representative papers are highlighted
lab members indicated in bold · [+] indicates equal contribution
2024
101Genetic and molecular architecture of complex traits
T Lappalainen, YI Li, S Ramachandran, A Gusev. Cell. 2024
100Cancer Type and Histology Influence Cutaneous Immunotherapy Toxicities: A Multi-Institutional Cohort Study
G Wan, S Khattab, BW Leung, S Zhang, N Nguyen, M Tran, C Lin, C Chang, N Alexander, R Jairath, J Phillipps, K Tang, A Rajeh, L Zubiri, ST Chen, S Demehri, K Yu, A Gusev, SG Kwatra, NR LeBoeuf, KL Reynolds, YR Semenov. Br J Dermatol. 2024
99Development and validation of time-to-event models to predict metastatic recurrence of localized cutaneous melanoma
G Wan, BW Leung, MS DeSimone, N Nguyen, A Rajeh, MR Collier, H Rashdan, K Roster, X Zhou, CB Moseley, AJ Nirmal, RJ Pelletier, Z Maliga, G Marko-Varga, IB Németh, H Tsao, MM Asgari, A Gusev, AM Stagner, CG Lian, MS Hurlbert, F Liu, K Yu, PK Sorger, YR Semenov. Journal of the American Academy of Dermatology. 2024
98Pre-existing inflammatory disease predicts cutaneous immunotherapy toxicity development: A multi-institutional cohort study
G Wan, N Nguyen, BW Leung, H Rashdan, K Tang, K Roster, MR Collier, PO Ugwu-Dike, NS Raval, NA Alexander, R Jairath, J Phillipps, M Amadife, S Zhang, A Gusev, ST Chen, KL Reynolds, NR LeBoeuf, SG Kwatra, YR Semenov. Journal of the American Academy of Dermatology. 2024
97Lung cancer in patients who have never smoked—an emerging disease
J LoPiccolo, A Gusev, DC Christiani, PA Jänne. Nature Reviews Clinical Oncology. 2024
96A comprehensive analysis of clinical and polygenic germline influences on somatic mutational burden
K Taraszka, S Groha, D King, R Tell, K White, E Ziv, N Zaitlen, A Gusev. The American Journal of Human Genetics. 2024
2023
95Scalable genetic screening for regulatory circuits using compressed Perturb-seq
D Yao, L Binan, J Bezney, B Simonton, J Freedman, CJ Frangieh, K Dey, K Geiger-Schuller, B Eraslan, A Gusev[+], A Regev[+], Brian Cleary[+]. Nature Biotechnology. 2023
94Pre-Existing Inflammatory Disease Predicts Cutaneous Immunotherapy Toxicity Development: A Multi-Institutional Cohort Study
G Wan, N Nguyen, B Leung, H Rashdan, K Tang, K Roster, M Collier, P Ugwu-Dike, N Raval, N Alexander, R Jairath, J Phillipps, M Amadife, S Zhang, A Gusev, S Chen, K Reynolds, N LeBoeuf, S Kwatra, Y Yevgeniy, R Semenov. Journal of the American Academy of Dermatology. 2023
93Development and Validation of Time-to-Event Models to Predict Metastatic Recurrence of Localized Cutaneous Melanoma
G Wan, B Leung, M DeSimone, N Nguyen, A Rajeh, M Collier, H Rashdan, K Roster, X Zhou, C Moseley, A Nirmal, R Pelletier, Z Maliga, G Gyorgy, M Marko-Varga, I Németh, H Tsao, M Asgari, A Gusev, A Stagner, C Lian, M Hurlbert, F Liu, K Yu, P Sorger, Y Semenov. Journal of the American Academy of Dermatology. 2023
92Enzyme-mediated depletion of methylthioadenosine restores T cell function in MTAP-deficient tumors and reverses immunotherapy resistance
D Gjuka, E Adib, K Garrison, J Chen, Y Zhang, W Li, D Boutz, C Candice, L Lamb, Y Tanno, A Nassar, T Zarif, N Kale, M Rakaee, T Mouhieddine, S Abou, A Alaiwi, A Gusev, T Rogers, J Gao, G Georgiou, D Kwiatkowski, E Stone. Cancer Cell. 2023
91Germline mechanisms of immunotherapy toxicities in the era of genome‐wide association studies
A Gusev. Immunological Reviews. 2023
90A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15. 33 prostate cancer risk locus
S Spisak, V Tisza, P Nuzzo, J Seo, B Balint, P Pataki, D Ribli, Z Sztupinszki, C Bell, M Mersedeh, R Rohanizadegan, D Stillman, S Alaiwi, A Bartels, M Marton, P Papp, A Shetty, F Abbasi, X Lin, K Lawrenson, S A, G Gayther, M Pomerantz, S Baca, N Solymosi, I Csabai, , Z Szallasi, A Gusev, M Freedman. Nature Communications. 2023
89Collaborative privacy-preserving analysis of oncological data using multiparty homomorphic encryption
