF are available in all common programming languages.
Connectome imaging for mapping human brain pathways.Publications2017-05-02BDDSConnectome imaging for mapping human brain pathways.

Shi Y, Toga AW

Mol. Psychiatry pmid: 28461700 doi: 10.1038/mp.2017.92
T2-Imaging Changes in the Nigrosome-1 Relate to Clinical Measures of Parkinson's Disease.Publications2016-10-20BDDST2-Imaging Changes in the Nigrosome-1 Relate to Clinical Measures of Parkinson's Disease.

Fu KA, Nathan R, Dinov ID, Li J, Toga AW

Front Neurol pmid: 27812347 doi: 10.3389/fneur.2016.00174
Diverging volumetric trajectories following pediatric traumatic brain injury.Publications2017-03-31ENIGMADiverging volumetric trajectories following pediatric traumatic brain injury.

Dennis EL, Faskowitz J, Rashid F, Babikian T, Mink R, Babbitt C, Johnson J, Giza CC, Jahanshad N, Thompson PM, Asarnow RF

Neuroimage Clin pmid: 28507895 doi: 10.1016/j.nicl.2017.03.014
The C677T variant in MTHFR modulates associations between brain integrity, mood, and cognitive functioning in old age.Publications2017-04ENIGMAThe C677T variant in MTHFR modulates associations between brain integrity, mood, and cognitive functioning in old age.

Roussotte FF, Hua X, Narr KL, Small GW, Thompson PM

Biol Psychiatry Cogn Neurosci Neuroimaging pmid: 28435933 doi: 10.1016/j.bpsc.2016.09.005
Female-specific association of NOS1 genotype with white matter microstructure in ADHD patients and controls.Publications2017-06-07ENIGMAFemale-specific association of NOS1 genotype with white matter microstructure in ADHD patients and controls.

van Ewijk H, Bralten J, van Duin EDA, Hakobjan M, Buitelaar JK, Heslenfeld DJ, Hoekstra PJ, Hartman C, Hoogman M, Oosterlaan J, Franke B

J Child Psychol Psychiatry pmid: 28589541 doi: 10.1111/jcpp.12742
Positive symptoms associate with cortical thinning in the superior temporal gyrus via the ENIGMA Schizophrenia consortium.Publications2017-05ENIGMAPositive symptoms associate with cortical thinning in the superior temporal gyrus via the ENIGMA Schizophrenia consortium.

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Acta Psychiatr Scand pmid: 28369804 doi: 10.1111/acps.12718
Shape Analysis with Hyperbolic Wasserstein Distance.Publications2016-06ENIGMAShape Analysis with Hyperbolic Wasserstein Distance.

Shi J, Zhang W, Wang Y

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit pmid: 28392672 doi: 10.1109/CVPR.2016.546
Continuous representations of brain connectivity using spatial point processes.Publications2017-04-28ENIGMAContinuous representations of brain connectivity using spatial point processes.

Moyer D, Gutman BA, Faskowitz J, Jahanshad N, Thompson PM

Med Image Anal pmid: 28487128 doi: 10.1016/j.media.2017.04.013
Widespread Allelic Heterogeneity in Complex Traits.Publications2017-05-04ENIGMAWidespread Allelic Heterogeneity in Complex Traits.

Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segre AV, Joo JWJ, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E

Am. J. Hum. Genet. pmid: 28475861 doi: 10.1016/j.ajhg.2017.04.005
Novel genetic loci associated with hippocampal volume.Publications2017-01-18ENIGMANovel genetic loci associated with hippocampal volume.

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Nat Commun pmid: 28098162 doi: 10.1038/ncomms13624
Inattention and Reaction Time Variability Are Linked to Ventromedial Prefrontal Volume in Adolescents.Publications2017-01-13ENIGMAInattention and Reaction Time Variability Are Linked to Ventromedial Prefrontal Volume in Adolescents.

