Representative Publications

Topic Publication
Polygenic score in diverse populations

Polygenic scoring accuracy varies across the genetic ancestry continuum.
Ding et al. Nature. 2023.

Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification.
Ding*, Hou*, et al. Nat Genet. 2022.

Methods for admixed populations

Impact of cross-ancestry genetic architecture on GWASs in admixed populations.
Mester et al. AJHG. 2023.

Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals.
Hou et al. Nat Genet. 2023.

Review on methods for analyses of GWAS summary data Dissecting the genetics of complex traits using summary association statistics.
Pasaniuc and Price. Nat Rev Genet. 2017.
SNP-heritability and genetic correlation of complex traits under minimal assumptions on genetic architecture

Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture.
Hou*, Burch*, et al. Nat Genet. 2019.

Local genetic correlation gives insights into the shared genetic architecture of complex traits.
Shi et al. AJHG. 2017.

Contrasting the Genetic Architecture of 30 Complex Traits from Summary Association Data.
Shi et al. AJHG. 2016.

Transcriptome-wide association studies (TWAS)

Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits.
Mancuso et al. AJHG. 2017.

Integrative approaches for large-scale transcriptome-wide association studies.
Gusev et al. Nat Genet. 2016.

Statistical fine-mapping

Probabilistic fine-mapping of transcriptome-wide association studies.
Mancuso et al. Nat Genet. 2019.

Improved methods for multi-trait fine mapping of pleiotropic risk loci.
Kichaev*, Roytman*, et al. Bioinformatics. 2017.

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Kichaev et al. PLoS Genetics. 2014. Nature Genetics research highlight.

Methods for transethnic analysis that leverage population-specific components of genetic architecture

Localizing Components of Shared Transethnic Genetic Architecture of Complex Traits from GWAS Summary Data.
Shi*, Burch*, et al. AJHG. 2020.

Leveraging functional annotation data in trans-ethnic fine-mapping studies.
Kichaev and Pasaniuc. AJHG. 2015.

Contribution of low-frequency/rare variants to complex traits The contribution of rare variation to prostate cancer heritability.
Mancuso*, Rohland* et al. Nat Genet. 2015.

 

Preprints (bioRxiv/medRxiv)

* – denotes equal contributions; members of the group are underlined.

Month Year Preprint
Feb 2023 Polygenic scores for tobacco use provide insights into systemic health risks in a diverse EHR-linked biobank in Los Angeles.
Vidhya Venkateswaran, Kristin Boulier, Yi Ding, Ruth Johnson, Arjun Bhattacharya, Bogdan Pasaniuc. doi: https://doi.org/10.1101/2023.02.05.23285493

 

