Alon Keinan

Alon Keinan

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Alon Keinan

Publications by authors named "Alon Keinan"

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Combining Sparse Group Lasso and Linear Mixed Model Improves Power to Detect Genetic Variants Underlying Quantitative Traits.

Front Genet 2019 10;10:271. Epub 2019 Apr 10.

Department of Computational Biology, Cornell University, Ithaca, NY, United States.

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http://dx.doi.org/10.3389/fgene.2019.00271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469383PMC
April 2019

Gene-Based Nonparametric Testing of Interactions Using Distance Correlation Coefficient in Case-Control Association Studies.

Genes (Basel) 2018 Dec 5;9(12). Epub 2018 Dec 5.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

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http://www.mdpi.com/2073-4425/9/12/608
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http://dx.doi.org/10.3390/genes9120608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316506PMC
December 2018

Crowdsourced genealogies and genomes.

Science 2018 04;360(6385):153-154

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1126/science.aat2634DOI Listing
April 2018

Dietary adaptation of FADS genes in Europe varied across time and geography.

Nat Ecol Evol 2017 May 26;1:167. Epub 2017 May 26.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/s41559-017-0167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672832PMC
May 2017

Explosive genetic evidence for explosive human population growth.

Curr Opin Genet Dev 2016 Dec 4;41:130-139. Epub 2016 Oct 4.

Department of Biological Statistics and Computational Biology, Ithaca, NY 14850, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161661PMC
December 2016

Association of mitochondrial DNA variants with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) symptoms.

J Transl Med 2016 12 20;14(1):342. Epub 2016 Dec 20.

Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1186/s12967-016-1104-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175376PMC
December 2016

The genetic history of Cochin Jews from India.

Hum Genet 2016 10 4;135(10):1127-43. Epub 2016 Jul 4.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1007/s00439-016-1698-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020127PMC
October 2016

Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity.

Genome Res 2016 05 7;26(5):579-87. Epub 2016 Apr 7.

Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;

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http://dx.doi.org/10.1101/gr.199240.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864454PMC
May 2016

Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions.

PLoS One 2015 25;10(3):e0121644. Epub 2015 Mar 25.

Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America; Human Genetic Center, University of Texas Health Science Center, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121644PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373932PMC
March 2016

Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes.

Mol Biol Evol 2016 Feb 22;33(2):384-93. Epub 2015 Oct 22.

Department of Biological Statistics and Computational Biology, Cornell University

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http://dx.doi.org/10.1093/molbev/msv225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751236PMC
February 2016

XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome.

J Hered 2015 Sep-Oct;106(5):666-71. Epub 2015 Aug 12.

From the Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853 (Gao, Chang, Biddanda, Ma, Guo, Zhou, and Keinan); Program in Computational Biology and Medicine, Cornell University, Ithaca, NY 14853 (Chang and Keinan); Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740 (Ma); and School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China (Guo).

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http://dx.doi.org/10.1093/jhered/esv059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567842PMC
January 2016

Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models.

Genetics 2016 Jan 8;202(1):235-45. Epub 2015 Oct 8.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853

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http://dx.doi.org/10.1534/genetics.115.180570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701087PMC
January 2016

Mitochondrial DNA variants correlate with symptoms in myalgic encephalomyelitis/chronic fatigue syndrome.

J Transl Med 2016 Jan 20;14:19. Epub 2016 Jan 20.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1186/s12967-016-0771-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4719218PMC
January 2016

Host genetic variation impacts microbiome composition across human body sites.

Genome Biol 2015 Sep 15;16:191. Epub 2015 Sep 15.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1186/s13059-015-0759-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570153PMC
September 2015

Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits.

Methods Mol Biol 2015 ;1253:35-45

Department of Animal and Avian Sciences, University of Maryland, Bldg 142, College Park, MD, 20742, USA,

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http://dx.doi.org/10.1007/978-1-4939-2155-3_3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930274PMC
July 2015

Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases.

PLoS One 2014 5;9(12):e113684. Epub 2014 Dec 5.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America; Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, United States of America; Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113684PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257614PMC
July 2015

X-inactivation informs variance-based testing for X-linked association of a quantitative trait.

BMC Genomics 2015 Mar 25;16:241. Epub 2015 Mar 25.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14850, USA.

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http://dx.doi.org/10.1186/s12864-015-1463-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381508PMC
March 2015

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 15;79:64-72. Epub 2014 Nov 15.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1016/j.jhevol.2014.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381881PMC
February 2015

Principal component analysis characterizes shared pathogenetics from genome-wide association studies.

PLoS Comput Biol 2014 Sep 11;10(9):e1003820. Epub 2014 Sep 11.

Department of Biological Statistics & Computational Biology, Cornell University, Ithaca, New York, United States of America; Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161298PMC
September 2014

Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals.

Proc Natl Acad Sci U S A 2014 Jul 7;111(29):10654-9. Epub 2014 Jul 7.

Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853;

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http://dx.doi.org/10.1073/pnas.1403521111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115537PMC
July 2014

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 22;234(2):249-53. Epub 2014 Mar 22.

Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, USA; Center for Cardiovascular Disease Prevention, Methodist DeBakey Heart and Vascular Center, Houston, TX, USA; Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.atherosclerosis.2014.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078400PMC
June 2014

Contrasting X-linked and autosomal diversity across 14 human populations.

Am J Hum Genet 2014 Jun 15;94(6):827-44. Epub 2014 May 15.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121480PMC
June 2014

Neutral genomic regions refine models of recent rapid human population growth.

