representative papers are highlighted

lab members indicated in bold · [+] indicates equal contribution

Pre-prints from the lab

Allele-specific epigenetic activity in prostate cancer and normal prostate tissue implicates prostate cancer risk mechanisms. Shetty A, Seo JH, Bell CA, O’Connor EP, Pomerantz M, Freedman ML, Gusev A

Seeing beyond the target: Leveraging off-target reads in targeted clinical tumor sequencing to identify prognostic biomarkers.
Mangul S, Brito JJ, Groha SM, Zaitlen N, Gusev A. 2021 software
 

Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation.
Baca S, Singler C, Zacharia S, Seo J, Morova T, Hach F, Ding Y, Schwarz T, Huang CF, Kalita C, Groha S, Pomerantz MM, Wang V, Linder S, Sweeney CJ, Zwart W, Lack NA, Pasaniuc B, Takeda DY, Gusev A[+], Freedman ML[+]. 2021 software
 

Constructing germline research cohorts from the discarded reads of clinical tumor sequences.
Gusev A, Groha SM, Taraszka K, Semenov YR, Zaitlen N. 2021 software
 

A General Framework for Survival Analysis and Multi-State Modelling.
Groha S, Schmon SM, Gusev A. 2021 software
 

Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma.
Gusev A[+], Spisak S[+], Fay AP, Carol H, Vavra KC, Signoretti S, Tisza V, Pomerantz M, Abbasi F, Seo J, Choueiri TK, Lawrenson K, Freedman ML. 2019 software
 

2021

58Immunotherapy-Mediated Thyroid Dysfunction: Genetic Risk and Impact on Outcomes with PD-1 Blockade in Non–Small Cell Lung Cancer.
Luo J, Martucci VL, Quandt Z, Groha S, Murray MH, Lovly CM, Rizvi H, Egger JV, Plodkowski AJ, Abu-Akeel M, Schulze I, Merghoub T, Cardenas E, Huntsman S, Li M, Hu D, Gubens MA, Gusev A[+], Aldrich MC[+], Hellmann MD[+], Ziv E[+]. Clin Cancer Res. 2021

57Clinical Inflection Point Detection on the Basis of EHR Data to Identify Clinical Trial-Ready Patients With Cancer.
Kehl KL, Groha S, Lepisto EM, Elmarakeby H, Lindsay J, Gusev A, Van Allen EM, Hassett MJ, Schrag D. JCO Clin Cancer Inform. 2021

56Gene fusions create partner and collateral dependencies essential to cancer cell survival.
Gillani R, Seong BKA, Crowdis J, Conway JR, Dharia NV, Alimohamed S, Haas BJ, Han K, Park J, Dietlein F, He MX, Imamovic A, Ma C, Bassic MC, Boehm JS, Vazquez F, Gusev A, Liu D, Janeway KA, McFarland JM, Stegmaier K, EM Van Allen. Cancer Res. 2021

55CDKN2A Alterations and Response to Immunotherapy in Solid Tumors.
Adib E, Nassar AH, Akl EW, Alaiwi SA, Nuzzo PV, Mouhieddine TH, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi SF, Shukla SA, Gusev A, Braun DA, Choueiri TK, Kiwatkowski DJ. Clin Cancer Res. 2021

54Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improve the power of transcriptome-wide association studies.
Feng H, Mancuso N, Gusev A, Majumdar A, Major M, Pasaniuc B, Kraft P. PLOS Genetics. 2021

53Prediction of severe immune-related adverse events requiring hospital admission in patients on immune checkpoint inhibitors: study of a population level insurance claims database from the USA.
Kalinich M, Murphy W, Wongvibulsin S, Pahalyants V, Yu KH, Lu C, Wang F, Zubiri L, Naranbhai V, Gusev A, Kwatra SG, Reynolds KL, Semenov YR. J Immunother Cancer. 2021

52Trans-ethnic variation in germline variants of patients with renal cell carcinoma.
Alaiwi SA[+], Nassar AH[+], Adib E, Groha S, Akl EW, McGregor BA, Esplin ED, Yang S, Hatchell K, Fusaro V, Nielsen S, Kwiatkowski DJ, Sonpavde GP, Pomerantz M, Garber JE, Freedman ML, Rana HQ, Gusev A[+], Choueiri TK[+]. Cell Reports. 2021

51Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations.
Carrot-Zhang J, Soca G, Patterson NJ, Watson J, Thorner A, Nag A, Genovese G, Rodriguez Ariza J, Gelbard MK, Corrales-Rodriguez L, Mitsuishi Y, Ha G, Campbell JD, Oxnard G, Arrieta O, Cardona AF[+], Gusev A[+], Meyerson M[+]. Cancer Discovery. 2021

2020

50Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations.
Saada JN, Kalantzis G, Shyr D, Cooper F, Robinson M, Gusev A[+] and Palamara PF[+]. Nature Communications. 2020
software 2 software 1 web data

49Prostate cancer reactivates developmental epigenomic programs during metastatic progression.
Pomerantz M, Qiu, … Freedman ML. Nature Genetics. 2020