Publications

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

Year Publication
2023 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 May 17:S0002-9297(23)00158-1. doi: 10.1016/j.ajhg.2023.05.001. PMID: 37224807
2023 Polygenic scoring accuracy varies across the genetic ancestry continuum.
Ding Y, Hou K, Xu Z, Pimplaskar A, Petter E, Boulier K, Privé F, Vilhjálmsson BJ, Olde Loohuis LM, Pasaniuc B. Nature. 2023 May 17. doi: 10.1038/s41586-023-06079-4. Online ahead of print. PMID: 37198491
2023 twas_sim, 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
2023 Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals.
Hou K, Ding Y, Xu Z, Wu Y, Bhattacharya A, Mester R, Belbin GM, Buyske S, Conti DV, Darst BF, Fornage M, Gignoux C, Guo X, Haiman C, Kenny EE, Kim M, Kooperberg C, Lange L, Manichaikul A, North KE, Peters U, Rasmussen-Torvik LJ, Rich SS, Rotter JI, Wheeler HE, Wojcik GL, 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
2023 Genome-Wide Analyses Characterize Shared Heritability Among Cancers and Identify Novel Cancer Susceptibility Regions.
Lindström S, Wang L, Feng H, Majumdar A, Huo S, Macdonald J, Harrison T, Turman C, Chen H, Mancuso N, Bammler T; Breast Cancer Association Consortium (BCAC); Gallinger S, Gruber SB, Gunter MJ, Le Marchand L, Moreno V, Offit K; Colorectal Transdisciplinary Study (CORECT), Colon Cancer Family Registry Study (CCFR), Genetics And Epidemiology Of Colorectal Cancer Consortium (GECCO); de Vivo I, O'Mara TA, Spurdle AB, Tomlinson I; Endometrial Cancer Association Consortium (ECAC); Fitzgerald R, Gharahkhani P, Gockel I, Jankowski J, Macgregor S, Schumacher J, Barnholtz-Sloan J, Bondy ML, Houlston RS, Jenkins RB, Melin B, Wrensch M, Brennan P, Christiani D, Johansson M, Mckay J, Aldrich MC, Amos CI, Landi MT, Tardon A; International Lung Cancer Consortium (ILCCO); Bishop DT, Demenais F, Goldstein AM, Iles MM, Kanetsky PA, Law MH; Ovarian Cancer Association Consortium (OCAC); Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM; Pancreatic Cancer Cohort Consortium (Panscan); Klein A, Petersen G, Risch H; Pancreatic Cancer Case-Control Consortium (Panc4); PRACTICAL Consortium; Chanock SJ, Purdue MP, Scelo G, Pharoah P, Kar S, Hung RJ, Pasaniuc B, Kraft P. J Natl Cancer Inst. 2023 Mar 17:djad043. doi: 10.1093/jnci/djad043. PMID: 36929942
2023 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. https://doi.org/10.1016/j.xgen.2022.100243
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
2022 Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.
Kneppers J, Severson TM, Siefert JC, Schol P, Joosten SEP, Yu IPL, Huang CF, Morova T, Altıntaş UB, Giambartolomei C, Seo JH, Baca SC, Carneiro I, Emberly E, Pasaniuc B, Jerónimo C, Henrique R, Freedman ML, Wessels LFA, Lack NA, Bergman AM, Zwart W. Nat Commun. 2022 Nov 30;13(1):7367. doi: 10.1038/s41467-022-35135-2. PMID: 36450752
2022 Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJ, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A; COVID-19 Host Genetics Initiative; DeCOI Host Genetics Group; GEN-COVID Multicenter Study (Italy); Mount Sinai Clinical Intelligence Center; GEN-COVID consortium (Spain); GenOMICC Consortium; Japan COVID-19 Task Force; Regeneron Genetics Center; Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. PLoS Genet. 2022 Nov 3;18(11):e1010367. doi: 10.1371/journal.pgen.1010367. eCollection 2022 Nov. PMID: 36327219
2022 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
2022 Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the 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
2022 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 Oct;54(10):1572-1580. doi: 10.1038/s41588-022-01167-z. Epub 2022 Sep 1. PMID: 36050550
2022 Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative.
Johnson R, Ding Y, Venkateswaran V, Bhattacharya A, Boulier K, Chiu A, Knyazev S, Schwarz T, Freund M, Zhan L, Burch KS, Caggiano C, Hill B, Rakocz N, Balliu B, Denny CT, Sul JH, Zaitlen N, Arboleda VA, Halperin E, Sankararaman S, Butte MJ; 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
2022 Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward 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, Sjöström 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 Sep 2;12(9):2074-2097. doi: 10.1158/2159-8290.CD-21-0576. PMID: 35754340
2022 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;54(9):1364-1375. doi: 10.1038/s41588-022-01168-y. Epub 2022 Sep 7. PMID: 36071171
2022 Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies.
BLu 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
2022 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. eCollection 2022 Jul 14. PMID: 35519825
2022 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
2022 Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies disease-relevant 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
2022 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
2022 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. eCollection 2022. PMID: 35370621
2022 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
2021 Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification.
Ding Y*, Hou K*, Burch KS, Lapinska S, Privé F, Vilhjálmsson B, Sankararaman S, Pasaniuc B. Nat Genet. 2022 Jan;54(1):30-39. doi: 10.1038/s41588-021-00961-5. PMID: 34931067
2021 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. 2021 Dec 23. doi: 10.1038/s41431-021-00996-6. PMID: 34949768
2021 Fast estimation of genetic correlation for biobank-scale data.
Wu Y, Burch KS, Ganna A, Pajukanta P, Pasaniuc B, Sankararaman S. Eur J Hum Genet. 2021 Dec 23. doi: 10.1038/s41431-021-00996-6. PMID: 34949768
2021 On powerful GWAS in admixed populations.
Hou K, Bhattacharya A, Mester R,Burch KS,Pasaniuc B. Eur J Hum Genet. 2021 Dec 23. doi: 10.1038/s41431-021-00996-6. PMID: 34949768
2021 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. PMID: 34822763
2021 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, Rodríguez-Malavé 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
2021 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
2021 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, Gocke 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, Kote-Jarai 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, Lindström S. HGG Adv. 2021 Jul 8;2(3):100041. doi: 10.1016/j.xhgg.2021.100041.PMID: 34355204
2021 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
2021 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, Măndoiu 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
2021 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. PMID: 34237774
2021 Multitrait transcriptome-wide association study (TWAS) tests.
Feng H, Mancuso N, Pasaniuc B, Kraft P. Genet Epidemiol. 2021 Jun 3. doi: 10.1002/gepi.22391. PMID: 34082479
2021 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
2021 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. PMID: 33997789
2021 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
2021 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. PMID: 33811807
2021 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
2021 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. PMID: 33615196
2021 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. PMID: 33637304
2021 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. PMID: 33453114
2020 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
2020 Transcriptomic Insight 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. 2021 Jan 1;89(1):54-64. doi: 10.1016/j.biopsych.2020.06.005. PMID: 32792264
2020 Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders.
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. PMID: 32690948
‌2020

