Publications

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

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

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

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

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.

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

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

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

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

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

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.

Integrative approaches for large-scale transcriptome-wide association studies.
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.[TWAS software]

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.

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. 2015 Nov 24. pii: ddv462..

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 Nov 16. doi: 10.1038/ng.3446.

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

A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data. 
Shi HPasaniuc B, Lange K. Bioinformatics. 2015 Jul 2. pii: btv397.

Leveraging functional annotation data in trans-ethnic fine-mapping studies. 
Kichaev GPasaniuc B. Am J Hum Genet. 2015 Aug 6;97(2):260-71. doi: 10.1016/j.ajhg.2015.06.007. Epub 2015 Jul 16.

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.

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.

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.

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 ConsortiumThe American Journal of Human Genetics 2014.

Spatial Localization of Recent Ancestors for Admixed Individuals. 
Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc BG3 (Bethesda). 2014 Nov 3. pii: g3.114.014274. doi: 10.1534/g3.114.014274.

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.

Identifying causal variants at loci with multiple signals of association.
Hormozdiari F*, Kostem E*, Kang EY, Pasaniuc B*, Eskin E*. Genetics 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.

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.

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

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

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals.
Brown R,Pasaniuc B. PLoS Computational Biology 2014. Software.

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.

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 .

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.

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.

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).

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.

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).

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 .

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

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

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 (and before)

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.

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.

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.

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.

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.

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.

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.

Optimal testing of digital microfluidic biochips. 
Pasaniuc B, Garfinkel R, Mandoiu I, Zelikovsky A. INFORMS Journal on Computing. 2011; 23(4):518-529.

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.

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.

Imputation-Based Local Ancestry Inference in Admixed Populations. 
Pasaniuc B, Kennedy J, Mandoiu II.  ISBRA 2009: 221-233.

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.

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.

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.