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Itsik G. Pe'er - Publications

Affiliations: 
Computer Science Columbia University, New York, NY 
Area:
Computational Biology, Genomics, Bioinformatics
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71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Yuan J, Xing H, Lamy AL, Lencz T, Pe'er I. Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts. Plos Genetics. 16: e1009015. PMID 32956347 DOI: 10.1371/Journal.Pgen.1009015  0.416
2020 Lencz T, Yu J, Khan R, Lam M, Atzmon G, Pe'er I. Cadherin and Protocadherin Genes Implicated by Novel Ultra-Rare Variants in Schizophrenia Cases From a Founder Population Biological Psychiatry. 87. DOI: 10.1016/J.Biopsych.2020.02.308  0.354
2019 Joseph TA, Pe'er I. Inference of Population Structure from Time-Series Genotype Data. American Journal of Human Genetics. PMID 31256878 DOI: 10.1016/j.ajhg.2019.06.002  0.324
2019 Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R. arcasHLA: high resolution HLA typing from RNAseq. Bioinformatics (Oxford, England). PMID 31173059 DOI: 10.1093/Bioinformatics/Btz474  0.325
2019 Lencz T, Yu J, Khan R, Lam M, Atzmon G, Pe'er I. 92 Novel Ultra-Rare Exonic Variants Identified In A Founder Population Implicate Cadherins, Protocadherins, And Autism/Id Genes In Schizophrenia European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2019.07.233  0.382
2018 Lencz T, Yu J, Palmer C, Carmi S, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Joseph V, Klein R, Lipkin S, Offit K, et al. High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Human Genetics. PMID 29705978 DOI: 10.1007/S00439-018-1886-Z  0.379
2018 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, et al. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Science Translational Medicine. 10. PMID 29321258 DOI: 10.1126/Scitranslmed.Aai7795  0.323
2017 Palmer CD, Pe'er IG. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies. Plos Genetics. 13: 1-18. PMID 28715421 DOI: 10.1371/Journal.Pgen.1006916  0.431
2017 Xue J, Lencz T, Darvasi A, Pe'er I, Carmi S. The time and place of European admixture in Ashkenazi Jewish history. Plos Genetics. 13: e1006644. PMID 28376121 DOI: 10.1371/Journal.Pgen.1006644  0.436
2016 Chuang LS, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Ng SM, Zhang W, Hsu NY, Facey JA, Luong T, Fernandez-Hernandez H, Li D, Rivas M, et al. A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GMCSF. Gastroenterology. PMID 27377463 DOI: 10.1053/J.Gastro.2016.06.045  0.505
2016 Palmer C, Pe'er I. Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation. Plos Genetics. 12: e1006091. PMID 27310603 DOI: 10.1371/journal.pgen.1006091  0.341
2016 Yang S, Carmi S, Pe'er I. Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27104872 DOI: 10.1089/Cmb.2016.0016  0.355
2015 Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. American Journal of Human Genetics. PMID 26581902 DOI: 10.1016/J.Ajhg.2015.10.006  0.729
2015 Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A. ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs. Plos One. 10: e0131038. PMID 26110827 DOI: 10.1371/Journal.Pone.0131038  0.371
2015 Trampush JW, Lencz T, Knowles E, Davies G, Guha S, Pe'er I, Liewald DC, Starr JM, Djurovic S, Melle I, Sundet K, Christoforou A, Reinvang I, Mukherjee S, DeRosse P, et al. Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics. 168: 363-73. PMID 25951819 DOI: 10.1002/Ajmg.B.32319  0.359
2014 Kreimer A, Pe'er I. Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks. Plos Genetics. 10: e1004587. PMID 25210734 DOI: 10.1371/Journal.Pgen.1004587  0.648
2014 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, et al. Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. Nature Communications. 5: 4835. PMID 25203624 DOI: 10.1038/Ncomms5835  0.45