‌Efficient variance components analysis across millions of genomes.
Pazokitoroudi A, Wu Y, Burch KS, Hou K, Pasaniuc B, Sankararaman S. Nat Commun. 2020 (In Press). doi: https://doi.org/10.1101/522003

2020 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, Gräwe 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. WNat Commun . 2020 Jun 1;11(1):2718. doi: 10.1038/s41467-020-16590-1. PMID: 32483191
2020 Transcriptomic insight into the polygenic mechanisms underlying psychiatric disorders.
Hernandez LM, Kim M, Hoftman GD, Haney JR, de la Torre Ubieta L, Pasaniuc B, Gandal MJ. Biological Psychiatry . 2020 Feb;19(1):113-114. doi: 10.1002/wps.20702. PMID: 31922671
2020 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. PMID:32442408
2020 BATMAN: Fast and Accurate Integration of Single-Cell RNA-Seq Datasets via Minimum-Weight Matching.
Mandric I, Hill BL, Freund MK, Thompson M, Halperin E. iScience . 2020 May 20;23(6):101185. doi: 10.1016/j.isci.2020.101185. PMID:32504875
‌2020 ‌Transcriptome‐wide association study of breast cancer risk by estrogen‐receptor status
Feng H, Gusev A, Pasaniuc B, et al. Genet Epidemiol. 2020 Mar 1; 44: 442–468. doi: https://doi.org/10.1002/gepi.22288
2019 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. PMID: 31626773
2019 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, 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. Nat Med. 2019 Oct 7. doi: 10.1038/s41591-019-0579-z. [Epub ahead of print]. PMID: 31591588
2019 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 Jul 30. [Epub ahead of print]. PMID: 31358995
2019 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
2019 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, Lindstrom S. Hum Genet. 2019 Jun 22. doi: 10.1007/s00439-019-02041-5. [Epub ahead of print]. PMID: 31230194
2019 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. [Epub ahead of print]. PMID: 31173064
2019 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 R*. Genet Epidemiol. 2019 May 13. doi: 10.1002/gepi.22209. [Epub ahead of print]. PMID: 31087417
2019 A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants.