Proc Natl Acad Sci U S A 2014 Jan 30;111(2):757-62. Epub 2013 Dec 30.

Departments of Biological Statistics and Computational Biology and Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853.

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http://dx.doi.org/10.1073/pnas.1310398110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896169PMC
January 2014

Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect.

Genetics 2013 Nov 26;195(3):969-78. Epub 2013 Aug 26.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853.

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http://dx.doi.org/10.1534/genetics.113.153973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813877PMC
November 2013

Genome-wide inference of natural selection on human transcription factor binding sites.

Nat Genet 2013 Jul 9;45(7):723-9. Epub 2013 Jun 9.

Department of Biological Statistics & Computational Biology, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1038/ng.2658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932982PMC
July 2013

Gene-based testing of interactions in association studies of quantitative traits.

PLoS Genet 2013 28;9(2):e1003321. Epub 2013 Feb 28.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585009PMC
June 2013

Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation.

PLoS Comput Biol 2012 5;8(7):e1002600. Epub 2012 Jul 5.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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https://dx.doi.org/10.1371/journal.pcbi.1002600
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http://dx.doi.org/10.1371/journal.pcbi.1002600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390358PMC
January 2013

Interaction between SNPs in the RXRA and near ANGPTL3 gene region inhibits apoB reduction after statin-fenofibric acid therapy in individuals with mixed dyslipidemia.

J Lipid Res 2012 Nov 15;53(11):2425-8. Epub 2012 Aug 15.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1194/jlr.M028829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466010PMC
November 2012

NRE: a tool for exploring neutral loci in the human genome.

BMC Bioinformatics 2012 Nov 14;13:301. Epub 2012 Nov 14.

Department of Biological Statistics and Computational Biology, Cornell University, 102 Weill Hall, Ithaca 14853, USA.

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http://dx.doi.org/10.1186/1471-2105-13-301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543337PMC
November 2012

Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations.

PLoS Genet 2012 24;8(5):e1002714. Epub 2012 May 24.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359971PMC
September 2012

Recent explosive human population growth has resulted in an excess of rare genetic variants.

Science 2012 May;336(6082):740-3

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1126/science.1217283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586590PMC
May 2012

Selection for translation efficiency on synonymous polymorphisms in recent human evolution.

Genome Biol Evol 2011 29;3:749-61. Epub 2011 Jul 29.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evr076/
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http://dx.doi.org/10.1093/gbe/evr076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163469PMC
December 2011

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.

Nat Genet 2011 Jul 24;43(8):741-3. Epub 2011 Jul 24.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145052PMC
July 2011

The history of African gene flow into Southern Europeans, Levantines, and Jews.

PLoS Genet 2011 Apr 21;7(4):e1001373. Epub 2011 Apr 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080861PMC
April 2011

Can a sex-biased human demography account for the reduced effective population size of chromosome X in non-Africans?

Mol Biol Evol 2010 Oct 7;27(10):2312-21. Epub 2010 May 7.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1093/molbev/msq117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944028PMC
October 2010

Integrating common and rare genetic variation in diverse human populations.

Nature 2010 Sep;467(7311):52-8

Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature09298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859PMC
September 2010

Human population differentiation is strongly correlated with local recombination rate.

PLoS Genet 2010 Mar 26;6(3):e1000886. Epub 2010 Mar 26.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845648PMC
March 2010

Detecting natural selection by empirical comparison to random regions of the genome.

Hum Mol Genet 2009 Dec 25;18(24):4853-67. Epub 2009 Sep 25.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/hmg/ddp457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778377PMC
December 2009

Accelerated genetic drift on chromosome X during the human dispersal out of Africa.

Nat Genet 2009 Jan 21;41(1):66-70. Epub 2008 Dec 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng.303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612098PMC
January 2009

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans.

Nat Genet 2007 Oct 9;39(10):1251-5. Epub 2007 Sep 9.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng2116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586588PMC
October 2007

Axiomatic scalable neurocontroller analysis via the Shapley value.

Artif Life 2006 ;12(3):333-52

School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1162/artl.2006.12.3.333DOI Listing
October 2006

Neurocontroller analysis via evolutionary network minimization.

Artif Life 2006 ;12(3):435-48

School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1162/artl.2006.12.3.435DOI Listing
October 2006

Neural processing of counting in evolved spiking and McCulloch-Pitts agents.

Artif Life 2006 ;12(1):1-16

School of Computer Science, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, 69978, Israel.

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http://dx.doi.org/10.1162/106454606775186428DOI Listing
April 2006

Quantitative analysis of genetic and neuronal multi-perturbation experiments.

PLoS Comput Biol 2005 Nov 25;1(6):e64. Epub 2005 Nov 25.

Interdisciplinary Center for Neural Computation, Hebrew University, Jerusalem, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.0010064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1289391PMC
November 2005

Fair localization of function via multi-lesion analysis.

Neuroinformatics 2004 ;2(2):163-8

School of Computer Science, Tel Aviv University, Israel.

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http://dx.doi.org/10.1385/NI:2:2:163DOI Listing
October 2004

Fair attribution of functional contribution in artificial and biological networks.

Neural Comput 2004 Sep;16(9):1887-915

School of Computer Sciences, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1162/0899766041336387DOI Listing
September 2004

Controlled analysis of neurocontrollers with informational lesioning.

Philos Trans A Math Phys Eng Sci 2003 Oct;361(1811):2123-44

School of Computer Sciences, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1098/rsta.2003.1253DOI Listing
October 2003