Publications

All:

Find us on Google, or Pubmed * – denotes equal contribution; members of the group are underlined.

2025:

• The Germline and Somatic Origins of Prostate Cancer Heterogeneity. Yamaguchi TN, Houlahan KE, Zhu H, Kurganovs N, Livingstone J, Fox NS, Yuan J, Sietsma Penington J, Jung CH, Schwarz T, Jaratlerdsiri W, van Riet J, Georgeson P, Mangiola S, Taraszka K, Lesurf R, Jiang J, Chow K, Heisler LE, Shiah YJ, Ramanand SG, Clarkson MJ, Nguyen A, Espiritu SMG, Stuchbery R, Jovelin R, HuangV, Bell C, O’Connor E, McCoy PJ, Lalansingh CM, Cmero M, Salcedo A, Chan EKF, Liu LY, Stricker PD, Bhandari V, Bornman RMS, Sendorek DH, Lonie A, Prokopec SD, Fraser M, Peters JS, Foucal A, Mutambirwa SBA, Mcintosh L, Orain M, Wakefield M, Picard V, Park DJ, Hovington H, Kerger M, Bergeron A, Sabelnykova V, Seo JH, Pomerantz MM, Zaitlen N, Waszak SM, Gusev A, Lacombe L, Fradet Y, Ryan A, Kishan AU, Lolkema MP, Weischenfeldt J, Tˆetu B, Costello AJ, Hayes VM, Hung RJ, He HH, McPherson JD, Pasaniuc B, van der Kwast T, Papenfuss AT, Freedman ML, Pope BJ, Bristow RG, Mani RS, Corcoran NM, Reimand J, Hovens CM, Boutros PC. Cancer Discov. 2025 Feb 13. doi: 10.1158/2159-8290.CD-23-0882. Epub ahead of print. PMID: 39945744.
• The PRIMED Consortium: Reducing disparities in polygenic risk assessment. Kullo IJ, Conomos MP, Nelson SC, Adebamowo SN, Choudhury A, Conti D, Fullerton SM, Gogarten SM, Heavner B, Hornsby WE, Kenny EE, Khan A, Khera AV, Li Y, Martin I, Mercader JM, Ng M, Raffield LM, Reiner A, Rowley R, Schaid D, Stilp A, Wiley K, Wilson R, Witte JS, Natarajan P, Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium. Am J Hum Genet. 2024 Dec 5;111(12):2594-2606. doi: 10.1016/j.ajhg.2024.10.010. Epub 2024 Nov 18. PMID: 39561770; PMCID: PMC11639095.
• Evaluating Performance and Agreement of Coronary Heart Disease Polygenic Risk Scores. Abramowitz SA, Boulier K, Keat K, Cardone KM, Shivakumar M, DePaolo J, Judy R, Bermudez F, Mimouni N, Neylan C, Kim D, Rader DJ, Ritchie MD, Voight BF, Pasaniuc B, Levin MG, Damrauer SM; Penn Medicine BioBank. JAMA. 2025 Jan 7;333(1):60-70. doi: 10.1001/jama.2024.23784. PMID: 39549270; PMCID: PMC11569413.

2024:

• Advancing Mental Health Research Through Strategic Integration of Transdiagnostic Dimensions and Genomics. Doyle AE, Bearden CE, Gur RE, Ledbetter DH, Martin CL, McCoy TH Jr, Pasaniuc B, Perlis RH, Smoller JW, Davis LK. Biol Psychiatry. 2025 Mar 1;97(5):450-460. doi: 10.1016/j.biopsych.2024.10.006. Epub 2024 Oct 16. PMID: 39424167.
• Temporally distinct 3D multi-omic dynamics in the developing human brain. Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski, TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. Nature. 2024 Nov;635(8038):481-489. doi: 10.1038/s41586-024-08030-7. Epub 2024 Oct 9. PMID: 39385032; PMCID: PMC11560841.
• Improving genetic risk modeling of dementia from real-world data in underrepresented populations. Fu M, Valiente-Banuet L, Wadhwa SS, Pasaniuc B, Vossel K, Chang TS. Commun Biol. 2024 Aug 25;7(1):1049. doi: 10.1038/s42003-024-06742-0. PMID: 39183196; PMCID: PMC11345412.
• Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B*, Xiao X*. Am J Hum Genet. 2024 Aug 8;111(8):1573-1587. doi: 10.1016/j.ajhg.2024.06.001. Epub 2024 Jun 25. PMID: 38925119; PMCID: PMC11339621.
• Calibrated prediction intervals for polygenic scores across diverse contexts. Hou K, Xu Z, Ding Y, Mandla R, Shi Z, Boulier K, Harpak A, Pasaniuc B. Nat Genet. 2024 Jul;56(7):1386-1396. doi: 10.1038/s41588-024-01792-w. Epub 2024 Jun 17. PMID: 38886587; PMCID: PMC11465192.
• Multi-ancestry polygenic risk scores for venous thromboembolism. Jee YH, Thibord F, Dominguez A, Sept C, Boulier K, Venkateswaran V, Ding Y, Cherlin T, Verma SS, Faro VL, Bartz TM, Boland A, Brody JA, Deleuze JF, Emmerich J, Germain M, Johnson AD, Kooperberg C, Morange PE, Pankratz N, Psaty BM, Reiner AP, Smadja DM, Sitlani CM, Suchon P, Tang W, Tr ́egou ̈et DA, Zo ̈llner S, Pasaniuc B, Damrauer SM, Sanna S, Snieder H; Lifelines Co- hort Study; Kabrhel C, Smith NL, Kraft P; Hum Mol Genet. 2024 Sep 3;33(18):1584-1591. doi: 10.1093/hmg/ddae097. PMID: 38879759; PMCID: PMC11373328.
• Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygu ̈n N, Walker RL, Chatzinakos C, Clarke D, Pratt H; PsychEN- CODE Consortium†; Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ, PsychENCODE Consortium. Science. 2024 May 24;384(6698):eadh0829. doi: 10.1126/science.adh0829. Epub 2024 May 24. PMID: 38781368.
• Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Science. 2024 May 24;384(6698):eadh7688. doi: 10.1126/science.adh7688. Epub 2024 May 24. PMID: 38781356.
• Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics. Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ. Sci Adv. 2024 May 24;10(21):eadn7655. doi: 10.1126/sciadv.adn7655. Epub 2024 May 23. PMID: 38781333; PMCID: PMC11114225.
• Generalizability of PGS313 for breast cancer risk in a Los Angeles biobank. Shang H, Ding Y, Venkateswaran V, Boulier K, Kathuria-Prakash N, Malidarreh PB, Luber JM, Pasaniuc B. HGG Adv. 2024 Jul 18;5(3):100302. doi: 10.1016/j.xhgg.2024.100302. Epub 2024 May 3. PMID: 38704641; PMCID: PMC11137525.
• Electronic health record signatures identify undiagnosed patients with common variable immunodeficiency disease. Johnson R, Stephens AV, Mester R, Knyazev S, Kohn LA, Freund MK, Bondhus L, Hill BL, Schwarz T, Zaitlen N, Arboleda VA, A Bastarache L, Pasaniuc B*, Butte MJ*. Sci Transl Med. 2024 May;16(745):eade4510. doi: 10.1126/scitranslmed.ade4510. Epub 2024 May 1. PMID: 38691621; PMCID: PMC11402387.
• Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Hou K, Gogarten S, Kim J, Hua X, Dias JA, Sun Q, Wang Y, Tan T; Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group; Atkinson EG, Martin A, Shortt J, Hirbo J, Li Y, Pasaniuc B, Zhang H. Bioinformatics. 2024 Mar 29;40(4):btae148. doi: 10.1093/bioinformatics/btae148. PMID: 38490256; PMCID: PMC10980565.
• Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders. Boltz T, Schwarz T, Bot M, Hou K, Caggiano C, Lapinska S, Duan C, Boks MP, Kahn RS, Zaitlen N, Pasaniuc B, Ophoff R. Am J Hum Genet. 2024 Feb 1;111(2):323-337. doi: 10.1016/j.ajhg.2023.12.018. PMID: 38306997; PMCID: PMC10870131.
• Polygenic scores for tobacco use provide insights into systemic health risks in a diverse EHR-linked biobank in Los Angeles. Venkateswaran V, Boulier K, Ding Y, Johnson R, Bhattacharya A, Pasaniuc B. Transl Psychiatry. 2024 Jan 18;14(1):38. doi: 10.1038/s41398-024-02743-z. PMID: 38238290; PMCID: PMC10796315.

2023:

• Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric disorders in the human brain. Bhattacharya A, Vo DD, Jops C, Kim M, Wen C, Hervoso JL, Pasaniuc B*, Gandal MJ*. Nat Genet. 2023 Dec;55(12):2117-2128. doi: 10.1038/s41588-023-01560-2. Epub 2023 Nov 30. PMID: 38036788; PMCID: PMC10703692.
• Inferring disease architecture and predictive ability with LDpred2-auto. Priv ́e F, Albin ̃ana C, Arbel J, Pasaniuc B, Vilhja ́lmsson BJ. Am J Hum Genet. 2023 Dec 7;110(12):2042- 2055. doi: 10.1016/j.ajhg.2023.10.010. Epub 2023 Nov 8. PMID: 37944514; PMCID: PMC10716363.
• A second update on mapping the human genetic architecture of COVID-19. COVID-19 Host Genetics Initiative. Nature. 2023 Sep;621(7977):E7-E26. doi: 10.1038/s41586-023- 06355-3. Epub 2023 Sep 6. PMID: 37674002
• A Bayesian method for estimating gene-level polygenicity under the framework of transcriptome-wide association study. Majumdar A, Pasaniuc B. Stat Med. 2023 Aug 29. doi: 10.1002/sim.9892. Online ahead of print. PMID: 37643728
• Principles and methods for transferring polygenic risk scores across global populations. Kachuri L, Chatterjee N, Hirbo J, Schaid DJ, Martin I, Kullo IJ, Kenny EE, Pasaniuc B; Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group; Witte JS, Ge T. Nat Rev Genet. 2023 Aug 24. doi: 10.1038/s41576-023-00637-2. Online ahead of print. PMID: 37620596
• Genotype error due to low-coverage sequencing induces uncertainty in polygenic scoring. Petter E, Ding Y, Hou K, Bhattacharya A, Gusev A, Zaitlen N, Pasaniuc B. Am J Hum Genet. 2023 Aug 3;110(8):1319-1329. doi: 10.1016/j.ajhg.2023.06.015. Epub 2023 Jul 24. PMID: 37490908
• Disease risk and healthcare utilization among ancestrally diverse groups in the Los Angeles region. Caggiano C, Boudaie A, Shemirani R, Mefford J, Petter E, Chiu A, Ercelen D, He R, Tward D, Paul KC, Chang TS, Pasaniuc B, Kenny EE, Shortt JA, Gignoux CR, Balliu B, Arboleda VA, Belbin G, Zaitlen N. Nat Med. 2023 Jul;29(7):1845-1856. doi: 10.1038/s41591-023-02425-1. Epub 2023 Jul 18. PMID: 37464048
• Impact of cross-ancestry genetic architecture on GWASs in admixed populations. Mester R, Hou K, Ding Y, Meeks G, Burch KS, Bhattacharya A, Henn BM, Pasaniuc B. Am J Hum Genet. 2023 Jun 1;110(6):927-939. doi: 10.1016/j.ajhg.2023.05.001. Epub 2023 May 23. PMID: 37224807
• Polygenic scoring accuracy varies across the genetic ancestry continuum. Ding Y, Hou K, Xu Z, Pimplaskar A, Petter E, Boulier K, Prive F, Vilhjalmsson BJ, Olde Loohuis LM, Pasaniuc B. Nature. 2023 Jun;618(7966):774-781. doi: 10.1038/s41586-023-06079-4. Epub 2023 May 17. PMID: 37198491
• twassim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis. Wang X, Lu Z, Bhattacharya A, Pasaniuc B, Mancuso N. Bioinformatics. 2023 May 4;39(5):btad288. doi: 10.1093/bioinformatics/btad288. PMID: 37099718
• Causal effects on complex traits are similar across segments of different continental ancestries within admixed individuals. Hou K, Ding Y, Xu X, Wu Y, Bhattacharya A, Mester R, Belbin G, Conti D, Darst BF, Fornage, Gignoux C, Guo X, Haiman X, Kenny E, Kim M, Kooperberg C, Lange L, Manichaikul A, North K, Nudelman N, Peters U, Rasmussen-Torvik L, Rich S, Rotter J, Wheeler H, Zhou Y, Sankararaman S, Pasaniuc B. Nat Genet. 2023 Apr;55(4):549-558. doi: 10.1038/s41588-023-01338-6. Epub 2023 Mar 20. PMID: 36941441
• The UCLA ATLAS Community Health Initiative: Promoting precision health research in a diverse biobank. Johnson R, Ding Y, Bhattacharya A, Knyazev S, Chiu A, Lajonchere C, Geschwind DH, Pasaniuc B. Cell Genom. 2023 Jan 11;3(1):100243. doi: 10.1016/j.xgen.2022.100243. eCollection 2023 Jan 11. PMID: 36777178

2022:

• Optimized high-throughput screening of non-coding variants identified from genome-wide association studies. Morova T, Ding Y, Huang CF, Sar F, Schwarz T, Giambartolomei C, Baca SC, Grishin D, Hach F, Gusev A, Freedman ML, Pasaniuc B, Lack NA. Nucleic Acids Res. 2022 Dec 22:gkac1198. doi:10.1093/nar/gkac1198. Online ahead of print. PMID: 36546757
• Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons fromthe Global Biobank Meta-analysis Initiative. Bhattacharya A, Hirbo JB, Zhou D, Zhou W, Zheng J, Kanai M; Global Biobank Meta-analysis Initiative; Pasaniuc B, Gamazon ER, Cox NJ. Cell Genom. 2022 Oct 12;2(10):100180. doi: 10.1016/j.xgen.2022.100180. PMID: 36341024
• Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Gandal MJ, Haney JR, Wamsley B, Yap CX, Parhami S, Emani PS, Chang N, Chen GT, Hoftman GD, de Alba D, Ramaswami G, Hartl CL, Bhattacharya A, Luo C, Jin T, Wang D, Kawaguchi R, Quintero D, Ou J, Wu YE, Parikshak NN, Swarup V, Belgard TG, Gerstein M, Pasaniuc B, Geschwind DH. Nature. 2022 Nov;611(7936):532-539. doi: 10.1038/s41586-022-05377-7. Epub 2022 Nov 2. PMID: 36323788
• Leveraging genomic diversity for discovery in an EHR-linked biobank: the UCLA ATLAS Community Health Initiative. Johnson R, Ding Y, Venkateswaran V, Bhattacharya A, Chiu A, Schwarz T, Freund M, Zhan L, Burch KS, Caggiano C, Hill B, Rakocz N, Balliu B, Sul JH, Zaitlen N, Arboleda VA, Halperin E, Sankararaman S, Butte M, UCLA Precision Health Data Discovery Repository Working Group, UCLA Precision Health ATLAS Working Group, Lajonchere C, Geschwind DH, Pasaniuc B. Genome Med. 2022 Sep 9;14(1):104. doi: 10.1186/s13073-022-01106-x. PMID: 36085083
• Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation. Baca SC, Singler C, Zacharia S, Seo JH, Morova T, Hach F, Ding Y, Schwarz T, Huang CF, Anderson J, Fay AP, Kalita C, Groha S, Pomerantz MM, Wang V, Linder S, Sweeney CJ, Zwart W, Lack NA, Pasaniuc B, Takeda DY, Gusev A, Freedman ML. Nat Genet. 2022 Sep 7. doi: 10.1038/s41588-022-01168-y. Online ahead of print. PMID: 36071171
• Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Zhang MJ*, Hou K*, Dey KK, Sakaue S, Jagadeesh KA, Weinand K, Taychameekiatchai A, Rao P, Pisco AO, Zou J, Wang B, Gandal M, Raychaudhuri S, Pasaniuc B*, Price AL*. Nat Genet. 2022 Sep 1. doi: 10.1038/s41588-022-01167-z. Online ahead of print. PMID: 36050550
• Multi-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. Am J Hum Genet. 2022 Aug 4;109(8):1388-1404. doi: 10.1016/j.ajhg.2022.07.002. PMID: 35931050.
• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence. Linder S, Hoogstraat M, Stelloo S, Eickhoff N, Schuurman K, de Barros H, Alkemade M, Bekers EM, Severson TM, Sanders J, Huang CF, Morova T, Altintas UB, Hoekman L, Kim Y, Baca SC, Sjostrom M, Zaalberg A, Hintzen DC, de Jong J, Kluin RJC, de Rink I, Giambartolomei C, Seo JH, Pasaniuc B,, Altelaar M, Medema RH, Feng FY, Zoubeidi A, Freedman ML, Wessels LFA, Butler LM, Lack NA, van der Poel H, Bergman AM, Zwart W. Cancer Discov. 2022 Jun 27:candisc.0576.2021- 5-3 12:14:47.513. doi: 10.1158/2159-8290.CD-21-0576. Epub ahead of print. PMID: 35754340.
• Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Gazal S, Weissbrod O, Hormozdiari F, Dey KK, Nasser J, Jagadeesh KA, Weiner DJ, Shi H, Fulco CP, O’Connor LJ, Pasaniuc B, Engreitz JM, Price AL. Nat Genet. 2022 Jun;54(6):827-836. doi: 10.1038/s41588-022-01087-y. Epub 2022 Jun 6. PMID: 35668300.
• Powerful eQTL mapping through low-coverage RNA sequencing. Schwarz T, Boltz T, Hou K, Bot M, Duan C, Loohuis LO, Boks MP, Kahn RS, Ophoff RA, Pasaniuc B. HGG Adv. 2022 Apr 2;3(3):100103. doi: 10.1016/j.xhgg.2022.100103. PMID: 35519825; PMCID: PMC9062329.
• Unlocking capacities of genomics for the COVID-19 response and future pandemics. Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Nat Methods. 2022 Apr;19(4):374-380. doi: 10.1038/s41592-022-01444-z. PMID: 35396471.
• Phenome-Wide Association Study of Polygenic Risk Score for Alzheimer’s Disease in Electronic Health Records. Fu M; UCLA Precision Health Data Discovery Repository Working Group; UCLA Precision Health ATLAS Working Group, Chang TS. Front Aging Neurosci. 2022 Mar 15;14:800375. doi: 10.3389/fnagi.2022.800375. PMID: 35370621; PMCID: PMC8965623.
• Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies diseaserelevant genes. Burch KS, Hou K, Ding Y, Wang Y, Gazal S, Shi H, Pasaniuc B. Am J Hum Genet. 2022 Apr 7;109(4):692-709. doi: 10.1016/j.ajhg.2022.02.012. Epub 2022 Mar 9. PMID: 35271803; PMCID: PMC9069080.
• Genetically regulated multi-omics study for symptom clusters of posttraumatic stress disorder highlights pleiotropy with hematologic and cardio-metabolic traits. Pathak GA, Singh K, Wendt FR, Fleming TW, Overstreet C, Koller D, Tylee DS, De Angelis F, Cabrera Mendoza B, Levey DF, Koenen KC, Krystal JH, Pietrzak RH, O’ Donell C, Gaziano JM, Falcone G, Stein MB, Gelernter J, Pasaniuc B, Mancuso N, Davis LK, Polimanti R. Mol Psychiatry. 2022 Mar;27(3):1394-1404. doi: 10.1038/s41380-022- 01488-9. Epub 2022 Mar 3. PMID: 35241783; PMCID: PMC9210390.
• A summary-statistics-based approach to examine the role of serotonin transporter promoter tandem repeat polymorphism in psychiatric phenotypes. Majumdar A, Patel P, Pasaniuc B, Ophoff RA. Eur J Hum Genet. 2022 May;30(5):547-554. doi: 10.1038/s41431-021-00996-6. Epub 2021 Dec 23. PMID: 34949768; PMCID: PMC9091198.
• Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification. Ding Y, Hou K, Burch KS, Lapinska S, Prive F, Vilhalmsoon B, Sankararaman S, Pasaniuc B. Nat Genet. 2022 Jan;54(1):30-39. doi: 10.1038/s41588-021-00961-5. Epub 2021 Dec 20. PMID: 34931067; PMCID: PMC8758557.
• Fast estimation of genetic correlation for biobank-scale data. Wu Y, Burch KS, Ganna A, Pajukanta P, Pasaniuc B, Sankararaman S. Am J Hum Genet. 2022 Jan 6;109(1):24-32. doi: 10.1016/j.ajhg.2021.11.015. Epub 2021 Dec 2. PMID: 34861179; PMCID: PMC8764132.
• On powerful GWAS in admixed populations. Hou K, Bhattacharya A, Mester R, Burch KS, Pasaniuc B. Nat Genet. 2021 Dec;53(12):1631-1633. doi: 10.1038/s41588-021-00953-5. Epub 2021 Nov 25. PMID: 34824480; PMCID: PMC8939372.
• H3K27ac 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 SC, Gusev A, Mancuso N, Pasaniuc B*, Freedman ML*. Am J Hum Genet. 2021 Dec 2;108(12):2284-2300. doi: 10.1016/j.ajhg.2021.11.007. Epub 2021 Nov 24. PMID: 34822763; PMCID: PMC8715276.
• Predicting master transcription factors from pan-cancer expression data. Reddy J, Fonseca MAS, Corona RI, Nameki R, Segato Dezem F, Klein IA, Chang H, Chaves-Moreira D, Afeyan LK, Malta TM, Lin X, Abbasi F, Font-Tello A, Sabedot T, Cejas P, RodriquezMalav N, Seo JH, Lin DC, Matulonis U, Karlan BY, Gayther SA, Pasaniuc B, Gusev A, Noushmehr H, Long H, Freedman ML, Drapkin R, Young RA, Abraham BJ, Lawrenson K. Sci Adv. 2021 Nov 26;7(48):eabf6123. doi: 10.1126/sciadv.abf6123. Epub 2021 Nov 24. PMID: 34818047; PMCID: PMC8612691.
• Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits. Johnson R, Burch KS, Hou K, Paciuc M, Pasaniuc B*, Sankararaman S*. PLoS Comput Biol. 2021 Oct 21;17(10):e1009483. doi: 10.1371/journal.pcbi.1009483. PMID: 34673766; PMCID: PMC8562817.
• Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals. Chen H, Majumdar A, Wang L, Kar S, Brown KM, Feng H, Turman C, Dennis J, Easton D, Michailidou K, Simard J; Breast Cancer Association Consortium (BCAC), Bishop T, Cheng IC, Huyghe JR, Schmit SL; Colorectal Transdisciplinary Study (CORECT); Colon Cancer Family Registry Study (CCFR); Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), O’Mara TA, Spurdle AB; Endometrial Cancer Association Consortium (ECAC), Gharahkhani P, Schumacher J, Jankowski J, Gockel I; Esophageal Cancer GWAS Consortium, Bondy ML, Houlston RS, Jenkins RB, Melin B; Glioma International Case Control Consortium (GICC), Lesseur C, Ness AR, Diergaarde B, Olshan AF; Head-Neck Cancer GWAS Consortium, Amos CI, Christiani DC, Landi MT, McKay JD; International Lung Cancer Consortium (ILCCO), Brossard M, Iles MM, Law MH, MacGregor S; Melanoma GWAS Consortium, Beesley J, Jones MR, Tyrer J, Winham SJ; Ovarian Cancer Association Consortium (OCAC), Klein AP, Petersen G, Li D, Wolpin BM; Pancreatic Cancer Case-Control Consortium (PANC4); Pancreatic Cancer Cohort Consortium (PanScan), Eeles RA, Haiman CA, KoteJarai Z, Schumacher FR; PRACTICAL consortium; CRUK; BPC3; CAPS; PEGASUS, Brennan P, Chanock SJ, Gaborieau V, Purdue MP; Renal Cancer GWAS Consortium, Pharoah P, Hung RJ, Amundadottir LT, Kraft P, Pasaniuc B, Lindstroem S. HGG Adv. 2021 Jul 8;2(3):100041. doi: 10.1016/j.xhgg.2021.100041. Epub 2021 Jun 12. PMID: 34355204; PMCID: PMC8336922.
• Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization. Pathak GA, Singh K, Miller-Fleming TW, Wendt FR, Ehsan N, Hou K, Johnson R, Lu Z, Gopalan S, Yengo L, Mohammadi P, Pasaniuc B, Polimanti R, Davis LK, Mancuso N. Nat Commun. 2021 Jul 27;12(1):4569. doi: 10.1038/s41467-021-24824-z. PMID: 34315903; PMCID: PMC8316582.
• Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. Rondel FM, Hosseini R, Sahoo B, Knyazev S, Mandric I, Stewart F, Mandoiu II, Pasaniuc B, Porozov Y, Zelikovsky A. J Comput Biol. 2021 Aug;28(8):842-855. doi: 10.1089/cmb.2021.0053. Epub 2021 Jul 14. PMID: 34264744; PMCID: PMC8575064.
• Mapping the human genetic architecture of COVID-19. COVID-19 Host Genetics Initiative. Nature. 2021 Dec;600(7889):472-477. doi: 10.1038/s41586-021-03767-x. Epub 2021 Jul 8. PMID: 34237774; PMCID: PMC8674144.
• Multi-trait transcriptome-wide association study (TWAS) tests. Feng H, Mancuso N, Pasaniuc B, Kraft P. Genet Epidemiol. 2021 Sep;45(6):563-576. doi: 10.1002/gepi.22391. Epub 2021 Jun 3. PMID: 34082479.
• Leveraging eQTLs to identify individual-level tissue of interest for a complex trait. Majumdar A, Giambartolomei C, Cai N, Haldar T, Schwarz T, Gandal M, Flint J, Pasaniuc B. PLoS Comput Biol. 2021 May 21;17(5):e1008915. doi: 10.1371/journal.pcbi.1008915. PMID: 34019542; PMCID: PMC8174686.
• CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. Watt AC, Cejas P, DeCristo MJ, Metzger-Filho O, Lam EYN, Qiu X, BrinJones H, Kesten N, Coulson R, Font-Tello A, Lim K, Vadhi R, Daniels VW, Montero J, Taing L, Meyer CA, Gilan O, Bell CC, Korthauer KD, Giambartolomei C, Pasaniuc B, Seo JH, Freedman ML, Ma C, Ellis MJ, Krop I, Winer E, Letai A, Brown M, Dawson MA, Long HW, Zhao JJ, Goel S. Nat Cancer. 2021 Jan;2(1):34-48. doi: 10.1038/s43018-020-00135-y. Epub 2020 Nov 9. PMID: 33997789; PMCID: PMC8115221.
• Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies. Feng H, Mancuso N, Gusev A, Majumdar A, Major M, Pasaniuc B, Kraft P. PLoS Genet. 2021 Apr 8;17(4):e1008973. doi: 10.1371/journal.pgen.1008973. PMID: 33831007; PMCID: PMC8057593.
• Quantifying the contribution of dominance deviation effects to complex trait variation in biobank-scale data. Pazokitoroudi A, Chiu AM, Burch KS, Pasaniuc B, Sankararaman S. Am J Hum Genet. 2021 May 6;108(5):799-808. doi: 10.1016/j.ajhg.2021.03.018. Epub 2021 Apr 2. PMID: 33811807; PMCID: PMC8206203.
• Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O’Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Nat Commun. 2021 Mar 30;12(1):1979. doi: 10.1038/s41467-021-22139-7. PMID: 33785741; PMCID: PMC8010057.
• Gene Expression Imputation Across Multiple Tissue Types Provides Insight Into the Genetic Architecture of Frontotemporal Dementia and Its Clinical Subtypes. Reus LM, Pasaniuc B, Posthuma D, Boltz T; International FTD-Genomics Consortium, Pijnenburg YAL, Ophoff RA. . Biol Psychiatry. 2021 Apr 15;89(8):825-835. doi: 10.1016/j.biopsych.2020.12.023. Epub 2021 Jan 9. PMID: 33637304; PMCID: PMC8415425.
• Pre-existing conditions in Hispanics/Latinxs that are COVID-19 risk factors. Chang TS, Ding Y, Freund MK, Johnson R, Schwarz T, Yabu JM, Hazlett C, Chiang JN, Wulf DA; UCLA Precision Health Data Discovery Repository Working Group, Geschwind DH, Butte MJ, Pasaniuc B. iScience. 2021 Mar 19;24(3):102188. doi: 10.1016/j.isci.2021.102188. Epub 2021 Feb 12. PMID: 33615196; PMCID: PMC7879099.
• A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes. Majumdar A, Burch KS, Haldar T, Sankararaman S, Pasaniuc B, Gauderman WJ, Witte JS. Bioinformatics. 2021 Jan 16:btaa1083. doi: 10.1093/bioinformatics/btaa1083. Epub ahead of print. PMID: 33453114.