Gusev A*, Lawrenson K*, Lin X, Lyra Jr PC, Kar S, Vavra KC, Segato S, Fonseca MAS, Lee J, Pejovic T, Liu G, Ovarian Cancer Association Consortium, Karlan BY, Freedman ML, Noushmehr H, Monteiro AN, Pharoah PDP, Pasaniuc B**, Gayther SA**. Nat Genet. 2019 May;51(5):815-823. doi: 10.1038/s41588-019-0395-x. Epub 2019 May 1. PMID: 31043753

Press release "Scientists identify genes tied to increased risk of ovarian cancer" featured by UCLA Jonsson Comprehensive Cancer Center and Cedars-Sinai

Featured in the Daily Bruin

2019 Opportunities and challenges for transcriptome-wide association studies.
Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles D, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Bjorkegren JLM*, Im HK*, Pasaniuc B*, Rivas MA*, Kundaje A*. Nat Genet. 2019 Apr;51(4):592-599. doi: 10.1038/s41588-019-0385-z. Epub 2019 Mar 29. PMID: 30926968 
2019 Probabilistic fine-mapping of transcriptome-wide association studies.
Mancuso N, Freund MK, Johnson R, Shi H, Kichaev G, 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
2019 Shared heritability and functional enrichment across six solid cancers.
Jiang X, Finucane HK, [...], Pharoah PDP, Price AL, Pasaniuc B, Amos CI, Kraft P, Lindström S. Nat Commun. 2019 Jan 25;10(1):431. doi: 10.1038/s41467-018-08054-4. PMID: 30683880.
2019

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. 2018 Dec 14. pii: S0002-9297(18)30411-7. doi: 10.1016/j.ajhg.2018.11.008. [Epub ahead of print]. PMID: 30595370.