R Geva, A Gusev, Y Polyakov, L Liram, O Rosolio, A Alexandru, N Genise, M Blatt, Z Duchin, B Waissengrin, D Mirelman, F Bukstein, D T, B Blumenthal, I Wolf, S Pelles-Avraham, T Schaffer, L Lavi, D Micciancio, V Vaikuntanathan, A Badawi, S Goldwasser. Proceedings of the National Academy of Sciences. 2023
88Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary
I Moon, J LoPiccolo, S Baca, L Sholl, K Kehl, M Hassett, D Liu, D Schrag, A Gusev. Nature Medicine. 2023
87Genotype error due to low-coverage sequencing induces uncertainty in polygenic scoring
E Petter, Y Ding, K Hou, A Bhattacharya, A Gusev, N Zaitlen, B Pasaniuc. The American Journal of Human Genetics. 2023
86Influence of melanoma type on incidence and downstream implications of cutaneous immune-related adverse events in the setting of immune checkpoint inhibitor therapy
N Nguyen, G Wan, P Ugwu-Dike, N Alexander, N Raval, S Zhang, R Jairath, J Phillipps, B Leung, K Roster, J Seo, C Lu, K Tang, M Seok, C Choi, M DeSimone, N Theodosakis, M Amadife, N Cox, T Le, F Liu, W Chen, X Bai, G Boland, D Liu, M Hurlbert, N LeBoeuf, K L, R Reynolds, K Yu, H Tsao, M Asgari, A Gusev, S Kwatra, Y Semenov. Journal of the American Academy of Dermatology. 2023
85A polygenic risk score for predicting racial and genetic susceptibility to prurigo nodularis
C Vasavda, G Wan, M Szeto, M Marani, N Sutaria, A Rajeh, C Lu, K Lee, N Nguyen, W Adawi, J Deng, V Parthasarathy, Z Bordeaux, M Taylor, M Alphonse, M Kwatra, S Kang, Y Semenov, A Gusev, S Kwatra. Journal of Investigative Dermatology. 2023
84Cutaneous immune-related adverse events are associated with longer overall survival in advanced cancer patients on immune checkpoint inhibitors: A multi-institutional cohort study
S Zhang, K Tang, G Wan, N Nguyen, C Lu, P Ugwu-Dike, N Raval, J Seo, N Alexander, R Jairath, J Phillipps, B Leung, K Roster, W Wenxin, C Chen, L Zubiri, G Boland, S Chen, H Tsao, S Demehri, N LeBoeuf, K Reynolds, K Yu, A Gusev, S Kwatra, Y Semenov. Journal of the American Academy of Dermatology. 2023
83Germline cancer gene expression quantitative trait loci are associated with local and global tumor mutations
Liu Y, Gusev A, Kraft P. Cancer Research. 2023
82The lingering effects of Neanderthal introgression on human complex traits
X Wei, C Robles, A Pazokitoroudi, A Ganna, A Gusev, A Durvasula, S Gazal, P Loh, D Reich, S Sankararaman. eLife. 2023
81Elucidating analytic bias due to informative cohort entry in cancer clinico-genomic datasets
K Kehl, H Uno, A Gusev, S Groha, S Brown, J Lavery, D Schrag, K Panageas. Cancer Epidemiology, Biomarkers & Prevention. 2023
80Optimized high-throughput screening of non-coding variants identified from genome-wide association studies
T Morova, Y Ding, C Huang, F Sar, T Schwarz, C Giambartolomei, S Baca, D Grishin, F Hach, A Gusev, M Freedman, B Pasaniuc, N Lack. Nucleic Acids Research. 2023
79Epigenomic charting and functional annotation of risk loci in renal cell carcinoma
A Nassar, S Alaiwi, S Baca, E Adib, R Corona, J Seo, M Fonseca, S Spisak, T Zarif, V Tisza, D Braun, H Du, M He, A Flaifel, M Alchoueiry, T Denize, S Matar, A Acosta, S Shukla, Y Hou, J Steinharter, G Bouchard, J Berchuck, E O’Connor, C Bell, P Pier, V Nuzzo, G Lee, S Signoretti, M Hirsch, M Pomerantz, E Henske, A Gusev, K Lawrenson, T Choueiri, D Kwiatkowski, M Freedman. Nature Communications. 2023
2022
78Germline variants associated with toxicity to immune checkpoint blockade.
Groha S, Alaiwi SA, Xu W, Naranbhai V, Nassar AH, Bakouny Z, Adib E, Nuzzo PV, Schmidt AL, Labaki C, Zarif TE, Ricciuti B, Alessi JV, Braun DA, Shukla SA, Keenan TE, Allen EV, Awad MM, Manos M, Rahma O, Zubiri L, Villani A, Hammer C, Khan Z, Reynolds K, Semenov Y, Schrag D, Kehl KL, Freedman ML[+], Choieiri TK[+], Gusev A[+]. Nature Medicine. 2022 datanews
77IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma.