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Biol. Psychiatry pmid: 28237458 doi: 10.1016/j.biopsych.2017.01.003
Effects of dopaminergic genes, prenatal adversities, and their interaction on attention-deficit/hyperactivity disorder and neural correlates of response inhibition.Publications2017-03ENIGMAEffects of dopaminergic genes, prenatal adversities, and their interaction on attention-deficit/hyperactivity disorder and neural correlates of response inhibition.

van der Meer D, Hartman CA, van Rooij D, Franke B, Heslenfeld DJ, Oosterlaan J, Faraone SV, Buitelaar JK, Hoekstra PJ

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Identifying disordered eating behaviours in adolescents: how do parent and adolescent reports differ by sex and age?Publications2017-06ENIGMAIdentifying disordered eating behaviours in adolescents: how do parent and adolescent reports differ by sex and age?

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Eur Child Adolesc Psychiatry pmid: 28050706 doi: 10.1007/s00787-016-0935-1
Heritability of the shape of subcortical brain structures in the general population.Publications2016-12-15ENIGMAHeritability of the shape of subcortical brain structures in the general population.

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Childhood adversity impacts on brain subcortical structures relevant to depression.Publications2017-03ENIGMAChildhood adversity impacts on brain subcortical structures relevant to depression.

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Relationship of a common OXTR gene variant to brain structure and default mode network function in healthy humans.Publications2017-02-15ENIGMARelationship of a common OXTR gene variant to brain structure and default mode network function in healthy humans.

Wang J, Braskie MN, Hafzalla GW, Faskowitz J, McMahon KL, de Zubicaray GI, Wright MJ, Yu C, Thompson PM

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Human subcortical brain asymmetries in 15,847 people worldwide reveal effects of age and sex.Publications2016-10-13ENIGMAHuman subcortical brain asymmetries in 15,847 people worldwide reveal effects of age and sex.

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Brain Imaging Behav pmid: 27738994 doi: 10.1007/s11682-016-9629-z
Ruminative brooding is associated with salience network coherence in early pubertal youth.Publications2017-02-01ENIGMARuminative brooding is associated with salience network coherence in early pubertal youth.

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The C677T variant in MTHFR modulates associations between blood-based and cerebrospinal fluid biomarkers of neurodegeneration.Publications2016-08-17ENIGMAThe C677T variant in MTHFR modulates associations between blood-based and cerebrospinal fluid biomarkers of neurodegeneration.

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Volumetric and shape analyses of subcortical structures in United States service members with mild traumatic brain injury.Publications2016-10ENIGMAVolumetric and shape analyses of subcortical structures in United States service members with mild traumatic brain injury.

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Blockwise Human Brain Network Visual Comparison Using NodeTrix Representation.Publications2017-01ENIGMABlockwise Human Brain Network Visual Comparison Using NodeTrix Representation.



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Cortical abnormalities in adults and adolescents with major depression based on brain scans from 20 cohorts worldwide in the ENIGMA Major Depressive Disorder Working Group.Publications2017-06ENIGMACortical abnormalities in adults and adolescents with major depression based on brain scans from 20 cohorts worldwide in the ENIGMA Major Depressive Disorder Working Group.

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Effect of Electroconvulsive Therapy on Striatal Morphometry in Major Depressive Disorder.Publications2016-09ENIGMAEffect of Electroconvulsive Therapy on Striatal Morphometry in Major Depressive Disorder.

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Testing differential susceptibility: Plasticity genes, the social environment, and their interplay in adolescent response inhibition.Publications2017-06ENIGMATesting differential susceptibility: Plasticity genes, the social environment, and their interplay in adolescent response inhibition.

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Age, APOE and sex: Triad of risk of Alzheimer's disease.Publications2016-06ENIGMAAge, APOE and sex: Triad of risk of Alzheimer's disease.

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Early developmental gene enhancers affect subcortical volumes in the adult human brain.Publications2016-05ENIGMAEarly developmental gene enhancers affect subcortical volumes in the adult human brain.

Becker M, Guadalupe T, Franke B, Hibar DP, Renteria ME, Stein JL, Thompson PM, Francks C, Vernes SC, Fisher SE

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J Neurol Neurosci pmid: 28503392 doi: 10.21767/2171-6625.1000159
Genes influence the amplitude and timing of brain hemodynamic responses.Publications2016-01-01ENIGMAGenes influence the amplitude and timing of brain hemodynamic responses.

