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Guo Y, Wu C, Guo M, Zou Q, Liu X, Keinan A. Combining Sparse Group Lasso and Linear Mixed Model Improves Power to Detect Genetic Variants Underlying Quantitative Traits. Front Genet. 2019;10:271. doi: 10.3389/fgene.2019.00271. eCollection 2019. PubMed PMID: 31024614; PubMed Central PMCID: PMC6469383.
Guo Y, Wu C, Guo M, Liu X, Keinan A. Gene-Based Nonparametric Testing of Interactions Using Distance Correlation Coefficient in Case-Control Association Studies. Genes (Basel). 2018 Dec 5;9(12). doi: 10.3390/genes9120608. PubMed PMID: 30563156; PubMed Central PMCID: PMC6316506.
Lussier AA, Keinan A. Crowdsourced genealogies and genomes. Science. 2018 Apr 13;360(6385):153-154. doi: 10.1126/science.aat2634. PubMed PMID: 29650659; NIHMSID:NIHMS967283.
Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, Devine SE. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res. 2017 Nov;27(11):1916-1929. doi: 10.1101/gr.218032.116. Epub 2017 Aug 30. PubMed PMID: 28855259; PubMed Central PMCID: PMC5668948.
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P. Alignment of 1000 Genomes Project reads to reference assembly GRCh38. Gigascience. 2017 Jul 1;6(7):1-8. doi: 10.1093/gigascience/gix038. PubMed PMID: 28531267; PubMed Central PMCID: PMC5522380.
Ye K, Gao F, Wang D, Bar-Yosef O, Keinan A. Dietary adaptation of FADS genes in Europe varied across time and geography. Nat Ecol Evol. 2017 May 26;1:167. doi: 10.1038/s41559-017-0167. PubMed PMID: 29094686; PubMed Central PMCID: PMC5672832.
D'Amico F, Skarmoutsou E, Lo LJ, Granata M, Trovato C, Rossi GA, Bellocchi C, Marchini M, Scorza R, Mazzarino MC, Keinan A. Association between rs2294020 in X-linked CCDC22 and susceptibility to autoimmune diseases with focus on systemic lupus erythematosus. Immunol Lett. 2017 Jan;181:58-62. doi: 10.1016/j.imlet.2016.11.011. Epub 2016 Nov 22. PubMed PMID: 27888057; PubMed Central PMCID: PMC5222889.
Hanson MR, Gu Z, Keinan A, Ye K, Germain A, Billing-Ross P. Association of mitochondrial DNA variants with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) symptoms. J Transl Med. 2016 Dec 20;14(1):342. doi: 10.1186/s12967-016-1104-5. PubMed PMID: 27998272; PubMed Central PMCID: PMC5175376.
Gao F, Keinan A. Explosive genetic evidence for explosive human population growth. Curr Opin Genet Dev. 2016 Dec;41:130-139. doi: 10.1016/j.gde.2016.09.002. Epub 2016 Oct 4. Review. PubMed PMID: 27710906; PubMed Central PMCID: PMC5161661.
Waldman YY, Biddanda A, Dubrovsky M, Campbell CL, Oddoux C, Friedman E, Atzmon G, Halperin E, Ostrer H, Keinan A. The genetic history of Cochin Jews from India. Hum Genet. 2016 Oct;135(10):1127-43. doi: 10.1007/s00439-016-1698-y. Epub 2016 Jul 4. PubMed PMID: 27377974; PubMed Central PMCID: PMC5020127.
Kothapalli KS, Ye K, Gadgil MS, Carlson SE, O'Brien KO, Zhang JY, Park HG, Ojukwu K, Zou J, Hyon SS, Joshi KS, Gu Z, Keinan A, Brenna JT. Positive Selection on a Regulatory Insertion-Deletion Polymorphism in FADS2 Influences Apparent Endogenous Synthesis of Arachidonic Acid. Mol Biol Evol. 2016 Jul;33(7):1726-39. doi: 10.1093/molbev/msw049. Epub 2016 Mar 29. PubMed PMID: 27188529; PubMed Central PMCID: PMC4915354.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, Bustamante CD, Tyler-Smith C. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016 Jun;48(6):593-9. doi: 10.1038/ng.3559. Epub 2016 Apr 25. Review. PubMed PMID: 27111036; PubMed Central PMCID: PMC4884158.
Pinto Y, Gabay O, Arbiza L, Sams AJ, Keinan A, Levanon EY. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. Genome Res. 2016 May;26(5):579-87. doi: 10.1101/gr.199240.115. Epub 2016 Apr 7. PubMed PMID: 27056836; PubMed Central PMCID: PMC4864454.
Waldman YY, Biddanda A, Davidson NR, Billing-Ross P, Dubrovsky M, Campbell CL, Oddoux C, Friedman E, Atzmon G, Halperin E, Ostrer H, Keinan A. The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry. PLoS One. 2016;11(3):e0152056. doi: 10.1371/journal.pone.0152056. eCollection 2016. PubMed PMID: 27010569; PubMed Central PMCID: PMC4806850.
Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res. 2016 Feb;26(2):151-62. doi: 10.1101/gr.191478.115. Epub 2016 Jan 4. PubMed PMID: 26728717; PubMed Central PMCID: PMC4728368.
Slavney A, Arbiza L, Clark AG, Keinan A. Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes. Mol Biol Evol. 2016 Feb;33(2):384-93. doi: 10.1093/molbev/msv225. Epub 2015 Oct 22. PubMed PMID: 26494842; PubMed Central PMCID: PMC4751236.
Billing-Ross P, Germain A, Ye K, Keinan A, Gu Z, Hanson MR. Mitochondrial DNA variants correlate with symptoms in myalgic encephalomyelitis/chronic fatigue syndrome. J Transl Med. 2016 Jan 20;14:19. doi: 10.1186/s12967-016-0771-6. PubMed PMID: 26791940; PubMed Central PMCID: PMC4719218.
Gao F, Keinan A. Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models. Genetics. 2016 Jan;202(1):235-45. doi: 10.1534/genetics.115.180570. Epub 2015 Oct 8. PubMed PMID: 26450922; PubMed Central PMCID: PMC4701087.
Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. PubMed PMID: 26432245; PubMed Central PMCID: PMC4750478.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. PubMed PMID: 26432246; PubMed Central PMCID: PMC4617611.
Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 2015 Sep 15;16:191. doi: 10.1186/s13059-015-0759-1. PubMed PMID: 26374288; PubMed Central PMCID: PMC4570153.
Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, Chiavacci RM, Kim CE, Wang F, Snyder J, Richie MD, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Russell RK, Wilson DC, Silverberg MS, Annese V, Lie BA, Punaro M, Dubinsky MC, Monos DS, Strisciuglio C, Staiano A, Miele E, Kugathasan S, Ellis JA, Munro JE, Sullivan KE, Wise CA, Chapel H, Cunningham-Rundles C, Grant SF, Orange JS, Sleiman PM, Behrens EM, Griffiths AM, Satsangi J, Finkel TH, Keinan A, Prak ET, Polychronakos C, Baldassano RN, Li H, Keating BJ, Hakonarson H. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nat Med. 2015 Sep;21(9):1018-27. doi: 10.1038/nm.3933. Epub 2015 Aug 24. PubMed PMID: 26301688; PubMed Central PMCID: PMC4863040.
Gao F, Chang D, Biddanda A, Ma L, Guo Y, Zhou Z, Keinan A. XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome. J Hered. 2015 Sep-Oct;106(5):666-71. doi: 10.1093/jhered/esv059. Epub 2015 Aug 12. PubMed PMID: 26268243; PubMed Central PMCID: PMC4567842.
Ma L, Hoffman G, Keinan A. X-inactivation informs variance-based testing for X-linked association of a quantitative trait. BMC Genomics. 2015 Mar 25;16:241. doi: 10.1186/s12864-015-1463-y. PubMed PMID: 25880738; PubMed Central PMCID: PMC4381508.
Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E. Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One. 2015;10(3):e0121644. doi: 10.1371/journal.pone.0121644. eCollection 2015. PubMed PMID: 25807536; PubMed Central PMCID: PMC4373932.
Sams AJ, Hawks J, Keinan A. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection. J Hum Evol. 2015 Feb;79:64-72. doi: 10.1016/j.jhevol.2014.10.009. Epub 2014 Nov 15. PubMed PMID: 25467111; PubMed Central PMCID: PMC4381881.
Ma L, Keinan A, Clark AG. Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits. Methods Mol Biol. 2015;1253:35-45. doi: 10.1007/978-1-4939-2155-3_3. PubMed PMID: 25403526; PubMed Central PMCID: PMC4930274.
Chang D, Gao F, Slavney A, Ma L, Waldman YY, Sams AJ, Billing-Ross P, Madar A, Spritz R, Keinan A. Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PLoS One. 2014;9(12):e113684. doi: 10.1371/journal.pone.0113684. eCollection 2014. PubMed PMID: 25479423; PubMed Central PMCID: PMC4257614.
Siepel A, Arbiza L. Cis-regulatory elements and human evolution. Curr Opin Genet Dev. 2014 Dec;29:81-9. doi: 10.1016/j.gde.2014.08.011. Epub 2014 Sep 16. Review. PubMed PMID: 25218861; PubMed Central PMCID: PMC4258466.
Willems T, Gymrek M, Highnam G, Mittelman D, Erlich Y. The landscape of human STR variation. Genome Res. 2014 Nov;24(11):1894-904. doi: 10.1101/gr.177774.114. Epub 2014 Aug 18. PubMed PMID: 25135957; PubMed Central PMCID: PMC4216929.
