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Items: 1 to 50 of 96

1.

Inference of Population Structure from Time-Series Genotype Data.

Joseph TA, Pe'er I.

Am J Hum Genet. 2019 Aug 1;105(2):317-333. doi: 10.1016/j.ajhg.2019.06.002. Epub 2019 Jun 27.

PMID:
31256878
2.

FEAST: fast expectation-maximization for microbial source tracking.

Shenhav L, Thompson M, Joseph TA, Briscoe L, Furman O, Bogumil D, Mizrahi I, Pe'er I, Halperin E.

Nat Methods. 2019 Jul;16(7):627-632. doi: 10.1038/s41592-019-0431-x. Epub 2019 Jun 10.

PMID:
31182859
3.

arcasHLA: high resolution HLA typing from RNAseq.

Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R.

Bioinformatics. 2019 Jun 7. pii: btz474. doi: 10.1093/bioinformatics/btz474. [Epub ahead of print]

PMID:
31173059
4.

Autoencoding Topographic Factors.

Moretti A, Stirn A, Marks G, Pe'er I.

J Comput Biol. 2019 Jun;26(6):546-560. doi: 10.1089/cmb.2018.0176. Epub 2018 Dec 7.

PMID:
30526005
5.

Identity inference of genomic data using long-range familial searches.

Erlich Y, Shor T, Pe'er I, Carmi S.

Science. 2018 Nov 9;362(6415):690-694. doi: 10.1126/science.aau4832. Epub 2018 Oct 11.

PMID:
30309907
6.

High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation.

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, Ostrer H, Ozelius LJ, Peter I, Atzmon G, Pe'er I.

Hum Genet. 2018 Apr;137(4):343-355. doi: 10.1007/s00439-018-1886-z. Epub 2018 Apr 28.

PMID:
29705978
7.

Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease.

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.

Sci Transl Med. 2018 Jan 10;10(423). pii: eaai7795. doi: 10.1126/scitranslmed.aai7795.

8.

2-Way k-Means as a Model for Microbiome Samples.

Jackson WJ, Agarwal I, Pe'er I.

J Healthc Eng. 2017;2017:5284145. doi: 10.1155/2017/5284145. Epub 2017 Sep 5.

9.

Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

Palmer C, Pe'er I.

PLoS Genet. 2017 Jul 17;13(7):e1006916. doi: 10.1371/journal.pgen.1006916. eCollection 2017 Jul.

10.

The time and place of European admixture in Ashkenazi Jewish history.

Xue J, Lencz T, Darvasi A, Pe'er I, Carmi S.

PLoS Genet. 2017 Apr 4;13(4):e1006644. doi: 10.1371/journal.pgen.1006644. eCollection 2017 Apr.

11.

Elevated GM3 plasma concentration in idiopathic Parkinson's disease: A lipidomic analysis.

Chan RB, Perotte AJ, Zhou B, Liong C, Shorr EJ, Marder KS, Kang UJ, Waters CH, Levy OA, Xu Y, Shim HB, Pe'er I, Di Paolo G, Alcalay RN.

PLoS One. 2017 Feb 17;12(2):e0172348. doi: 10.1371/journal.pone.0172348. eCollection 2017.

12.

A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF.

Chuang LS, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Evelyn Ng SM, Zhang W, Hsu NY, Facey JA, Luong T, Fernandez-Hernandez H, Li D, Rivas M, Schiff ER, Gusev A, Schumm LP, Bowen BM, Sharma Y, Ning K, Remark R, Gnjatic S, Legnani P, George J, Sands BE, Stempak JM, Datta LW, Lipka S, Katz S, Cheifetz AS, Barzilai N, Pontikos N, Abraham C, Dubinsky MJ, Targan S, Taylor K, Rotter JI, Scherl EJ, Desnick RJ, Abreu MT, Zhao H, Atzmon G, Pe'er I, Kugathasan S, Hakonarson H, McCauley JL, Lencz T, Darvasi A, Plagnol V, Silverberg MS, Muise AM, Brant SR, Daly MJ, Segal AW, Duerr RH, Merad M, McGovern DP, Peter I, Cho JH.

