[+] indicates equal contribution

pre-prints

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Gusev A, Mancuso N, Finucane H, Reshef Y, Song L, Safi A, Oh E, SCZ Working Group of the Psychiatric Genomics Consortium, McCaroll S, Neale B, Ophoff R, O’Donovan MC, Katsanis N, Crawford GE, Sullivan PF, Pasaniuc B[+], Price AL[+]. bioRxiv. 2016

Correcting subtle stratification in summary association statistics. Bhatia G, Furlotte N, Loh P, Liu X, Finucane H, Gusev A, Price AL. bioRxiv. 2016

Subtle stratification confounds estimates of heritability from rare variants. Bhatia G, Gusev A, Loh P, Finucane H, Vilhjalmsson B, Ripke S, SCZ Working Group of the Psychiatric Genomics Consortium, Purcell S, Stahl E, Daly M, de Candia T, Lee SH, Neale BM, Keller MC, Zaitlen NA, Pasaniuc B, Patterson N, Yang J, Price AL. bioRxiv. 2016

Linkage disequilibrium dependent architecture of human complex traits reveals action of negative selection. Gazal S, Finucane H, Furlotte NA, Loh P, Palamara PF, Liu X, Schoech A, Bulik-Sullivan B, Neale BM, Gusev A, Price AL. bioRxiv. 2016

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types Finucane H, Reshef Y, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh P, Genovese G, Saunders A, Macosko E, Pollack S, The Brainstorm Consortium, Perry JRB, Raychaudhuri S, McCarroll S, Neale B, Price AL. bioRxiv 2017

Estimating the proportion of disease heritability mediated by gene expression levels O’Connor L, Gusev A, Liu X, Loh P, Finucane H, Price AL. bioRxiv 2017

2017

30 Functional partitioning of local and distal gene expression regulation in multiple human tissues. Liu X, Finucane H, Gusev A, Bhatia G, Gazal S, O’Connor L, Bulik-Sullivan B, Wright F, Sullivan P, Neale B, Price AL. The American Journal of Human Genetics. 2017

29 Integrating gene expression with summary association statistics to identify susceptibility genes for 30 complex traits. Mancuso N, Shi H, Goddard P, Kichaev G, Gusev A[+], Pasaniuc B[+]. The American Journal of Human Genetics. 2017

2016

28 Integrative approaches for large-scale transcriptome-wide association studies. Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx B, Jansen R, Geus E, Boomsma D, Wright F., Sullivan PF, Nikkola E, Alvarez M, Civelek M, Lusis AJ, Lehtimäki T, Raitoharju E, Kähönen M, Seppälä I, Raitakari OT, Kuusisto J, Laakso M, Price AL, Pajukanta P, Pasaniuc B. Nature Genetics. 2016

27 Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJ, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A; PRACTICAL consortium, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Nature communications. 2016

26 A frameshift in CSF2RB predominant among Ashkenazi Jews increases risk for Crohn’s disease and reduces monocyte signaling via GM-CSF. Chuang LS, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Evelyn Ng SM, Zhang W, Hsu NY, Facey JA, Luong T, Fernandez-Hernandez H, Li D, Rivas M, Schiff ER, Gusev A, Schumm LP, 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 DP, Peter I, Cho JH. Gastroenterology. 2016

2015

25 Modeling linkage disequilibrium increases accuracy of polygenic risk scores. Vilhjálmsson BJ, Yang J, Finucane HK, Gusev A, Lindström S, Ripke S, Genovese G, Loh PR, Bhatia G, Do R, Hayeck T, Won HH; Schizophrenia Working Group of the Psychiatric Genomics Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Kathiresan S, Pato M, Pato C, Tamimi R, Stahl E, Zaitlen N, Pasaniuc B, Belbin G, Kenny EE, Schierup MH, De Jager P, Patsopoulos NA, McCarroll S, Daly M, Purcell S, Chasman D, Neale B, Goddard M, Visscher PM, Kraft P, Patterson N, Price AL. The American Journal of Human Genetics. 2015

24 Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. Loh PR, Bhatia G, Gusev A, Finucane HK, Bulik-Sullivan BK, Pollack SJ; Schizophrenia Working Group of Psychiatric Genomics Consortium, de Candia TR, Lee SH, Wray NR, Kendler KS, O’Donovan MC, Neale BM, Patterson N, Price AL. Nature Genetics. 2015

23 Leveraging local ancestry to detect gene-gene interactions in genome-wide data. Aschard H, Gusev A, Brown R, Pasaniuc B. BMC Genetics. 2015

22 Partitioning heritability by functional annotation using genome-wide association summary statistics. Finucane H[+], Bulik-Sullivan B[+], Gusev A, Trynka G, Reshef Y, Loh P, Anttila V, Xu H, Zang C, Farh K, Ripke S, Day FR, ReproGen Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, RACI Consortium, Purcell S, Stahl E, Lindstrom S, Perry JR, Okada Y, Raychaudhuri S, Daly MJ, Patterson N, Neale BM, Price AL. Nature Genetics. 2015

21 Genome-wide mapping of identical-by-descent segments in an Ashkenazi Parkinson disease cohort identifies associated haplotypes Vacic V, Ozelius L, Clark L, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny E, Liu X, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe’er I, Bressman SB, Orr-Urtreger A.

