Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R. arcasHLA: high-resolution HLA typing from RNAseq . Bioinformatics. 2020 Jan 1;36(1):33-40. doi: 10.1093/bioinformatics/btz474.

Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med. 2018 Jan 10.

Jackson WJ, Agarwal I, Pe'er I. 2-Way k-Means as a Model for Microbiome Samples. J Healthc Eng. 2017;2017:5284145. Epub 2017 Sep 5.

Palmer C, Pe'er I. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies. PLoS Genet. 2017 Jul 17. 

Xue J, Lencz T, Darvasi A, Pe'er I, Carmi S. The time and place of European admixture in Ashkenazi Jewish history. PLoS Genet. 2017 Apr 4;13(4):e1006644. eCollection 2017 April. 

Carmi S, Hui KY, Kochav E, Liu X, Xue J, Grady F, Guha S, Upadhyay K, Ben-Avraham D, Mukherjee S, Bowen BM, Thomas T, Vijai J, Cruts M, Froyen G, Lambrechts D, Plaisance S, Van Broeckhoven C, Van Damme P, Van Marck H, Barzilai N, Darvasi A, Offit K, Bressman S, Ozelius LJ, Peter I, Cho JH, Ostrer H, Atzmon G, Clark LN, Lencz T, Pe'er I.  Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins . Nat Commun. 2014 Sep 9;5:4835.

Gusev A, Shah MJ, Kenny EE, et al. Low-pass genomewide sequencing and variant imputation using identity-by-descent in an isolated population . Genetics. 2012 Feb;190(2):679-89.

Dewal N, Hu Y, Freedman M, LaFramboise T, Pe'er I. Calling amplified haplotypes in next generation tumor sequence data . Genome Res. 2012 Feb;22(2):362-74.

Gusev A, Palamara P, Darvasi A, Gregersen P, Pe'er I. The architecture of long-range haplotypes shared across populations . Mol Biol Evol. 2012 Feb;29(2):473-86.

Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe’er I. DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation . Am J Hum Genet. 2011 Jun 10;88(6):706-17.

Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. Whole population, genome-wide mapping of hidden relatedness . Genome Res. 2009 Feb;19(2):318-26.