• PLEIO: a method to map and interpret pleiotropic loci with GWAS summary statistics. Lee CH, Shi H, Pasaniuc B, Eskin E, Han B. Am J Hum Genet. 2021 Jan 7;108(1):36-48. doi: 10.1016/j.ajhg.2020.11.017. Epub 2020 Dec 21. PMID: 33352115; PMCID: PMC7820744.
• Integrative analyses identify susceptibility genes underlying COVID-19 hospitalization. Pathak GA, Singh K, Miller-Fleming TW, Wendt FR, Ehsan N, Hou K, Johnson R, Lu Z, Gopalan S, Yengo L, Mohammadi P, Pasaniuc B, Polimanti R, Davis LK, Mancuso N. medRxiv [Preprint]. 2020 Dec 8:2020.12.07.20245308. doi: 10.1101/2020.12.07.20245308. Update in: Nat Commun. 2021 Jul 27;12(1):4569. PMID: 33330876; PMCID: PMC7743085.
• Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis. Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E. Nat Commun. 2020 Oct 30;11(1):5504. doi: 10.1038/s41467- 020-19365-w. PMID: 33127880; PMCID: PMC7599215.
• Transcriptomic Insights Into the Polygenic Mechanisms Underlying Psychiatric Disorders. Hernandez LM, Kim M, Hoftman GD, Haney JR, de la Torre-Ubieta L, Pasaniuc B, Gandal MJ. Biol Psychiatry. 2020 Jun 12:S0006-3223(20)31674-7. doi: 10.1016/j.biopsych.2020.06.005. Online ahead of print. PMID: 32792264
• Efficient variance components analysis across millions of genomes. Pazokitoroudi A, Wu Y, Burch KS, Hou K, Zhou A, Pasaniuc B, Sankararaman S. Nat Commun. 2020 Aug 11;11(1):4020. doi: 10.1038/s41467-020-17576-9. PMID: 32782262; PMCID: PMC7419517.
• Prostate cancer reactivates developmental epigenomic programs during metastatic progression. Pomerantz MM, Qiu X, Zhu Y, Takeda DY, Pan W, Baca SC, Gusev A, Korthauer KD, Severson TM, Ha G, Viswanathan SR, Seo JH, Nguyen HM, Zhang B, Pasaniuc B, Giambartolomei C, Alaiwi SA, Bell CA, O’Connor EP, Chabot MS, Stillman DR, Lis R, Font-Tello A, Li L, Cejas P, Bergman AM, Sanders J, van der Poel HG, Gayther SA, Lawrenson K, Fonseca MAS, Reddy J, Corona RI, Martovetsky G, Egan B, Choueiri T, Ellis L, Garraway IP, Lee GM, Corey E, Long HW, Zwart W, Freedman ML. Nat Genet. 2020 Aug;52(8):790-799. doi: 10.1038/s41588-020-0664-8. Epub 2020 Jul 20. PMID: 32690948.
• Localizing Components of Shared Transethnic Genetic Architecture of Complex Traits from GWAS Summary Data. Shi H, Burch KS, Johnson R, Freund MK, Kichaev G, Mancuso N, Manuel AM, Dong N, Pasaniuc B. Am J Hum Genet. 2020 Jun 4;106(6):805-817. doi: 10.1016/j.ajhg.2020.04.012. Epub 2020 May 21. PMID: 32442408; PMCID: PMC7273527.
• Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Choi J, Zhang T, Vu A, Ablain J, Makowski MM, Colli LM, Xu M, Hennessey RC, Yin J, Rothschild H, GrA˜€we C, Kovacs MA, Funderburk KM, Brossard M, Taylor J, Pasaniuc B, Chari R, Chanock SJ, Hoggart CJ, Demenais F, Barrett JH, Law MH, Iles MM, Yu K, Vermeulen M, Zon LI, Brown KM. Nat Commun. 2020 Jun 1;11(1):2718. doi: 10.1038/s41467-020-16590-1. PMID: 32483191; PMCID: PMC7264232.
• Transcriptome-wide association study of breast cancer risk by estrogen-receptor status. Feng H, Gusev A, Pasaniuc B, Wu L, Long J, Abu-Full Z, ... , Wendt C, Winqvist R, Yang XR, Yannoukakos D, Ziogas A, Milne RL, Easton DF, Chenevix-Trench G, Zheng W, Kraft P, Jiang X. Genet Epidemiol. 2020 Jul;44(5):442-468. doi: 10.1002/gepi.22288. Epub 2020 Mar 1. PMID: 32115800.  
• Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms. Walker RL, Ramaswami G, Hartl C, Mancuso N, Gandal MJ, de la Torre-Ubieta L, Pasaniuc B, Stein JL, Geschwind DH. Cell. 2019 Oct 17;179(3):750-771.e22. doi: 10.1016/j.cell.2019.09.021. Erratum in: Cell. 2020 Apr 16;181(2):484. Erratum in: Cell. 2020 Apr 30;181(3):745. PMID: 31626773.
• Genome-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, TAtu 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. Nat Med. 2019 Oct;25(10):1615-1626. doi: 10.1038/s41591-019-0579-z. Epub 2019 Oct 7. PMID: 31591588
• Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture. Hou K, Burch KS, Majumdar A, Shi H, Mancuso N, Wu Y, Sankararaman S, Pasaniuc B. Nat Genet. 2019 Aug;51(8):1244-1251. doi: 10.1038/s41588-019-0465-0. Epub 2019 Jul 29.
• Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues. Chen H, Kichaev G, Bien SA, MacDonald JW, Wang L, Bammler TK, Auer P, Pasaniuc B, Lindstroem S. Hum Genet. 2019 Jun 22. doi: 10.1007/s00439-019-02041-5. [Epub ahead of print] PMID: 31230194
• RAISS: Robust and Accurate imputation from Summary Statistics. Julienne H, Shi H, Pasaniuc B, Aschard H. Bioinformatics. 2019 Jun 7. pii: btz466. doi: 10.1093/bioinformatics/btz466. PMID: 31173064
• Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants. Wu L, Wang J, Cai Q, Cavazos TB, Emami NC, Long J, Shu XO, Lu Y, Guo X, Bauer JA, Pasaniuc B, Penney KL, Freedman ML, Kote-Jarai Z, Witte JS, Haiman CA, Eeles RA, Zheng W; and the PRACTICAL, CRUK, BPC3, CAPS, PEGASUS Consortia. Cancer Res. 2019 Jul 1;79(13):3192-3204. doi: 10.1158/0008-5472.CAN-18-3536. Epub 2019 May 17. PMID: 31101764
• Integrative analysis of Dupuytren’s disease identifies novel risk locus and reveals a shared genetic etiology with BMI. Major M, Freund MK, Burch KS, Mancuso N, Ng M, Furniss D, Pasaniuc B*, Ophoff RA*. Genet Epidemiol. 2019 Sep;43(6):629-645. doi: 10.1002/gepi.22209. Epub 2019 May 13. PMID: 31087417
• Multi-Tissue Transcriptome-Wide Association Studies Identify 21 Novel Candidate Susceptibility Genes for High Grade Serous Epithelial Ovarian Cancer. Gusev A*, Lawrenson K*, Segato F, Fonseca M, Kar S, Lee J, Pejovic T, Ovarian Cancer Association Consortium, Karlan B, Freedman M, Noushmehr H, Pharoah P, Pasaniuc B*, Gayther S* Nat Genet. 2019 May;51(5):815-823. doi: 10.1038/s41588- 019-0395-x. Epub 2019 May 1. PMID: 31043753
• Probabilistic fine-mapping of transcriptome-wide association studies. Mancuso N, Kichaev G, Shi H, Freund M, Gusev A, Pasaniuc B. Nat Genet. 2019 Apr;51(4):675-682. doi: 10.1038/s41588-019- 0367-1. Epub 2019 Mar 29. PMID: 30926970
• Transcriptome-wide association studies: opportunities and challenges. Wainberg M, Sinnot-Armstrong N, Mancuso N, Barbeira AN, Knowles D, Golan D, Ermel R, Ruusalepp A, Quertermos T, Hao K, Bjorkegren J*, Im HK*, Pasaniuc B*, Rivas M*, Kundaje A*. Nat Genet. 2019 Apr;51(4):592-599. doi: 10.1038/s41588-019-0385-z. Epub 2019 Mar 29. Review. PMID: 30926968
• Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Kichaev G, Bhatia G, Loh PR, Gazal S, Burch K, Freund MK, Schoech A, Pasaniuc B*, Price AL*. Am J Hum Genet. 2019 Jan 3;104(1):65-75. doi: 10.1016/j.ajhg.2018.11.008. Epub 2018 Dec 27. PubMed PMID: 30595370.
• GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes. Franceschini N, Giambartolomei C, de Vries PS, Finan C, Bis JC,..., Pasaniuc B,..., Gudnason V, Hingorani AD, Bjarkegen, JLM, Casas JP, O’Donnell CJ. Nat Comm. 2018 Dec 3;9(1):5141. doi: 10.1038/s41467-018-07340-5. PubMed PMID: 30510157; PubMed Central PMCID: PMC6277418.
• Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. Freund MK, Burch KS, Shi H, Mancuso N, Kichaev G, Garske KM, Pan DZ, Miao Z, Mohlke KL, Laakso M, Pajukanta P, Pasaniuc B*, Arboleda VA*. Am J Hum Genet. 2018 Oct 4;103(4):535-552. doi: 10.1016/j.ajhg.2018.08.017. PubMed PMID: 30290150; PubMed Central PMCID: PMC6174356.
• Large-scale transcriptome-wide association study identifies new prostate cancer risk regions. Mancuso N, Gayther S, Gusev A, Zheng W, Penney KL, PRACTICAL consortium, Kote-Jarai Z, Eeles R, Freedman M, Haiman C, Pasaniuc B. Nat Comm. 2018 Oct 4;9(1):4079. doi: 10.1038/s41467-018- 06302-1. PubMed PMID: 30287866; PubMed Central PMCID: PMC6172280.
• A unifying framework for joint trait analysis under a non-infinitesimal model. Johnson R, Shi H, Pasaniuc B*, Sankararaman S*. Bioinformatics. 2018 Jul 1;34(13):i195-i201. doi: 10.1093/bioinformatics/bty254. PubMed PMID: 29949958; PubMed Central PMCID: PMC6022541.
• Transcriptome-wide association studies accounting for colocalization using Egger regression. Barfield R, Feng H, Gusev A, Wu L, Zheng W, Pasaniuc B, Kraft P. Genet Epidemiol. 2018 Jul;42(5):418- 433. doi: 10.1002/gepi.22131. Epub 2018 May 29. PubMed PMID: 29808603.
• Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Gusev A, Mancuso N, Finucane HK, Reshef Y, Song L, Safi A, Oh E, SCZ working group of PGC, McCaroll S, Neale B, Ophoff R, O’Donovan M, Katsanis N, Crawford GE, Sullivan PF, Pasaniuc B*, Price AL*. Nat Genet. 2018 Apr;50(4):538-548. doi: 10.1038/s41588-018-0092-1. Epub 2018 Apr 9. PMID: 29632383
• A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics. Giambartolomei C, Zhenli Liu J, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE; CommonMind Consortium, Pasaniuc B, Roussos P. Bioinformatics. 2018 Mar 19. doi: 10.1093/bioinformatics/bty147. PMID: 29579179
• Methods for fine-mapping with chromatin and expression data. Roytman M, Kichaev G, Gusev A, Pasaniuc B. PLoS Genet. 2018 Feb 26;14(2):e1007240. doi: 10.1371/journal.pgen.1007240. eCollection 2018 Feb. PMID: 29481575
• Local genetic correlation gives insights into the shared genetic architecture of complex traits. Shi H, Mancuso N, Spendlove S, Pasaniuc B. Am J Hum Genet. 2017 Nov 2;101(5):737-751. doi: 10.1016/j.ajhg.2017.09.022. PMID: 29100087
• A multi-stage genome-wide association study of uterine fibroids in African Americans. Hellwege JN, Jeff JM, Wise LA,..., Pasaniuc B,..., Morton CC, Kenny EE, Edwards TL, Velez Edwards DR. Hum Genet. 2017 Aug 23. doi: 10.1007/s00439-017-1836-1. PMID: 28836065
• Widespread allelic heterogeneity in complex traits. Hormozdiari F, Zhu A, Kichaev G, V. Segre A, Ju CT, Wha Joo J, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E Am J Hum Genet. 2017 May 4;100(5):789-802. doi: 10.1016/j.ajhg.2017.04.005. PMID: 28475861
• A Genetic Population Isolate in The Netherlands Showing Extensive Haplotype Sharing and Long Regions of Homozygosity. Somers M, Olde Loohuis LM, Aukes MF, Pasaniuc B, de Visser KCL, Kahn RS, Sommer IE, Ophoff RA. Genes (Basel). 2017 May 4;8(5). pii: E133. doi: 10.3390/genes8050133. PMID: 28471380
• Enhanced methods to detect haplotypic effects on gene expression. Brown R, Kichaev G, Mancuso N, Boocock J, Pasaniuc B. Bioinformatics. 2017 Aug 1;33(15):2307-2313. doi: 10.1093/bioinformatics/btx142. PMID: 28369161
• Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits. Mancuso N, Shi H, Goddard P, Kichaev G, Gusev A*, Pasaniuc B*. Am J Hum Genet. 2017 Mar 2;100(3):473-487. doi: 10.1016/j.ajhg.2017.01.031. PMID: 28238358
• Colocalization of GWAS and eQTL Signals Detects Target Genes. Hormozdiari F, van de Bunt M, Segre, 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. PMID: 27866706
• Dissecting the genetics of complex traits using summary association statistics. Pasaniuc B, Price AL. Nat Rev Genet. 2016 Nov 14. doi: 10.1038/nrg.2016.142. PMID: 27840428
• Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Zubair N, Graff M, Ambite JL, ... , Pasaniuc B, ..., North KE, Kooperberk C, Carthu CL. Human Mol. Genetics. Dec 15;25(24):5500-5512. doi: 10.1093/hmg/ddw358. PMID: 28426890
• Improved methods for multi-trait fine mapping of pleiotropic risk loci. Kichaev G, Roytman M, Johnson R, Eskin E, Lindstroem S, Kraft P, Pasaniuc B. Bioinformatics. 2016 Sep 22. pii: btw615.