Featured in Broad Institute Research Roundup, Jan 2019

2018 GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes.
Franceschini N*, Giambartolomei C*, […], Pasaniuc B, […], Björkegren JLM, Casas JP & O’Donnell CJ. Nat Commun. 2018; 9: 5141. Published online 2018 Dec 3. doi: 10.1038/s41467-018-07340-5. PMCID: PMC6277418
2018 Large-scale transcriptome-wide association study identifies new prostate cancer risk regions.
Mancuso N, Gayther S, Gusev A, Zheng W, Penney KL, the PRACTICAL consortium, Kote-Jarai Z, Eeles R, Freedman M, Haiman C, Pasaniuc B. Nat Commun. 2018 Oct 4;9(1):4079. doi: 10.1038/s41467-018-06302-1. PMID: 30287866
2018 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. PMID: 30290150
2018 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. PMID: 29949958
2018 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. PMID: 29808603
2018 Transcriptome-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; Schizophrenia Working Group of the Psychiatric Genomics Consortium, McCarroll S, Neale BM, Ophoff RA, O'Donovan MC, Crawford GE, Geschwind DH, Katsanis N, 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
2018 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 Aug 1;34(15):2538-2545. doi: 10.1093/bioinformatics/bty147. PMID: 29579179
2018 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
2017 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
2017 Widespread Allelic Heterogeneity in Complex Traits.
Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segrè AV, Joo JWJ, 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
2017 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
2017 Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci.
Zubair N, Graff M, Luis Ambite J, Bush WS, Kichaev G, Lu Y, Manichaikul A, Sheu WH, Absher D, Assimes TL, Bielinski SJ, Bottinger EP, Buzkova P, Chuang LM, Chung RH, Cochran B, Dumitrescu L, Gottesman O, Haessler JW, Haiman C, Heiss G, Hsiung CA, Hung YJ, Hwu CM, Juang JJ, Le Marchand L, Lee IT, Lee WJ, Lin LA, Lin D, Lin SY, Mackey RH, Martin LW, Pasaniuc B, Peters U, Predazzi I, Quertermous T, Reiner AP, Robinson J, Rotter JI, Ryckman KK, Schreiner PJ, Stahl E, Tao R, Tsai MY, Waite LL, Wang TD, Buyske S, Ida Chen YD, Cheng I, Crawford DC, Loos RJF, Rich SS, Fornage M, North KE, Kooperberg C, Carty CL. Hum Mol Genet. 2016. Dec 15;25(24):5500-5512. doi: 10.1093/hmg/ddw358. PMID: 28426890
2017 Enhanced methods to detect haplotypic effects on gene expression.
Brown R, Kichaev G, Mancuso N, Boocock J, Pasaniuc B. Bioinformatics. 2017 Mar 22. doi: 10.1093/bioinformatics/btx142.
2017 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. Epub 2017 Feb 23.PMID: 28238358
2017 Dissecting the genetics of complex traits using summary association statistics.
Pasaniuc B, Price AL. Nat Rev Genet. 2017 Feb;18(2):117-127. doi: 10.1038/nrg.2016.142. Epub 2016 Nov 14. Review. PMID:27840428
2016 Colocalization of GWAS and eQTL Signals Detects Target Genes.
Hormozdiari F, van de Bunt M, Segrè AV, 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. Epub 2016 Nov 17.PMID:27866706
2016 Improved methods for multi-trait fine mapping of pleiotropic risk loci.
Kichaev G*, Roytman M*, Johnson R, Eskin E, Lindström S, Kraft P, Pasaniuc B. Bioinformatics. 2016 Sep 22. pii: btw615.PMID: 27663501
2016 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. Epub 2016 Jun 23.PMID: 27346688
2016 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, PRACTICAL consortium, AAPC consortium, BPC3 consortium, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Nat Commun. 2016 Apr 7;7:10979. doi: 10.1038/ncomms10979. PMID: 27052111
2016 Integrative approaches for large-scale transcriptome-wide association studies. [TWAS software]
Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx B, Jansen R, de Geus E, Boomsma DI, Wright F, Sullivan PF, Nikkola E, Alvarez E, Civelek M, Lusis AJ, Lehtimaki T, Raitoharju E, Kahonen M, Seppala I, Raitakari O, Kuusisto J, Laakso M, Price ALP, Pajukanta P, Pasaniuc B. Nat Genet. 2016 Mar;48(3):245-52. doi: 10.1038/ng.3506. Epub 2016 Feb 8. PMID: 26854917
2016 Prostate Cancer Susceptibility in Men of African Ancestry at 8q24.
Han Y, Rand KA, Hazelett DJ, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Schumacher FR, Berndt SI, Wang Z, Xu J, Rohland N, Reich D, Tandon A, Pasaniuc B, Allen A, Quinque D, Mallick S, Notani D, Rosenfeld MG, Jayani RS, Kolb S, Gapstur SM, Stevens VL, 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, Zheng SL, Witte JS, Casey G, Lubwama A, Pooler LC, Sheng X, Coetzee GA, Cook MB, Chanock SJ, Stram DO, Watya S, Blot WJ, 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
2016

Whole-exome sequencing of over 4,100 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. 2016 Jan 15;25(2):371-81. doi: 10.1093/hmg/ddv462. Epub 2015 Nov 24. PMID: 2660413

2015 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, the PRACTICAL consortium, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman C**, Pasaniuc B**, Reich D**. Nat Genet. 2015 Jan;48(1):30-5. doi: 10.1038/ng.3446. Epub 2015 Nov 16. PMID: 26569126
2015 Leveraging local ancestry to detect gene-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
2015

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. Am J Hum Genet. 2015 Oct 1;97(4):576-92. doi: 10.1016/j.ajhg.2015.09.001. PMID: 2643080