Gastroenterology. 2016 Oct;151(4):710-723.e2. doi: 10.1053/j.gastro.2016.06.045. Epub 2016 Jul 1.

13.

Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation.

Palmer C, Pe'er I.

PLoS Genet. 2016 Jun 16;12(6):e1006091. doi: 10.1371/journal.pgen.1006091. eCollection 2016 Jun.

14.

Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.

Yang S, Carmi S, Pe'er I.

J Comput Biol. 2016 Jun;23(6):495-507. doi: 10.1089/cmb.2016.0016. Epub 2016 Apr 22.

15.

Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.

Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S; Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL.

Am J Hum Genet. 2015 Dec 3;97(6):775-89. doi: 10.1016/j.ajhg.2015.10.006. Epub 2015 Nov 12.

16.

Expanded genetic screening panel for the Ashkenazi Jewish population.

Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, Darvasi A, Ozelius L, Peter I, Cho JH, Atzmon G, Clark L, Yu J, Lencz T, Pe'er I, Ostrer H, Oddoux C.

Genet Med. 2016 May;18(5):522-8. doi: 10.1038/gim.2015.123. Epub 2015 Sep 3.

17.

ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs.

Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A.

PLoS One. 2015 Jun 25;10(6):e0131038. doi: 10.1371/journal.pone.0131038. eCollection 2015.

18.

Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment.

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, Lundervold A, Steen VM, John M, Espeseth T, Räikkönen K, Widen E, Palotie A, Eriksson JG, Giegling I, Konte B, Ikeda M, Roussos P, Giakoumaki S, Burdick KE, Payton A, Ollier W, Horan M, Scult M, Dickinson D, Straub RE, Donohoe G, Morris D, Corvin A, Gill M, Hariri A, Weinberger DR, Pendleton N, Iwata N, Darvasi A, Bitsios P, Rujescu D, Lahti J, Le Hellard S, Keller MC, Andreassen OA, Deary IJ, Glahn DC, Malhotra AK.

Am J Med Genet B Neuropsychiatr Genet. 2015 Jul;168B(5):363-73. doi: 10.1002/ajmg.b.32319. Epub 2015 May 7.

19.

Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks.

Kreimer A, Pe'er I.

PLoS Genet. 2014 Sep 11;10(9):e1004587. doi: 10.1371/journal.pgen.1004587. eCollection 2014 Sep.

20.

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.

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.

Nat Commun. 2014 Sep 9;5:4835. doi: 10.1038/ncomms5835.

21.

A renewal theory approach to IBD sharing.

Carmi S, Wilton PR, Wakeley J, Pe'er I.

Theor Popul Biol. 2014 Nov;97:35-48. doi: 10.1016/j.tpb.2014.08.002. Epub 2014 Aug 18.

22.

Excess of homozygosity in the major histocompatibility complex in schizophrenia.

Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra AK, Pe'er I, Darvasi A, Lencz T.

Hum Mol Genet. 2014 Nov 15;23(22):6088-95. doi: 10.1093/hmg/ddu308. Epub 2014 Jun 18.

23.

Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.

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, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe'er I, Bressman SB, Orr-Urtreger A.

Hum Mol Genet. 2014 Sep 1;23(17):4693-702. doi: 10.1093/hmg/ddu158. Epub 2014 May 19.

24.

Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder.

Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, DeRosse P, John M, Cheng L, Zhang C, Badner JA, Ikeda M, Iwata N, Cichon S, Rietschel M, Nöthen MM, Cheng AT, Hodgkinson C, Yuan Q, Kane JM, Lee AT, Pisanté A, Gregersen PK, Pe'er I, Malhotra AK, Goldman D, Darvasi A.

Nat Commun. 2013;4:2739. doi: 10.1038/ncomms3739.

25.

Variants in exons and in transcription factors affect gene expression in trans.

Kreimer A, Pe'er I.

Genome Biol. 2013 Jul 11;14(7):R71. doi: 10.1186/gb-2013-14-7-r71.