• Contrasting the genetic architecture of 30 complex traits from summary association data. Shi H, Kichaev G, Pasaniuc B. Am J Hum Genet. 2016 Jul 7;99(1):139-53. doi: 10.1016/j.ajhg.2016.05.013. PMID: 27346688. [Genetics highlight]
• Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Gusev A, Shi H, Kichaev G, PRACTICAL Consortium, AAPC consortium, BPC3 consortium, Freedman M, Haiman C, Pasaniuc B. Nature Communications. 2016 Apr 7;7:10979. doi: 10.1038/ncomms10979. PMID: 27052111
• Integrative approaches for large-scale transcriptome-wide association studies. Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BW, Jansen R, de Geus EJ, Boomsma DI, Wright FA, Sullivan PF, Nikkola E, Alvarez M, Civelek M, Lusis AJ, Lehtimaki T, Raitoharju E, Kahanen M, Seppala I, Raitakari OT, Kuusisto J, Laakso M, Price AL, Pajukanta P Pasaniuc B. Nat Genet. 2016 Mar;48(3):245-52. doi: 10.1038/ng.3506. Epub 2016 Feb 8. PMID: 26854917. [Nat Rev Genetics highlight]
• Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk. Rand KA, Rohland N, Tandon A, Stram A, Sheng X, Do R, Pasaniuc B, Allen A, Quinque D, Mallick S, Le Marchand L, Kaggwa S, Lubwama A; African Ancestry Prostate Cancer GWAS Consortium; ELLIPSE/GAME-ON Consortium, Stram DO, Watya S, Henderson BE, Conti DV, Reich D, Haiman CA. Hum Mol Genet. 2015 Nov 24. pii: ddv462. [Epub ahead of print] PMID: 26604137
• Prostate Cancer Susceptibility in Men of African Ancestry at 8q24. Han Y, Rand KA, Hazelett DJ, ... , Pasaniuc B, ... , Conti DV, Henderson BE, Haiman CA. J Natl Cancer Inst. 2016 Jan 27;108(7). pii: djv431. doi: 10.1093/jnci/djv431. Print 2016 Jul. PMID: 26823525
• The contribution of rare variation to prostate cancer heritability. Mancuso N*, Rohland N*, Rand K,Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA; PRACTICAL consortium, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman C*, Pasaniuc B*, Reich D*. Nature Genetics. 2016 Jan;48(1):30-5. doi: 10.1038/ng.3446. Epub 2015 Nov 16. PMID: 26569126
• Leveraging local ancestry to detect gene-by-gene interactions in genome-wide data. Aschard H, Gusev A, Brown R, Pasaniuc B. BMC Genet. 2015 Oct 24;16:124. doi: 10.1186/s12863-015-0283-z. PMID: 26498930
• Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores. Vilhjalmsson B, Yang J, Finucane H, Gusev A, Lindstrom S, Ripke S, Genovese G, Loh P, Bhatia G, Do R, Hayeck T, Won H, Psychiatric Genomics Consortium, DRIVE, Kathiresan S, Pato M, Pato C, Tamimi R, Stahl E, Zaitlen N, Pasaniuc B, Schierup M, De Jager P, Patsopoulos N, McCarroll S, Daly M, Purcell S, Chasman D, Neale B, Goddard M, Visscher P, Kraft P, Patterson N, Price AL. Am J Hum Genet. 2015 Oct 1;97(4):576-92. doi: 10.1016/j.ajhg.2015.09.001. PMID: 26430803
• Leveraging functional annotation data in trans-ethnic fine-mapping studies. Kichaev G, Pasaniuc B. Am J Hum Genet. 2015 Aug 6;97(2):260-71. doi: 10.1016/j.ajhg.2015.06.007. Epub 2015 Jul 16. PMID: 26189819. (Winner of the CW Cotterman award for best paper by trainee in Am J Hum Genet during 2015).
• A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data. Shi H, Pasaniuc B, Lange KL. Bioinformatics. 2015 Jul 2. pii: btv397. [Epub ahead of print] PMID: 26139633
• Identification of causal genes for complex traits. Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E. Bioinformatics. 2015 Jun 15;31(12):i206-i213. doi: 10.1093/bioinformatics/btv240. PMID: 26072484 (best paper award at ISMB 2015).
• Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders. Brown R, Lee H, Eskin A, Kichaev G, Lohmueller KE, Reversade B, Nelson SF, Pasaniuc B. Eur J Hum Genet. 2015 Apr 22. doi: 10.1038/ejhg.2015.68. [Epub ahead of print]
• Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Gusev A, Hong Lee S, Neale B, Trynka G, Vilhjalmsson B, Finucane H, Xu H, Zang C, Ripke S, Stahl E, Kahler AK, Hultman CM, Purcell S, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Wray N, Raychaudhuri S, Price AL. Am J Hum Genet. 2014 Nov 6;95(5):535-52. doi: 10.1016/j.ajhg.2014.10.004. Epub 2014 Nov 6. PMID: 25439723 .
• Leveraging population admixture to explain missing heritability of complex traits. Zaitlen N, Pasaniuc B, Sakararaman S, Bhatia G, Zhang K, Gusev A, Young T, Tandon A, Pollack S, Vilhjalmsson, Assimes T, Franceschini N,. Lange LA, Patterson N, Reich D, Whitsel EA, Haiman C, Wilson J, Kooperberg C, Stram D, Reiner AP, Tang HA, Price AL. Nature Genetics. 2014 Dec;46(12):1356-62. doi: 10.1038/ng.3139. Epub 2014 Nov 10. PMID: 25383972
• Spatial Localization of Recent Ancestors for Admixed Individuals. Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc B. G3: Genes, Genomes, Genetics, 2014 Nov 3;4(12):2505-18. doi: 10.1534/g3.114.014274. PMID: 25371484
• Integrating functional data to prioritize causal variants in statistical fine-mapping studies. Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P, Pasaniuc B. PloS Genetics. Oct 30;10(10):e1004722. 2014. [Nat Genetics highlight].
• Identifying Causal Variants at Loci with Multiple Signals of Association. Hormozdiari F, Kostem E, Kang EY, Pasaniuc B*, Eskin E*. Genetics. 2014 Aug 7. PMID: 25104515. 30. Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Pasaniuc B, Zaitlen N, Bhatia G, Gusev A, Pickrell JK, Hirschhorn J, Strachan DP, Patterson N, Price AL. Bioinformatics. 2014 Jul 1. pii: btu416.
• Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. Ko A, Cantor RM, Weissglas-Volkov D, Nikkola E, Reddy PM, Sinsheimer JS, Pasaniuc B, Brown R, Alvarez M, Rodriguez A, Rodriguez-Guillen R, Bautista IC, Arellano-Campos O, Munoz-Hernandez LL, Salomaa V, Kaprio J, Jula A, Jauhiainen M, Helivaara M, Raitakari O, Lehtimaki T, Eriksson JG, Perola M, Lohmueller KE, Matikainen N, Taskinen MR, Rodriguez-Torres M, Riba L, Tusie-Luna T, Aguilar-Salinas CA, Pajukanta P. Nat Comm. June 2;5:3983. doi: 10.1038/ncomms4983. 2014
• A Spatial Haplotype Copying Model with Applications to Genotype Imputation. Yang WY, F Hormozdiari F, Eskin E, Pasaniuc B. Journal of Computational Biology 2015 May;22(5):451-62. doi: 10.1089/cmb.2014.0151. Epub 2014 Dec 19. PMID: 25526526.