Shan ZY, Vinkhuyzen AA, Thompson PM, McMahon KL, Blokland GA, de Zubicaray GI, Calhoun V, Martin NG, Visscher PM, Wright MJ, Reutens DC

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Heritability of the network architecture of intrinsic brain functional connectivity.Publications2015-11-01ENIGMAHeritability of the network architecture of intrinsic brain functional connectivity.

Sinclair B, Hansell NK, Blokland GA, Martin NG, Thompson PM, Breakspear M, de Zubicaray GI, Wright MJ, McMahon KL

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Penalized least squares regression methods and applications to neuroimaging.Publications2011-04-15ENIGMAPenalized least squares regression methods and applications to neuroimaging.

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An algorithm for direct causal learning of influences on patient outcomes.Publications2017-01BDTGAn algorithm for direct causal learning of influences on patient outcomes.

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Artif Intell Med pmid: 28363452 doi: 10.1016/j.artmed.2016.10.003
Genome graphs and the evolution of genome inference.Publications2017-05BDTGGenome graphs and the evolution of genome inference.

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Mapping DNA methylation with high-throughput nanopore sequencing.Publications2017-04BDTGMapping DNA methylation with high-throughput nanopore sequencing.

Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B

Nat. Methods pmid: 28218897 doi: 10.1038/nmeth.4189
Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.Publications2017-05BDTGImproved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.

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Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.Publications2017-03-14CCDRevealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.

Chen V, Paisley J, Lu X

BMC Genomics pmid: 28361690 doi: 10.1186/s12864-017-3494-z
Binary Classifier Calibration Using an Ensemble of Linear Trend Estimation.Publications2016-05CCDBinary Classifier Calibration Using an Ensemble of Linear Trend Estimation.

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Proc SIAM Int Conf Data Min pmid: 28357158 doi: 10.1137/1.9781611974348.30
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.Publications2017-04-20CCDChromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.

Sauerwald N, Zhang S, Kingsford C, Bahar I

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A million variables and more: the Fast Greedy Equivalence Search algorithm for learning high-dimensional graphical causal models, with an application to functional magnetic resonance images.Publications2017-03CCDA million variables and more: the Fast Greedy Equivalence Search algorithm for learning high-dimensional graphical causal models, with an application to functional magnetic resonance images.

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Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models.Publications2016-12CCDBinary Classifier Calibration using an Ensemble of Near Isotonic Regression Models.

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Predicting structured metadata from unstructured metadata.Publications2016-01-01CEDARPredicting structured metadata from unstructured metadata.

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Experimental Design on a Budget for Sparse Linear Models and Applications.Publications2016-06CPCPExperimental Design on a Budget for Sparse Linear Models and Applications.

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Structure-Leveraged Methods in Breast Cancer Risk Prediction.Publications2016-12CPCPStructure-Leveraged Methods in Breast Cancer Risk Prediction.

Fan J, Wu Y, Yuan M, Page D, Liu J, Ong IM, Peissig P, Burnside E

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SCnorm: robust normalization of single-cell RNA-seq data.Publications2017-06CPCPSCnorm: robust normalization of single-cell RNA-seq data.

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Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data.Publications2016-07CPCPBaseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data.

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Computational Drug Repositioning Using Continuous Self-Controlled Case Series.Publications2016-08CPCPComputational Drug Repositioning Using Continuous Self-Controlled Case Series.

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Temporally Factorized Network Modeling for Evolutionary Network Analysis.Publications2017-02HeartBD2KTemporally Factorized Network Modeling for Evolutionary Network Analysis.

Yu W, Aggarwal CC, Wang W

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Mutation of WIF1: a potential novel cause of a Nail-Patella-like disorder.Publications2017-04-06HeartBD2KMutation of WIF1: a potential novel cause of a Nail-Patella-like disorder.