2015 A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data.
Shi H, Pasaniuc B, Lange K. Bioinformatics. 2015 Nov 1;31(21):3514-21. doi: 10.1093/bioinformatics/btv397. Epub 2015 Jul 2. PMID: 26139633
2015 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
2015 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
2015 Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.
Brown B, Lee H, Eskin A, Kichaev G, Lohmueller K, Reversade B, Nelson SF, Pasaniuc B. Eur J Hum Genet. 2015 Apr 22. doi: 10.1038/ejhg.2015.68. PMID: 25898925
2014 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 BJ, 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 Nov 10. doi: 10.1038/ng.3139.
2014 Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases.
Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, 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; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium. The American Journal of Human Genetics 2014.
2014 Spatial Localization of Recent Ancestors for Admixed Individuals.
Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc B. G3 (Bethesda). 2014 Nov 3. pii: g3.114.014274. doi: 10.1534/g3.114.014274.
2014 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 2014. PAINTOR software. Nature Genetics research highlight.
2014 Identifying causal variants at loci with multiple signals of association.
Hormozdiari F*, Kostem E*, Kang EY, Pasaniuc B**, Eskin E**. Genetics 2014.
2014 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 DP, Patterson N, Price AL. Bioinformatics 2014. Software
2014 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, Muñoz-Hernández LL, Salomaa V, Kaprio J, Jula A, Jauhiainen M, Heliövaara M, Raitakari O, Lehtimäki 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 Commun. 2014 Jun 2;5:3983. doi: 10.1038/ncomms4983.
2014 IBD Genetics: Focus on (Dys) Regulation in Immune Cells and the Epithelium.
Kaser A, Pasaniuc B. Gastroenterology, Volume 146, Issue 4, April 2014, Pages 896–899
2014 A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation.
Yang WY, Hormozdiari F, Eskin E, Pasaniuc B. RECOMB 2014, Lecture Notes in Computer Science Volume 8394, 2014, pp 371-384
2014 Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals.
Brown R, Pasaniuc B. PLoS Computational Biology 2014. Software.
2013 Quantifying missing heritability at known GWAS loci.
Gusev S. Bhatia G, Zaitlen N, Vilhjalmsson B, Diogo D, Stahl E, Gregersen P, Worthington J, Klareskog L, Rayachaudhuri S, Plenge R, Pasaniuc B, Price AL. Plos Genetics, 2013.
2013

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY., Hormozdiari F., Wang Z., He D, Pasaniuc B, Eskin E. Bioinformatics, 2013

