2016 Publications

Xu K, Rosenstiel P, Paragas N, Hinze C, Gao X, Shen THuai, Werth M, Forster C, Deng R, Bruck E, Boles RW, Tornato A, Gopal T, Jones M, Konig J, Stauber J, D'Agati V, Erdjument-Bromage H, Saggi S, Wagener G, Schmidt-Ott KM, Tatonetti N, Tempst P, Oliver JA, Guarnieri P, Barasch J.  2016.  Unique Transcriptional Programs Identify Subtypes of AKI.. J Am Soc Nephrol. Go to Pubmed
Huang J, Kang BH, Ishida E, Zhou T, Griesman T, Sheng Z, Wu F, Doria-Rose NA, Zhang B, McKee K, O'Dell S, Chuang G-Y, Druz A, Georgiev IS, Schramm CA, Zheng A, M Joyce G, Asokan M, Ransier A, Darko S, Migueles SA, Bailer RT, Louder MK, S Alam M, Parks R, Kelsoe G, Von Holle T, Haynes BF, Douek DC, Hirsch V, Seaman MS, Shapiro L, Mascola JR, Kwong PD, Connors M.  2016.  Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.. Immunity. 45(5):1108-1121. Go to Pubmed
Tian M, Cheng C, Chen X, Duan H, Cheng H-L, Dao M, Sheng Z, Kimble M, Wang L, Lin S, Schmidt SD, Du Z, M Joyce G, Chen Y, DeKosky BJ, Chen Y, Normandin E, Cantor E, Chen RE, Doria-Rose NA, Zhang Y, Shi W, Kong W-P, Choe M, Henry AR, Laboune F, Georgiev IS, Huang P-Y, Jain S, McGuire AT, Georgeson E, Menis S, Douek DC, Schief WR, Stamatatos L, Kwong PD, Shapiro L, Haynes BF, Mascola JR, Alt FW.  2016.  Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires.. Cell. 166(6):1471-1484.e18. Go to Pubmed
Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SWai, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ.  2016.  DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome.. Am J Hum Genet. 99(3):555-66. Go to Pubmed
M Joyce G, Wheatley AK, Thomas PV, Chuang G-Y, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M, Kong W-P, Leung K, Narpala SN, Prabhakaran MS, Yang ESung, Zhang B, Zhang Y, Asokan M, Boyington JC, Bylund T, Darko S, Lees CR, Ransier A, Shen C-H, Wang L, Whittle JR, Wu X, Yassine HM, Santos C, Matsuoka Y, Tsybovsky Y, Baxa U, Mullikin JC, Subbarao K, Douek DC, Graham BS, Koup RA, Ledgerwood JE, Roederer M, Shapiro L, Kwong PD, Mascola JR, McDermott AB.  2016.  Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.. Cell. 166(3):609-23. Go to Pubmed
Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, Silva J, Stockwell BR, Califano A, Boehm JS, Vazquez F, Weir BA, Hahn WC, Khuri FR, Moreno CS, Johns M, Fu H, Nikolova O, Mendez E, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Warren EH, Riddell SR, McIntosh MW, Gevaert O, Kuo CJ, Ji HP, Dhruv H, Finlay D, Kiefer J, Kim S, Vuori K, Berens ME, Hangauer M, Boettcher M, Weissman JS, Bivona TG, Bandyopadhyay S, McManus MT, McCormick F, Aksoy O, Simonds EF, Zheng T, Chen J, An Z, Balmain A, Weiss WA, Chen K, Liang H, Scott KL, Mills GB, Posner BA, MacMillan J, Minna J, White M, Roth MG, Jagu S, Mazerik J.  2016.  Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance.. Mol Cancer Res. Go to Pubmed
Chuang L-S, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Ng SMeng Evely, Zhang W, Hsu N-Y, Facey J-A, Luong T, Fernandez-Hernandez H, Li D, Rivas M, Schiff ER, Gusev A, L Schumm P, Bowen BM, Sharma Y, Ning K, Remark R, Gnjatic S, Legnani P, George J, Sands BE, Stempak JM, Datta LW, Lipka S, Katz S, Cheifetz AS, Barzilai N, Pontikos N, Abraham C, Dubinsky MJ, Targan S, Taylor K, Rotter JI, Scherl EJ, Desnick RJ, Abreu MT, Zhao H, Atzmon G, Pe'er I, Kugathasan S, Hakonarson H, McCauley JL, Lencz T, Darvasi A, Plagnol V, Silverberg MS, Muise AM, Brant SR, Daly MJ, Segal AW, Duerr RH, Merad M, McGovern DPB, Peter I, Cho JH.  2016.  A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF.. Gastroenterology. 151(4):710-723.e2. Go to Pubmed
Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foá R, Rabadan R, Gaidano G, Rossi D.  2016.  The genetics of nodal marginal zone lymphoma.. Blood. Go to Pubmed
Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L.  2016.  The Genome Project-Write.. Science. Go to Pubmed
G Poznik D, Xue Y, Mendez FL, Willems TF, Massaia A, Sayres MAWilson, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GRS, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich, iv Y, Handsaker RE, Bustamante CD, Tyler-Smith C.  2016.  Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.. Nat Genet. Go to Pubmed
Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme K, Boutros PC, Caberlotto L, Caloian C, Campbell F, Neto EChaibub, Chang Y-C, Chen B, Chen C-Y, Chien T-Y, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJb, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong M-Y, Huang C, Hwang J, Ibrahim J, Inglese P, Jiang Q, Katsumata Y, Kauwe JSk, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Lyappan A, Ma M, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang Y-J, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung Y-A, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H et al.  2016.  Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.. Alzheimers Dement. Go to Pubmed
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WShing, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.  2016.  Inferring causal molecular networks: empirical assessment through a community-based effort.. Nat Methods. 13(4):310-8. Go to Pubmed
Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CGilberto, Tirapelli DPretti da, Rao A, Mikkelsen T, Lau CC, Yung WKAlfred, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH, Noushmehr H, Iavarone A, Verhaak RGW.  2016.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.. Cell. 164(3):550-63. Go to Pubmed
Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang G-Y, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, M Joyce G, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, Program NComparativ, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD.  2016.  Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.. Nat Struct Mol Biol. 23(1):81-90. Go to Pubmed