• IBD Genetics: Focus on (Dys) Regulation in Immune Cells and the Epithelium. Kaser A. Pasaniuc B. Gastroenterology 146 (4), 896-899. 2014 26. Enhanced methods for local ancestry assignment in sequenced admixed individuals. Brown R. Pasaniuc B. PLoS Computational Biology 10 (4), e1003555, 2014
• Quantifying missing heritability at known GWAS loci. Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson B, Diogo D, Stahl EA, Gregersen PK, Worthington J, Klareskog L, Rayachaudhuri S, Plenge RM, Pasaniuc B, Price AL. PLoS Genetics 9 (12), e1003993. 2013
• Leveraging Multi-SNP Reads from Sequencing Data for Haplotype Inference. Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E. Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3. 23. Enhanced Localization of Genetic Samples through Linkage Disequilibrium Correction. Baran Y, Quintela I, Carracedo A, Pasaniuc B*, Halperin E*. Am J Hum Genet. 2013 May 29. doi:pii: S0002- 9297(13)00210-3. 10.1016/j.ajhg.2013.04.023.  
• Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits. Zaitlen N, Kraft P, Patterson N, Pasaniuc B, Bhatia G, Pollack S, Price AL. PLoS Genetics. 2013 May;9(5):e1003520. doi: 10.1371/journal.pgen.1003520. Epub 2013 May 30
• Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. Pasaniuc B*, Sankararaman S*, Torgerson D, Gignoux C, Eng C, RodriguezCintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Chen GK, Le Marchand L, Henderson B, Reich D, Haiman C, Burchard EG, Halperin E. Bioinformatics. 2013 Jun 1;29(11):1407-15. doi: 10.1093/bioinformatics/btt166. Epub 2013 Apr 9.
• Using population admixture to help complete maps of the human genome. Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA. Nat Genet,. 2013 Feb 24. doi: 10.1038/ng.2565.
• Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li, H, Gupta N, Neale B, Daly M, Sklar P, Sullivan P, Bergen S, Moran J, Hultman C, Lichtenstein P, Magnusson P, Purcell S, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PIW, Reich D, Price AL. Nature Genetics, 2012 May 20;44(6):631-5. doi: 10.1038/ng.2283. (recommended by the Faculty of 1000).
• Informed conditioning on clinical covariates increases power in case-control association studies. Zaitlen N, Lindstrom S, Pasaniuc B, Cornelis M, Genovese G, Pollack S, Barton A, Bowden D, Eyre S, Freedman B, Friedman D, Field J, Groop L, Haugen A, Henderson BE, Hicks PJ, Hocking L, Kolonel L, Landi MT, Langefeld CD, Marchand L, Meister M, Morgan AW, Raji OY, Risch A, Scherf D, Steer S, Warshaw M, Waters KM, Wilson AG, Wordsworth P, Zienolddiny S, Haiman C, Hunter DJ, Plenge RM, Worthington J, Christiani D, Schaumberg DA, Chasman DI, Altshuler D, Voight B, Kraft P, Patterson N, Price AL. PLoS Genetics, 2012.
• Effective analysis of case-control association studies with known genetic effects. Zaitlen N, Pasaniuc B, Patterson N, Voight B., Groop L, Altshuler D, Henderson BE, Kolonel LN, Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL. Bioinformatics, 2012.
• Fast and accurate inference of local ancestry in Latino populations. Baran Y*, Pasaniuc B*, Sankararaman S*, Torgerson D, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E. Bioinformatics, 2012.
• Admixture Mapping Identifies Loci on 6q25 and 11p15 Associated with Breast Cancer Risk in US Latinas. Fejerman L, Chen G, Huntsman S, Hu D, Williams A, Pasaniuc B, John E, Via M, Gignoux C, Ingles S, Marchand L, Kolonel L, Torres-Meja G, Parez-Stable E, Burchard EG, Eng C, Henderson BE, Haiman C, Ziv E. . Human Molecular Genetics 2012 Jan 19. doi:10.1093/hmg/ddr617.
• New approaches to disease mapping in admixed populations. Seldin MF*, Pasaniuc B*, Price AL*. Nature Reviews Genetics, 2011 Jun 28. doi:10.1038/nrg3002.
• Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WH, Ruczinski I, Fornage M, Siscovick DS, Zhu X, Larkin E, Lange LA, Cupples LA, Yang Q, Akylbekova EL, Musani SK, Divers J, Mychaleckyj J, Li M, Papanicolaou GJ, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante SJ, Bandera EV, Ingles SA, Press MF, Chanock SJ, Deming SL, Rodriguez-Gil JL, Palmer CD, Buxbaum S, Ekunwe L, Hirschhorn JN, Henderson BE, Myers S, Haiman CA, Reich D, Patterson N, Wilson JG, Price AL. PLoS Genetics. 2011 Apr;7(4):e1001371. Epub 2011 Apr 21.
• Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer C, Adebowale A, Akylbekova E, Cupples LA, Divers J, Fornage M, Kao L, Lange L, Li M, Musani S, Mychaleckyuj J, Ogunniyi A, Papanicolaou G, Rotimi C, Rotter J, Ruczinzki I, Salako B, Siscovick S, Tayo B, Yahg Q, McCarrol S, Sabeti P, Lettre G, De Jagger P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL. Am J Hum Genet. 2011
• Combining effects from rare and common genetic variants in an exome-wide association study of sequence data. Aschard H, Qiu W, Pasaniuc B, Zaitlen N, Cho M and Carey V. BMC Proceedings 2011, 5(Suppl 9):S44
• Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal. Wang J, Geesman G, Hostikka S, Atallah M, Blackwell B, Lee E, Cook P, Pasaniuc B, Shariat G, Halperin E, Dobke M, Rosenfield MG, Jordan IK, Lunyak VV. Cell Cycle. 2011, Sept 1; 10:17
• Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. Pasaniuc B, Zaitlen N, Halperin E. Journal of Computational Biology. 2011 Mar;18(3):459-68.
• Genotyping common and rare variation using overlapping pool sequencing. He D, Zaitlen N, Pasaniuc B, Eskin E, Halperin E. BMC Bioinformatics. 2011, 12(Suppl 6):S2
• Optimal Testing of Digital Microfluidic Biochips. Pasaniuc B, Garfinkel R, Mandoiu I, Zelikovsky A. INFORMS Journal on computing. 2011.
• A Generic Coalescent-based Framework for the Selection of a Reference Panel for Imputation. Pasaniuc B, Avinery, R, Gur T, Skibola CF, Brooks PM, Halperin E. Genetic Epidemiology. 2010 Dec;34(8):773- 82.
• Leveraging genetic variability across populations for the identification of causal variants. Zaitlen N*, Pasaniuc B*, Gur T, Ziv E, Halperin E. Am J Hum Genet. 2010 Jan;86(1):23-33. 4. Imputation-Based Local Ancestry Inference in Admixed Populations. Pasaniuc B, Kennedy J, Mandoiu I. Proc. 5th International Symposium on Bioinformatics Research and Applications, pp. 221-233, 2009.
• Inference of locus-specific ancestry in closely related populations. Pasaniuc B*, Sankararaman S*, Kimmel G, Halperin E. Bioinformatics (special edition of ISMB 2009). 2009 Jun 15;25(12):i213-21.
• Genotype error detection using Hidden Markov Models of haplotype diversity. Kennedy J, Mandoiu I, Pasaniuc B. Journal of Computational Biology. 2008 Nov;15(9):1155-71.
• Highly scalable genotype phasing by entropy minimization. Gusev A, Mandoiu II, Pasaniuc B. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2008 Apr-Jun;5(2):252-61. (conference version: Highly scalable genotype phasing by entropy minimization. Pasaniuc B, Mandoiu I. Conf Proc IEEE Eng Med Biol Soc. 2006;1:3482-6.)