2013 Enhanced Localization of Genetic Samples through Linkage Disequilibrium Correction.
Baran Y., Quintela I., Carracedo A., Pasaniuc B*, Halperin E*. The American Journal of Human Genetics, 2013 May 30, doi:10.1016/j.ajhg.2013.04.023.
2013 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 30, doi:10.1371/journal.pgen.1003520.
2013 Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation.
Pasaniuc B*, Sankararaman S*, Torgerson DG, Gignoux C, Zaitlen N, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Chen GK, Le Marchand L, Henderson B, Reich D, Haiman C, Gonzàlez Burchard E, Halperin E. Bioinformatics. 2013 Apr 9. Error maps for local ancestry inference can be downloaded here. For reference panels for local ancestry inference in Latino populations please contact Bogdan (bpasaniuc_AT_mednet.ucla.edu).
2013 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. Nature Genetics. 2013 Feb 24. doi: 10.1038/ng.2565.
2012 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 BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PI, Reich D, Price AL. Nature Genetics. 2012 May 20;44(6):631-5. doi: 10.1038/ng.2283 Please see here how to run latest GATK to obtain likelihoods at all 1000G sites as in the manuscript (thanks to Marcus and ebanks).
2012 Informed conditioning on clinical covariates increases power in case-control association studies.
Zaitlen N, Lindström S, Pasaniuc B, Cornelis M, Genovese G, Pollack S, Barton A, Bickeböller H, Bowden DW, Eyre S, Freedman BI, Friedman DJ, Field JK, Groop L, Haugen A, Heinrich J, Henderson BE, Hicks PJ, Hocking LJ, Kolonel LN, Landi MT, Langefeld CD, Le Marchand L, Meister M, Morgan AW, Raji OY, Risch A, Rosenberger A, Scherf D, Steer S, Walshaw M, Waters KM, Wilson AG, Wordsworth P, Zienolddiny S, Tchetgen ET, Haiman C, Hunter DJ, Plenge RM, Worthington J, Christiani DC, Schaumberg DA, Chasman DI, Altshuler D, Voight B, Kraft P, Patterson N, Price AL. PLoS Genet. 2012;8(11):e1003032. doi: 10.1371/journal.pgen.1003032. Epub 2012 Nov 8 .
2012 Analysis of case-control association studies with known risk variants.
Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, Groop L, Altshuler D, Henderson BE, Kolonel LN, Le Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL. Bioinformatics. 2012 Jul 1;28(13):1729-37. Epub 2012 May 3
2012 Fast and accurate inference of local ancestry in Latino populations.
Baran Y*, Pasaniuc B*, Sankararaman S*, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E. Bioinformatics. 2012 May 15;28(10):1359-67. Epub 2012 Apr 11
2012 Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas.
Fejerman L, Chen GK, Eng C, Huntsman S, Hu D, Williams A, Pasaniuc B, John EM, Via M, Gignoux C, Ingles S, Monroe KR, Kolonel LN, Torres-Mejía G, Pérez-Stable EJ, Burchard EG, Henderson BE, Haiman CA, Ziv E. Hum Mol Genet. 2012 Apr 15;21(8):1907-17. Epub 2012 Jan 6.
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 MH, Carey V. BMC Proc. 2011 Nov 29;5 Suppl 9:S44.
2011 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. Epub 2011 Jul 28.
2011 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 CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WH, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL. Am J Hum Genet. 2011 Sep 9;89(3):368-81. doi: 10.1016/j.ajhg.2011.07.025.
2011 Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal.
Wang J, Geesman GJ, Hostikka SL, Atallah M, Blackwell B, Lee E, Cook PJ, Pasaniuc B, Shariat G, Halperin E, Dobke M, Rosenfeld MG, Jordan IK, Lunyak VV. Cell Cycle. 2011 Sep 1;10(17):3016-30. Epub 2011 Sep 1.
2011 New approaches to disease mapping in admixed populations.
Seldin MF*, Pasaniuc B*, Price AL*. Nature Reviews Genet. 2011 Jun 28;12(8):523-8. doi: 10.1038/nrg3002.
2011 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 Genet. 2011 Apr;7(4):e1001371. Epub 2011 Apr 21.
2011 Accurate estimation of expression levels of homologous genes in RNA-seq experiments.
Pasaniuc B, Zaitlen N, Halperin E. J Comput Biol. 2011 Mar;18(3):459-68.
2011 Optimal testing of digital microfluidic biochips.
Pasaniuc B, Garfinkel R, Mandoiu I, Zelikovsky A. INFORMS Journal on Computing. 2011; 23(4):518-529.
2010 A generic coalescent-based framework for the selection of a reference panel for imputation.
Pasaniuc B, Avinery R, Gur T, Skibola CF, Bracci PM, Halperin E. Genet Epidemiol. 2010 Dec;34(8):773-82.
2010 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.
2009 Imputation-Based Local Ancestry Inference in Admixed Populations.
Pasaniuc B, Kennedy J, Mandoiu II. ISBRA 2009: 221-233.
2009 Inference of locus-specific ancestry in closely related populations.
Pasaniuc B*, Sankararaman S*, Kimmel G, Halperin E. Bioinformatics. 2009 Jun 15;25(12):i213-21.
2008 Genotype error detection using Hidden Markov Models of haplotype diversity.
Kennedy J, Măndoiu I, Pasaniuc B. J Comput Biol. 2008 Nov;15(9):1155-71.
2008 Highly scalable genotype phasing by entropy minimization.
Gusev A, Măndoiu II, Pasaniuc B. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):252-61.