2014 Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra AK, Pe'er I, Darvasi A, Lencz T. Excess of homozygosity in the major histocompatibility complex in schizophrenia. Human Molecular Genetics. 23: 6088-95. PMID 24943592 DOI: 10.1093/Hmg/Ddu308  0.362
2014 Vacic V, Ozelius LJ, Clark LN, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny EE, Liu X, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, et al. Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes. Human Molecular Genetics. 23: 4693-702. PMID 24842889 DOI: 10.1093/Hmg/Ddu158  0.586
2013 Kreimer A, Pe'er I. Variants in exons and in transcription factors affect gene expression in trans. Genome Biology. 14: R71. PMID 23844908 DOI: 10.1186/Gb-2013-14-7-R71  0.581
2013 Palamara PF, Pe'er I. Inference of historical migration rates via haplotype sharing Bioinformatics. 29: i180-i188. PMID 23812983 DOI: 10.1093/Bioinformatics/Btt239  0.745
2013 Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell. 152: 633-41. PMID 23374354 DOI: 10.1016/J.Cell.2012.12.034  0.329
2013 Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I. The variance of identity-by-descent sharing in the wright-fisher model Genetics. 193: 911-928. PMID 23267057 DOI: 10.1534/Genetics.112.147215  0.738
2012 Palamara PF, Lencz T, Darvasi A, Pe'er I. Length distributions of identity by descent reveal fine-scale demographic history American Journal of Human Genetics. 91: 809-822. PMID 23103233 DOI: 10.1016/J.Ajhg.2012.08.030  0.75
2012 Zhuang Z, Gusev A, Cho J, Pe'er I. Detecting identity by descent and homozygosity mapping in whole-exome sequencing data. Plos One. 7: e47618. PMID 23071825 DOI: 10.1371/Journal.Pone.0047618  0.627
2012 Campbell CL, Palamara PF, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM, Burns E, Bustamante CD, Comas D, Friedman E, Pe'er I, et al. North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Proceedings of the National Academy of Sciences of the United States of America. 109: 13865-70. PMID 22869716 DOI: 10.1073/Pnas.1204840109  0.717
2012 Prabhu S, Pe'er I. Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease. Genome Research. 22: 2230-40. PMID 22767386 DOI: 10.1101/Gr.137885.112  0.634
2012 Henn BM, Hon L, Macpherson JM, Eriksson N, Saxonov S, Pe'er I, Mountain JL. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. Plos One. 7: e34267. PMID 22509285 DOI: 10.1371/Journal.Pone.0034267  0.544
2012 Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I. Inference of modules associated to eQTLs. Nucleic Acids Research. 40: e98. PMID 22447449 DOI: 10.1093/Nar/Gks269  0.664
2012 Kenny EE, Pe'er I, Karban A, Ozelius L, Mitchell AA, Ng SM, Erazo M, Ostrer H, Abraham C, Abreu MT, Atzmon G, Barzilai N, Brant SR, Bressman S, Burns ER, et al. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. Plos Genetics. 8: e1002559. PMID 22412388 DOI: 10.1371/Journal.Pgen.1002559  0.438
2012 Guha S, Rosenfeld JA, Malhotra AK, Lee AT, Gregersen PK, Kane JM, Pe'er I, Darvasi A, Lencz T. Implications for health and disease in the genetic signature of the Ashkenazi Jewish population. Genome Biology. 13: R2. PMID 22277159 DOI: 10.1186/Gb-2012-13-1-R2  0.486
2012 Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I. Calling amplified haplotypes in next generation tumor sequence data. Genome Research. 22: 362-74. PMID 22090379 DOI: 10.1101/Gr.122564.111  0.381
2012 Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe'er I. The architecture of long-range haplotypes shared within and across populations. Molecular Biology and Evolution. 29: 473-86. PMID 21984068 DOI: 10.1093/Molbev/Msr133  0.779
2012 Shen Y, Nicoletti P, Floratos A, Pirmohamed M, Molokhia M, Geppetti P, Benemei S, Giomi B, Schena D, Vultaggio A, Stern R, Daly MJ, John S, Nelson MR, Pe'er I, et al. Genome-wide association study of serious blistering skin rash caused by drugs. The Pharmacogenomics Journal. 12: 96-104. PMID 21221126 DOI: 10.1038/Tpj.2010.84  0.434