Taylor CA, Watson RA, Tong O, Ye W, Nassiri I, Gilchrist JJ, Aires AV, Sharma PK, Koturan S, Cooper RA, Woodcock V, Jungkurth E, Shine B, Coupe N, Payne MJ, Naranbhai V, Groha S, Emery P, Mankia K, Freedman ML, Choueiri TK, Middleton MR, Gusev A, Fairfax BP. Nature Medicine. 2022
76The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats.
Munro D, Wang T, Chitr AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Solberg Woods LC, Saba LM, Chen H, Palmer AA, Mohammadi P. Nucleic Acids Res. 2022
75Multi-context genetic modeling of transcriptional regulation resolves novel disease loci.
Thompson M, Gordon MG, Lu A, Tandon A, Halperin E, Gusev A, Ye CJ, Balliu B, Zaitlen N. Nature Communications. 2022
74Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors.
Nassar A[+], Adib E[+], Alaiwi S[+], Zarif T, Groha S, Akl E, Nuzzo P, Mouhieddine T, Perea-Chamblee T, Taraszka K, El-Khoury H, Labban M, Fong C, Arora KS, Labaki C, Xu W, Sonpavde G, Haddad R, Mouw K, Giannakis M, Hodi F, Zaitlen N, Schoenfeld AJ, Schultz N, Berger MF, MacConaill L, Ananda G, Kwiatkowski D, Choueiri T, Schrag D, Carrot-Zhang J[+], Gusev A[+]. Cancer Cell. 2022
73Genetic 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[+]. Nature Genetics. 2022 software
72Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies.
Lu Z, Gopalan S, Yuan D, Conti DV, Pasaniuc B, Gusev A, Mancuso N. The American Journal of Human Genetics. 2022
71SurvLatent ODE : A Neural ODE based time-to-event model with competing risks for longitudinal data improves cancer-associated Venous Thromboembolism (VTE) prediction.
Moon I, Groha S, Gusev A. Proceedings of Machine Learning Research. 2022 software
70DeCAF: A novel method to identify cell-type specific regulatory variants and their role in cancer risk.
Kalita C, Gusev A. Genome Biology. 2022 software
69Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms.
Grishin D, Gusev A. Nature Genetics. 2022 data
68Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology.
Adib E, Nassar AH, Alaiwi SA, Groha S, Akl EW, Sholl LM, Michael KS, Awad MM, Jӓnne PA, Gusev A, Kwiatkowski DJ. Genome Med. 2022
67Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1.
Restuadi R, Steyn FJ, Kabashi E, Ngo ST, Cheng F, Nabais MF, Thompson MJ, Qi T, Wu Y, Henders AK, Wallace L, Bye CR, Turner BJ, Ziser L, Mathers S, McCombe PA, Needham M, Schultz D, Kiernan MC, Rheenen Wv, Berg LH, Veldink JH, Ophoff R, Gusev A, Zaitlen N, McRae AF, Henderson RD, Wray NR, Giacomotto J, Garton FC. Genome Med. 2022
66Somatic mutational profiles and germline polygenic risk scores in human cancer.
Liu Y, Gusev A, Heng YJ, Alexanderov LB, Kraft P. Genome Med. 2022
65Pre-Existing Autoimmune Disease and Mortality in Patients Treated With Anti-PD-1 and Anti-PD-L1 Therapy.
Tang K, Tiu BC, Wan G, Zhang S, Nguyen N, Leung B, Gusev A, Reynolds KL, Kwatra SG, Semenov YR. J Natl Cancer Inst. 2022
64Association of Cutaneous Immune-Related Adverse Events With Increased Survival in Patients Treated With Anti–Programmed Cell Death 1 and Anti–Programmed Cell Death Ligand 1 Therapy.
Tang K, Seo J, Tiu BC, Le TK, Pahalyants V, Raval NS, Ugwu-Dike PO, Zubiri L, Naranbhai V, Carrington M, Gusev A, Reynolds KL, LeBoeuf NR, Asgari MM, Kwatra SG, Semenov YR. JAMA Dermatol. 2022
63HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study.
Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JK, Carrington M. The Lancet Oncology. 2022
2021
62Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset.
Kehl KL, Xu W, Gusev A, Bakouny Z, Choueiri TK, Riaz IB, Elmarakeby H, Van Allen EM, Schrag D. Nature Communications. 2021
61H3K27ac HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility.
Giambartolomei C, Seo JH, Schwarz T, Freund MK, Johnson RD, Spisak S, Baca S, Gusev A, Mancuso N, Pasaniuc B, Freedman ML. The American Journal of Human Genetics. 2021
60Constructing germline research cohorts from the discarded reads of clinical tumor sequences.
Gusev A[+], Groha SM, Taraszka K, Semenov YR, Zaitlen N[+]. Genome Medicine. 2021 software
59Allele-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. The American Journal of Human Genetics. 2021data
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