20 New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. Lee SH, Byrne EM, Hultman CM, Kähler A, Vinkhuyzen AA, Ripke S, Andreassen OA, Frisell T, Gusev A, Hu X, Karlsson R, Mantzioris VX, McGrath JJ, Mehta D, Stahl EA, Zhao Q, Kendler KS, Sullivan PF, Price AL, O’Donovan M, Okada Y, Mowry BJ, Raychaudhuri S, Wray NR; Schizophrenia Working Group of the Psychiatric Genomics Consortium and Rheumatoid Arthritis Consortium International. International journal of epidemiology. 2015

19 Leveraging distant relatedness to quantify human mutation and gene-conversion rates. Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S; Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe’er I, Price AL. The American Journal of Human Genetics. 2015

18 An atlas of genetic correlations across human diseases and traits. Bulik-Sullivan B[+], Finucane H[+], Anttila V, Gusev A, Day FR, Loh PR,; ReproGen Consortium; Psychiatric Genomics Consortium; Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium, Duncan L, Perry JR, Patterson N, Robinson EB, Daly MJ, Price AL, Neale BM Nature genetics. 2015

17 Mixed model with correction for case-control ascertainment increases association power. Hayeck T, Zaitlen N, Loh P, Vilhjalmsson B, Pollack S, Gusev A, Yang J, Chen GB, Goddard ME, Visscher PM, Patterson N, Price AL. The American Journal of Human Genetics. 2015

2014

16 Leveraging population admixture to characterize the heritability of complex traits. Zaitlen N, Pasaniuc B, Sankararaman S, Bhatia G, Zhang J, Gusev A, Young T, Tandon A, Pollack S, Vilhjálmsson B., Assimes TL, Berndt SI, Blot WJ, Chanock S, Franceschini N, Goodman PG, He J, Hennis AJ, Hsing A, Ingles SA, Isaacs W, Kittles RA, Klein EA, Lange LA, Nemesure B, Patterson N, Reich D, Rybicki BA, Stanford JL, Stevens VL, Strom SS, Whitsel EA, Witte JS, Xu J, Haiman C, Wilson JG, Kooperberg C, Stram D, Reiner AP, Tang H, Price AL. Nature genetics. 2014

15 Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Gusev A, Lee S, Trynka G, Finucane H, Vilhjálmsson B, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E., Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium, Kähler AK, Hultman CM, Purcell SM, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL. The American Journal of Human Genetics. 2014

14 Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes. Human molecular genetics. Vacic V, Ozelius L, Clark L, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny E, Liu X., Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe’er I, Bressman SB, Orr-Urtreger A. Hum Mol Genet. 2014

13 Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Pasaniuc B, Zaitlen N, Shi H, Bhatia G, Gusev A, Pickrell J, Hirschhorn J, Strachan D, Patterson N, Price AL. Bioinformatics. 2014

2013

12 Quantifying missing heritability at known GWAS loci. Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson B, Diogo D, Stahl E, Gregersen P, Worthington J, Klareskog L, Raychaudhuri S. Plenge RM, Pasaniuc B, Price AL. PLoS Genet. 2013

11 Extended haplotype association study in Crohn’s disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3. Zhang W, Hui K, Gusev A, Warner N, Ng S, Ferguson J, Choi M, Burberry A, Abraham C, Mayer L. Desnick RJ, Cardinale CJ, Hakonarson H, Waterman M, Chowers Y, Karban A, Brant SR, Silverberg MS, Gregersen PK, Katz S, Lifton RP, Zhao H, Nuñez G, Pe’er I, Peter I, Cho JH. Genes and immunity. 2013

2012

10 Detecting identity by descent and homozygosity mapping in whole-exome sequencing data. Zhuang Z, Gusev A, Cho J, Pe’er I. PloS one. 2012

09 Integration of Population-Specific Novel and Established Genetic Variation for the Identification of Crohn’s Disease-Associated Loci in Ashkenazi Jewish Individuals. Hui K, Zhang W, Gusev A, Pe’er I, Peter I, Cho J. Gastroenterology. 2012

08 Low-Pass Genome-Wide Sequencing and Variant Inference Using Identity-by-Descent in an Isolated Human Population. Gusev A, Shah M, Kenny E, Ramachandran A, Lowe J, Salit J, Lee C, Levandowsky E, Weaver T, Doan Q, Pe’er I. Genetics 2012

2011

07 The architecture of long-range haplotypes shared within and across populations. Gusev A[+], Palamara P[+], Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe’er I. MBE. 2011

06 HLA Type Inference via Haplotypes Identical by Descent. Setty M, Gusev A, Pe’er I. JCB. 2011

05 DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. Gusev A, Kenny E, Lowe J, Salit J, Saxena R, Kathiresan S, Altshuler D, Friedman J, Breslow J, Pe’er I. The American Journal of Human Genetics. 2011

2010

04 Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Kenny E, Kim M, Gusev A, Lowe J, Salit J, Smith J, Kovvali S, Kang H, Newton-Cheh C, Daly M, Pe’er, I. Hum Mol Genet. 2010

03 Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. Kenny E, Gusev A, Riegel K, Lütjohann D, Lowe J, Salit J, Maller J, Stoffel M, Daly M, Altshuler D. Pe’er, I. PNAS. 2009

2009

02 Whole population, genome-wide mapping of hidden relatedness. Gusev A, Lowe J, Stoffel M, Daly M, Altshuler D, Breslow J, Friedman J, Pe’er I. Genome res. 2009

2008

01 Highly scalable genotype phasing by entropy minimization. Gusev A, Măndoiu I, Paşaniuc B. IEEE/ACM TCBB. 2008