2012 Hui K, Zhang W, Gusev A, Pe'er I, Peter I, Cho JH. Tu1903 Integration of Population-Specific Novel and Established Genetic Variation for the Identification of Crohn's Disease-Associated Loci in Ashkenazi Jewish Individuals Gastroenterology. 142: S-873-S-874. DOI: 10.1016/S0016-5085(12)63390-3  0.607
2011 Shen Y, Gu Y, Pe'er I. A hidden Markov model for copy number variant prediction from whole genome resequencing data. Bmc Bioinformatics. S4. PMID 21989326 DOI: 10.1186/1471-2105-12-S6-S4  0.329
2011 Shen Y, Song R, Pe'er I. Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association Bioinformatics. 27: 1995-1997. PMID 21636589 DOI: 10.1093/Bioinformatics/Btr305  0.369
2011 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. American Journal of Human Genetics. 88: 706-17. PMID 21620352 DOI: 10.1016/J.Ajhg.2011.04.023  0.666
2011 Setty MN, Gusev A, Pe'er I. HLA type inference via haplotypes identical by descent. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 483-93. PMID 21385049 DOI: 10.1089/Cmb.2010.0258  0.555
2011 Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Kang HM, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL, et al. Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Human Molecular Genetics. 20: 827-39. PMID 21118897 DOI: 10.1093/Hmg/Ddq510  0.648
2010 LaFramboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML. Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis. Plos Genetics. 6: e1001086. PMID 20824129 DOI: 10.1371/Journal.Pgen.1001086  0.459
2010 Eriksson N, Macpherson JM, Tung JY, Hon LS, Naughton B, Saxonov S, Avey L, Wojcicki A, Pe'er I, Mountain J. Web-based, participant-driven studies yield novel genetic associations for common traits. Plos Genetics. 6: e1000993. PMID 20585627 DOI: 10.1371/Journal.Pgen.1000993  0.434
2010 Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PF, Morrow B, Friedman E, Oddoux C, Burns E, Ostrer H. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. American Journal of Human Genetics. 86: 850-9. PMID 20560205 DOI: 10.1016/J.Ajhg.2010.04.015  0.748
2010 Flowers EB, Poole RJ, Tursun B, Bashllari E, Pe'er I, Hobert O. The Groucho ortholog UNC-37 interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C. elegans. Development (Cambridge, England). 137: 1799-805. PMID 20431118 DOI: 10.1242/Dev.046219  0.327
2010 Dewal N, Freedman ML, LaFramboise T, Pe'er I. Power to detect selective allelic amplification in genome-wide scans of tumor data. Bioinformatics (Oxford, England). 26: 518-28. PMID 20031965 DOI: 10.1093/Bioinformatics/Btp694  0.321
2010 Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. European Journal of Human Genetics : Ejhg. 18: 309-16. PMID 19844264 DOI: 10.1038/Ejhg.2009.180  0.546
2009 Kenny EE, Gusev A, Riegel K, Lütjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe'er I, Sehayek E. Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. Proceedings of the National Academy of Sciences of the United States of America. 106: 13886-91. PMID 19667188 DOI: 10.1073/Pnas.0907336106  0.595
2009 Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, et al. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 460: 753-7. PMID 19571809 DOI: 10.1038/Nature08192  0.381
2009 Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR, Graham J, Park BK, Dillon JF, Bernal W, Cordell HJ, et al. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nature Genetics. 41: 816-9. PMID 19483685 DOI: 10.1038/Ng.379  0.368
2009 Prabhu S, Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Research. 19: 1254-61. PMID 19447964 DOI: 10.1101/Gr.088559.108  0.614
2009 Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Smith JG, Ji W, Noel M, Foo JN, Blundell ML, Skilling V, Garcia L, et al. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Plos Genetics. 5: e1000365. PMID 19197348 DOI: 10.1371/Journal.Pgen.1000365  0.543
2009 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 Research. 19: 318-26. PMID 18971310 DOI: 10.1101/Gr.081398.108  0.635
2008 Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. Plos One. 3: e4012. PMID 19107202 DOI: 10.1371/Journal.Pone.0004012  0.414