26.

Inference of historical migration rates via haplotype sharing.

Palamara PF, Pe'er I.

Bioinformatics. 2013 Jul 1;29(13):i180-8. doi: 10.1093/bioinformatics/btt239.

27.

De novo mutations in histone-modifying genes in congenital heart disease.

Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP.

Nature. 2013 Jun 13;498(7453):220-3. doi: 10.1038/nature12141. Epub 2013 May 12.

28.

Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.

Zhang W, Hui KY, Gusev A, Warner N, Ng SM, Ferguson J, Choi M, Burberry A, Abraham C, Mayer L, Desnick RJ, Cardinale CJ, Hakonarson H, Waterman M, Chowers Y, Karban A, Brant SR, Silverberg MS, Gregersen PK, Katz S, Lifton RP, Zhao H, Nuñez G, Pe'er I, Peter I, Cho JH.

Genes Immun. 2013 Jul-Aug;14(5):310-6. doi: 10.1038/gene.2013.19. Epub 2013 Apr 25.

29.
30.

Longitudinal study shows increasing obesity and hyperglycemia in micronesia.

Murdock D, Salit J, Stoffel M, Friedman JM, Pe'er I, Breslow JL, Bonnen PE.

Obesity (Silver Spring). 2013 Sep;21(9):E421-7. doi: 10.1002/oby.20041. Epub 2013 Apr 9.

31.

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.

Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML.

Cell. 2013 Jan 31;152(3):633-41. doi: 10.1016/j.cell.2012.12.034. Review.

32.

The variance of identity-by-descent sharing in the Wright-Fisher model.

Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I.

Genetics. 2013 Mar;193(3):911-28. doi: 10.1534/genetics.112.147215. Epub 2012 Dec 24.

33.

Length distributions of identity by descent reveal fine-scale demographic history.

Palamara PF, Lencz T, Darvasi A, Pe'er I.

Am J Hum Genet. 2012 Nov 2;91(5):809-22. doi: 10.1016/j.ajhg.2012.08.030. Epub 2012 Oct 25. Erratum in: Am J Hum Genet. 2012 Dec 7;91(6):1150.

34.

Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.

Zhuang Z, Gusev A, Cho J, Pe'er I.

PLoS One. 2012;7(10):e47618. doi: 10.1371/journal.pone.0047618. Epub 2012 Oct 11.

35.

Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.

Urban TJ, Shen Y, Stolz A, Chalasani N, Fontana RJ, Rochon J, Ge D, Shianna KV, Daly AK, Lucena MI, Nelson MR, Molokhia M, Aithal GP, Floratos A, Pe'er I, Serrano J, Bonkovsky H, Davern TJ, Lee WM, Navarro VJ, Talwalkar JA, Goldstein DB, Watkins PB; Drug-Induced Liver Injury Network; DILIGEN; EUDRAGENE; Spanish DILI Registry; International Serious Adverse Events Consortium.

Pharmacogenet Genomics. 2012 Nov;22(11):784-95. doi: 10.1097/FPC.0b013e3283589a76.

36.

North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.

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, Ostrer H.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13865-70. doi: 10.1073/pnas.1204840109. Epub 2012 Aug 6.

37.

Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.

Prabhu S, Pe'er I.

Genome Res. 2012 Nov;22(11):2230-40. doi: 10.1101/gr.137885.112. Epub 2012 Jul 5.

38.

Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples.

Henn BM, Hon L, Macpherson JM, Eriksson N, Saxonov S, Pe'er I, Mountain JL.

PLoS One. 2012;7(4):e34267. doi: 10.1371/journal.pone.0034267. Epub 2012 Apr 3.

39.

Inference of modules associated to eQTLs.

Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I.

Nucleic Acids Res. 2012 Jul;40(13):e98. doi: 10.1093/nar/gks269. Epub 2012 Mar 24.

40.

A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.