Ye K, Lu J, Ma F, Keinan A, Gu Z. Reply to Just et al.: Mitochondrial DNA heteroplasmy could be reliably detected with massively parallel sequencing technologies. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):E4548-50. doi: 10.1073/pnas.1415171111. Epub 2014 Oct 15. PubMed PMID: 25319265; PubMed Central PMCID: PMC4217444.
Chang D, Keinan A. Principal component analysis characterizes shared pathogenetics from genome-wide association studies. PLoS Comput Biol. 2014 Sep;10(9):e1003820. doi: 10.1371/journal.pcbi.1003820. eCollection 2014 Sep. PubMed PMID: 25211452; PubMed Central PMCID: PMC4161298.
Ye K, Lu J, Ma F, Keinan A, Gu Z. Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals. Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10654-9. doi: 10.1073/pnas.1403521111. Epub 2014 Jul 7. PubMed PMID: 25002485; PubMed Central PMCID: PMC4115537.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88. PubMed PMID: 24980144; PubMed Central PMCID: PMC4197830.
Saggie K, Keinan A, Ruppin E. Spikes that count: rethinking spikiness in neurally embedded systems. Neurocomputing. 2014 June; 58:303-311. doi: 10.1016/j.neucom.2004.01.060.
Delaneau O, Marchini J. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun. 2014 Jun 13;5:3934. doi: 10.1038/ncomms4934. PubMed PMID: 25653097; PubMed Central PMCID: PMC4338501.
Arbiza L, Gottipati S, Siepel A, Keinan A. Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet. 2014 Jun 5;94(6):827-44. doi: 10.1016/j.ajhg.2014.04.011. Epub 2014 May 15. PubMed PMID: 24836452; PubMed Central PMCID: PMC4121480.
Gao F, Ballantyne C, Ma L, Virani SS, Keinan A, Brautbar A. Rare LPL gene variants attenuate triglyceride reduction and HDL cholesterol increase in response to fenofibric acid therapy in individuals with mixed dyslipidemia. Atherosclerosis. 2014 Jun;234(2):249-53. doi: 10.1016/j.atherosclerosis.2014.03.010. Epub 2014 Mar 22. PubMed PMID: 24704626; PubMed Central PMCID: PMC4078400.
Gao F, Keinan A. High burden of private mutations due to explosive human population growth and purifying selection. BMC Genomics. 2014;15 Suppl 4:S3. doi: 10.1186/1471-2164-15-S4-S3. Epub 2014 May 20. PubMed PMID: 25056720; PubMed Central PMCID: PMC4083409.
Ma L, Ballantyne C, Brautbar A, Keinan A. Analysis of multiple association studies provides evidence of an expression QTL hub in gene-gene interaction network affecting HDL cholesterol levels. PLoS One. 2014;9(3):e92469. doi: 10.1371/journal.pone.0092469. eCollection 2014. PubMed PMID: 24651390; PubMed Central PMCID: PMC3961362.
Gazave E, Ma L, Chang D, Coventry A, Gao F, Muzny D, Boerwinkle E, Gibbs RA, Sing CF, Clark AG, Keinan A. Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):757-62. doi: 10.1073/pnas.1310398110. Epub 2013 Dec 30. PubMed PMID: 24379384; PubMed Central PMCID: PMC3896169.
Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M. FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol. 2014;15(10):480. doi: 10.1186/s13059-014-0480-5. PubMed PMID: 25273974; PubMed Central PMCID: PMC4203974.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet. 2013;9(12):e1004023. doi: 10.1371/journal.pgen.1004023. Epub 2013 Dec 26. PubMed PMID: 24385924; PubMed Central PMCID: PMC3873240.
Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res. 2013 Dec;23(12):2042-52. doi: 10.1101/gr.154625.113. Epub 2013 Sep 11. PubMed PMID: 24026178; PubMed Central PMCID: PMC3847774.
Gazave E, Chang D, Clark AG, Keinan A. Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect. Genetics. 2013 Nov;195(3):969-78. doi: 10.1534/genetics.113.153973. Epub 2013 Aug 26. PubMed PMID: 23979573; PubMed Central PMCID: PMC3813877.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587. PubMed PMID: 24092746; PubMed Central PMCID: PMC3947637.
Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet. 2013 Jul;45(7):723-9. doi: 10.1038/ng.2658. Epub 2013 Jun 9. PubMed PMID: 23749186; PubMed Central PMCID: PMC3932982.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11. PubMed PMID: 23478400; PubMed Central PMCID: PMC3638132.
Ma L, Clark AG, Keinan A. Gene-based testing of interactions in association studies of quantitative traits. PLoS Genet. 2013;9(2):e1003321. doi: 10.1371/journal.pgen.1003321. Epub 2013 Feb 28. PubMed PMID: 23468652; PubMed Central PMCID: PMC3585009.
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet. 2012 Dec 7;91(6):1022-32. doi: 10.1016/j.ajhg.2012.10.015. PubMed PMID: 23217326; PubMed Central PMCID: PMC3516590.
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