2008 Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe'er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM, Breslow JL. Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. Arteriosclerosis, Thrombosis, and Vascular Biology. 28: 2078-84. PMID 18802019 DOI: 10.1161/Atvbaha.108.172288  0.444
2008 Sarin S, Prabhu S, O'Meara MM, Pe'er I, Hobert O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nature Methods. 5: 865-7. PMID 18677319 DOI: 10.1038/Nmeth.1249  0.608
2008 Pe'er I, Yelensky R, Altshuler D, Daly MJ. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genetic Epidemiology. 32: 381-5. PMID 18348202 DOI: 10.1002/Gepi.20303  0.387
2008 Barzuza T, Beckmann JS, Shamir R, Pe'er I. Computational problems in perfect phylogeny haplotyping: Typing without calling the allele Ieee/Acm Transactions On Computational Biology and Bioinformatics. 5: 101-109. PMID 18245879 DOI: 10.1109/Tcbb.2007.1063  0.377
2008 Stoyanovich J, Pe'er I. MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinformatics (Oxford, England). 24: 440-2. PMID 18048395 DOI: 10.1093/Bioinformatics/Btm587  0.448
2007 Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe'er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, et al. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nature Genetics. 39: 1477-82. PMID 17982456 DOI: 10.1038/Ng.2007.27  0.376
2007 Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, Frazer KA, Ballinger DG, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 449: 913-8. PMID 17943131 DOI: 10.1038/Nature06250  0.483
2007 Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 449: 851-61. PMID 17943122 DOI: 10.1038/Nature06258  0.503
2007 Grossman I, Avidan N, Singer C, Goldstaub D, Hayardeny L, Eyal E, Ben-Asher E, Paperna T, Pe'er I, Lancet D, Beckmann JS, Miller A. Pharmacogenetics of glatiramer acetate therapy for multiple sclerosis reveals drug-response markers. Pharmacogenetics and Genomics. 17: 657-66. PMID 17622942 DOI: 10.1097/Fpc.0B013E3281299169  0.406
2007 Pe'er I, Yelensky R, Altshuler D, Daly MJ. Estimation of the Multiple Testing Burden for Genomewide Association Studies of Common Variants Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.359.1  0.398
2006 Pe'er I, de Bakker PI, Maller J, Yelensky R, Altshuler D, Daly MJ. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nature Genetics. 38: 663-7. PMID 16715096 DOI: 10.1038/Ng1816  0.441
2006 Wang H, Thomas DC, Pe'er I, Stram DO. Optimal two-stage genotyping designs for genome-wide association scans. Genetic Epidemiology. 30: 356-68. PMID 16607626 DOI: 10.1002/Gepi.20150  0.366
2006 Pe'er I, Chretien YR, de Bakker PI, Barrett JC, Daly MJ, Altshuler DM. Biases and reconciliation in estimates of linkage disequilibrium in the human genome. American Journal of Human Genetics. 78: 588-603. PMID 16532390 DOI: 10.1086/502803  0.401
2006 Bonnen PE, Pe'er I, Plenge RM, Salit J, Lowe JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman JM. Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nature Genetics. 38: 214-7. PMID 16429162 DOI: 10.1038/Ng1712  0.439
2005 de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D. Efficiency and power in genetic association studies. Nature Genetics. 37: 1217-23. PMID 16244653 DOI: 10.1038/Ng1669  0.404
2005 Singer C, Grossman I, Avidan N, Beckmann JS, Pe'er I. Trick or treat: The effect of placebo on the power of pharmacogenetic association studies Human Genomics. 2: 28-38. PMID 15814066 DOI: 10.1186/1479-7364-2-1-28  0.357
2004 Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckmann JS. Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins. 54: 20-40. PMID 14705021 DOI: 10.1002/Prot.10559  0.302
2002 Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics (Oxford, England). 18: 1116-23. PMID 12176835 DOI: 10.1093/Bioinformatics/18.8.1116  0.317
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