48Optimized homomorphic encryption solution for secure genome-wide association studies.
Blatt M, Gusev A, Polyakov Y, Rohloff K, Vaikuntanathan V. BMC Medical Genomics. 2020

47Quantifying genetic effects on disease mediated by assayed gene expression levels.
Yao D, O’Connor LJ, Price AL, Gusev A. Nature Genetics. 2020 software

46Secure large-scale genome-wide association studies using homomorphic encryption.
Blatt M[+], Gusev A[+], Polyakov Y[+], Goldwasser S[+]. PNAS. 2020 eprintsoftware

45Non-coding Somatic Mutations Converge on the PAX8 Pathway in Epithelial Ovarian Cancer.
Corona RI, Seo J, Lin X, Hazelett DJ, Reddy J, Fonseca MAS, Abassi F, Lin YG, Mhawech-Fauceglia PY, Shah SP, Huntsman DG, Gusev A, Karlan BY, Berman BP, Freedman ML [+], Gayther SA [+], Lawrenson [+]. Nature Communications. 2020

44Germline Features Associated with Immune Infiltration in Solid Tumors.
Shahamatdar S, He MX, Reyna M, Gusev A, AlDubayan SH, Van Allen EM, Ramachandran S. Cell Reports. 2020

43Transcriptome-wide association study of breast cancer risk by estrogen-receptor status.
Feng, Gusev A, et al. … Jiang. Genet Epidemiol. 2020

42Allele-Specific QTL Fine Mapping with PLASMA.
Wang AT, Shetty AH, O’Connor E, Bell C, Pomerantz MM, Freedman ML, Gusev A. The American Journal of Human Genetics. 2020
talksoftware

2019

41Genome-wide germline correlates of the epigenetic landscape of prostate cancer.
Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O’Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC. Nature Medicine. 2020

40Optimized Homomorphic Encryption Solution for Secure Genome-Wide Association Studies.
Blatt M, Gusev A, Polyakov Y, Rohloff K, Vaikuntanathan V. IACR. 2019

39A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants.
A Gusev[+], K Lawrenson[+], X Lin, PC Lyra, S Kar, KC Vavra, F Segato, MAS Fonseca, JM Lee, T Pejovic, G Liu, Ovarian Cancer Association Consortium, B Karlan, ML Freedman, H Noushmehr, AN Monteiro, PD Pharoah, B Pasaniuc[+], S Gayther[+]. Nature Genetics. 2019 data

38Probabilistic fine-mapping of transcriptome-wide association studies.
Mancuso N, Kichaev G, Shi H, Freund M, Giambartolomei C, Gusev A, Pasaniuc B. Nature Genetics. 2019

37Evidence for evolutionary shifts in the fitness landscape of human complex traits.
Urrichio L, Kitano H, Gusev A[+], Zaitlen N[+]. Evolution Letters. 2019 software

2018

36Large-scale transcriptome-wide association study identifies new prostate cancer risk regions.
N Mancuso, S Gayther, A Gusev, W Zheng, KL Penney, the PRACTICAL consortium, CRUK, BPC3, CAPS, PEGASUS, Z Kote-Jarai, R Eeles, ML Freedman, C Haiman, B Pasaniuc. Nature Communications. 2018

35A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer
Wu et al. Nature Genetics. 2018

34Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits
Hormozdiari F, Gazal S, van de Geijn B, Finucane H, Ju C, Loh P, Schoech A, Reshef Y, Liu X, O’Connor L, Gusev A, Eskin E, Price AL. Nature Genetics. 2018

33Transcriptome-wide association studies accounting for co-localization using Egger regression.
Barfield R, Feng H, Gusev A, Wu L, Zheng W, Pasaniuc B, Kraft P. Genetic Epidemiology. 2018

32Heritability 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, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S, The Brainstorm Consortium, Perry JRB, Buenrostro J, Bernstein B, Raychaudhuri S, McCarroll S, Neale B, Price AL. Nature Genetics. 2018

31Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Gusev A, Mancuso N, Won H, Kousi M, Finucane HK, Reshef Y, Song L, Safi A, SCZ Working Group of the Psychiatric Genomics Consortium, McCaroll S, Neale BM, Ophoff RA, O’Donovan MC, Crawford GE, Geschwind DH, Katsanis N, Sullivan PF, Pasaniuc B[+], Price AL[+]. Nature Genetics. 2018 data

30Methods for fine-mapping with chromatin and expression data.
Roytman M, Kichaev G, Gusev A, Pasaniuc B. PLoS Genet. 2018

2017

29Linkage disequilibrium-dependent architecture of human complex traits shows 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. Nature Genetics. 2017

28 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

27Integrating 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 web data

2016

26Integrative 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 software

25 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

24 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

23 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

22 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

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

20 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

19 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

18 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

17 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

16 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

15 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

14Partitioning 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

13 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

12 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

11Quantifying 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

10 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

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

08Low-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

07The 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

02Whole 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 software

2008

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