Jones MC, Topol SE, Rueda M, Oliveira G, Phillips T, Spencer EG, Torkamani A

Genet. Med. pmid: 28383544 doi: 10.1038/gim.2017.20
Cardiac Fibroblast Activation Post-Myocardial Infarction: Current Knowledge Gaps.Publications2017-05HeartBD2KCardiac Fibroblast Activation Post-Myocardial Infarction: Current Knowledge Gaps.

Ma Y, Iyer RP, Jung M, Czubryt MP, Lindsey ML

Trends Pharmacol. Sci. pmid: 28365093 doi: 10.1016/j.tips.2017.03.001
Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.Publications2017-02-03HeartBD2KQuantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.

Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW

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CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.Publications2017-01-31HeartBD2KCIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

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Influence of donor age on induced pluripotent stem cells.Publications2017-01HeartBD2KInfluence of donor age on induced pluripotent stem cells.

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Molecular Autopsy for Sudden Unexpected Death.Publications2016-10-11HeartBD2KMolecular Autopsy for Sudden Unexpected Death.

Torkamani A, Muse ED, Spencer EG, Rueda M, Wagner GN, Lucas JR, Topol EJ

JAMA pmid: 27727376 doi: 10.1001/jama.2016.11445
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.Publications2016-06-15HeartBD2KCombining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

Bravo A, Li TS, Su AI, Good BM, Furlong LI

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Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.Publications2016-07-01HeartBD2KBranch: an interactive, web-based tool for testing hypotheses and developing predictive models.

Gangavarapu K, Babji V, Meissner T, Su AI, Good BM

Bioinformatics pmid: 27153723 doi: 10.1093/bioinformatics/btw117
Genome-wide association studies of drug response and toxicity: an opportunity for genome medicine.Publications2017-01KnowengGenome-wide association studies of drug response and toxicity: an opportunity for genome medicine.

Giacomini KM, Yee SW, Mushiroda T, Weinshilboum RM, Ratain MJ, Kubo M

Nat Rev Drug Discov pmid: 27885282 doi: 10.1038/nrd.2016.234
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery.Publications2017-07LINCS-DCICSystemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery.

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Drug Discov. Today pmid: 28274840 doi: 10.1016/j.drudis.2017.02.004
Differential cytokine contributions of perivascular haematopoietic stem cell niches.Publications2017-03LINCS-DCICDifferential cytokine contributions of perivascular haematopoietic stem cell niches.

Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS

Nat. Cell Biol. pmid: 28218906 doi: 10.1038/ncb3475
The SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model of biliary atresia.Publications2017-04LINCS-DCICThe SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model of biliary atresia.

Mohanty SK, Donnelly B, Lobeck I, Walther A, Dupree P, Coots A, Meller J, McNeal M, Sestak K, Tiao G

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L1000CDS2: LINCS L1000 characteristic direction signatures search engine.Publications2016LINCS-DCICL1000CDS2: LINCS L1000 characteristic direction signatures search engine.

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VISAGE: Interactive Visual Graph Querying.Publications2016-06MD2KVISAGE: Interactive Visual Graph Querying.

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Interlandi M, Tetali SD, Gulzar MA, Noor J, Condie T, Kim M, Millstein T

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Privacy and Security in Mobile Health: A Research Agenda.Publications2016-06MD2KPrivacy and Security in Mobile Health: A Research Agenda.

Kotz D, Gunter CA, Kumar S, Weiner JP

Computer (Long Beach Calif) pmid: 28344359 doi: 10.1109/MC.2016.185
Programming and Runtime Support to Blaze FPGA Accelerator Deployment at Datacenter Scale.Publications2016-10MD2KProgramming and Runtime Support to Blaze FPGA Accelerator Deployment at Datacenter Scale.

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Effect of Physical Activity on Self-Reported Disability in Older Adults: Results from the LIFE Study.Publications2017-05MD2KEffect of Physical Activity on Self-Reported Disability in Older Adults: Results from the LIFE Study.