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, Chowers Y, Clark LN, Darvasi A, Doheny D, Duerr RH, Eliakim R, Giladi N, Gregersen PK, Hakonarson H, Jones MR, Marder K, McGovern DP, Mulle J, Orr-Urtreger A, Proctor DD, Pulver A, Rotter JI, Silverberg MS, Ullman T, Warren ST, Waterman M, Zhang W, Bergman A, Mayer L, Katz S, Desnick RJ, Cho JH, Peter I.

PLoS Genet. 2012;8(3):e1002559. doi: 10.1371/journal.pgen.1002559. Epub 2012 Mar 8.

41.

Implications for health and disease in the genetic signature of the Ashkenazi Jewish population.

Guha S, Rosenfeld JA, Malhotra AK, Lee AT, Gregersen PK, Kane JM, Pe'er I, Darvasi A, Lencz T.

Genome Biol. 2012 Jan 25;13(1):R2. doi: 10.1186/gb-2012-13-1-r2.

42.

Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population.

Gusev A, Shah MJ, Kenny EE, Ramachandran A, Lowe JK, Salit J, Lee CC, Levandowsky EC, Weaver TN, Doan QC, Peckham HE, McLaughlin SF, Lyons MR, Sheth VN, Stoffel M, De La Vega FM, Friedman JM, Breslow JL, Pe'er I.

Genetics. 2012 Feb;190(2):679-89. doi: 10.1534/genetics.111.134874. Epub 2011 Nov 30.

43.

Calling amplified haplotypes in next generation tumor sequence data.

Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I.

Genome Res. 2012 Feb;22(2):362-74. doi: 10.1101/gr.122564.111. Epub 2011 Nov 16.

44.

A hidden Markov model for copy number variant prediction from whole genome resequencing data.

Shen Y, Gu Y, Pe'er I.

BMC Bioinformatics. 2011;12 Suppl 6:S4. doi: 10.1186/1471-2105-12-S6-S4. Epub 2011 Jul 28.

45.

The architecture of long-range haplotypes shared within and across populations.

Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe'er I.

Mol Biol Evol. 2012 Feb;29(2):473-86. doi: 10.1093/molbev/msr133. Epub 2011 Oct 6.

46.

The impact of Converso Jews on the genomes of modern Latin Americans.

Velez C, Palamara PF, Guevara-Aguirre J, Hao L, Karafet T, Guevara-Aguirre M, Pearlman A, Oddoux C, Hammer M, Burns E, Pe'er I, Atzmon G, Ostrer H.

Hum Genet. 2012 Feb;131(2):251-63. doi: 10.1007/s00439-011-1072-z. Epub 2011 Jul 26.

PMID:
21789512
47.

Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.

Shen Y, Song R, Pe'er I.

Bioinformatics. 2011 Jul 15;27(14):1995-7. doi: 10.1093/bioinformatics/btr305. Epub 2011 Jun 2.

48.

DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.

Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I.

Am J Hum Genet. 2011 Jun 10;88(6):706-717. doi: 10.1016/j.ajhg.2011.04.023. Epub 2011 May 27.

49.

Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.

Lucena MI, Molokhia M, Shen Y, Urban TJ, Aithal GP, Andrade RJ, Day CP, Ruiz-Cabello F, Donaldson PT, Stephens C, Pirmohamed M, Romero-Gomez M, Navarro JM, Fontana RJ, Miller M, Groome M, Bondon-Guitton E, Conforti A, Stricker BH, Carvajal A, Ibanez L, Yue QY, Eichelbaum M, Floratos A, Pe'er I, Daly MJ, Goldstein DB, Dillon JF, Nelson MR, Watkins PB, Daly AK; Spanish DILI Registry; EUDRAGENE; DILIN; DILIGEN; International SAEC.

Gastroenterology. 2011 Jul;141(1):338-47. doi: 10.1053/j.gastro.2011.04.001. Epub 2011 Apr 12.

50.

HLA type inference via haplotypes identical by descent.

Setty MN, Gusev A, Pe'er I.

J Comput Biol. 2011 Mar;18(3):483-93. doi: 10.1089/cmb.2010.0258.

PMID:
21385049

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