Manini TM, Beavers DP, Pahor M, Guralnik JM, Spring B, Church TS, King AC, Folta SC, Glynn NW, Marsh AP, Gill TM

J Am Geriatr Soc pmid: 28168689 doi: 10.1111/jgs.14742
Control Engineering Methods for the Design of Robust Behavioral Treatments.Publications2017-05MD2KControl Engineering Methods for the Design of Robust Behavioral Treatments.

Bekiroglu K, Lagoa C, Murphy SA, Lanza ST

IEEE Trans Control Syst Technol pmid: 28344431 doi: 10.1109/TCST.2016.2580661
Just-in-Time Adaptive Interventions (JITAIs) in Mobile Health: Key Components and Design Principles for Ongoing Health Behavior Support.Publications2016-09-23MD2KJust-in-Time Adaptive Interventions (JITAIs) in Mobile Health: Key Components and Design Principles for Ongoing Health Behavior Support.

Nahum-Shani I, Smith SN, Spring BJ, Collins LM, Witkiewitz K, Tewari A, Murphy SA

Ann Behav Med pmid: 27663578 doi: 10.1007/s12160-016-9830-8
Actigraphy features for predicting mobility disability in older adults.Publications2016-09-21MD2KActigraphy features for predicting mobility disability in older adults.

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A SMART data analysis method for constructing adaptive treatment strategies for substance use disorders.Publications2017-05MD2KA SMART data analysis method for constructing adaptive treatment strategies for substance use disorders.

Nahum-Shani I, Ertefaie A, Lu XL, Lynch KG, McKay JR, Oslin DW, Almirall D

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Cultural Shift or Linguistic Drift? Comparing Two Computational Measures of Semantic Change.Publications2016-11MobilizeCultural Shift or Linguistic Drift? Comparing Two Computational Measures of Semantic Change.

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Online Actions with Offline Impact: How Online Social Networks Influence Online and Offline User Behavior.Publications2017-02MobilizeOnline Actions with Offline Impact: How Online Social Networks Influence Online and Offline User Behavior.

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SNAP: A General Purpose Network Analysis and Graph Mining Library.Publications2016-10MobilizeSNAP: A General Purpose Network Analysis and Graph Mining Library.

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Extracting Databases from Dark Data with DeepDive.Publications2016-06MobilizeExtracting Databases from Dark Data with DeepDive.

Zhang C, Shin J, Re C, Cafarella M, Niu F

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DeepDive: Declarative Knowledge Base Construction.Publications2016-03MobilizeDeepDive: Declarative Knowledge Base Construction.

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Preparatory co-activation of the ankle muscles may prevent ankle inversion injuries.Publications2017-02-08MobilizePreparatory co-activation of the ankle muscles may prevent ankle inversion injuries.

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Gait biomechanics in the era of data science.Publications2016-12-08MobilizeGait biomechanics in the era of data science.

Ferber R, Osis ST, Hicks JL, Delp SL

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Large-scale Analysis of Counseling Conversations: An Application of Natural Language Processing to Mental Health.Publications2016MobilizeLarge-scale Analysis of Counseling Conversations: An Application of Natural Language Processing to Mental Health.

Althoff T, Clark K, Leskovec J

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Scan Order in Gibbs Sampling: Models in Which it Matters and Bounds on How Much.Publications2016MobilizeScan Order in Gibbs Sampling: Models in Which it Matters and Bounds on How Much.

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L1-Regularized Least Squares for Support Recovery of High Dimensional Single Index Models with Gaussian Designs.Publications2016-05PIC-SUREL1-Regularized Least Squares for Support Recovery of High Dimensional Single Index Models with Gaussian Designs.

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Combining clinical and genomics queries using i2b2 - Three methods.Publications2017-04-07PIC-SURECombining clinical and genomics queries using i2b2 - Three methods.

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Augmented estimation for t-year survival with censored regression models.Publications2017-03-10PIC-SUREAugmented estimation for t-year survival with censored regression models.

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Testing Differential Networks with Applications to Detecting Gene-by-Gene Interactions.Publications2015-06PIC-SURETesting Differential Networks with Applications to Detecting Gene-by-Gene Interactions.

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