Alon Keinan

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc Recent explosive human population growth has resulted in an excess of rare genetic variants
    Alon Keinan
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Science 336:740-3. 2012
  2. pmc Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing
    Srikanth Gottipati
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Genet 43:741-3. 2011
  3. pmc Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation
    Diana Chang
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Comput Biol 8:e1002600. 2012
  4. pmc Human population differentiation is strongly correlated with local recombination rate
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1000886. 2010
  5. pmc Can a sex-biased human demography account for the reduced effective population size of chromosome X in non-Africans?
    Alon Keinan
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Mol Biol Evol 27:2312-21. 2010
  6. pmc Neutral genomic regions refine models of recent rapid human population growth
    Elodie Gazave
    Departments of Biological Statistics and Computational Biology and Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
    Proc Natl Acad Sci U S A 111:757-62. 2014
  7. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001373. 2011
  8. pmc Demographic history and rare allele sharing among human populations
    Simon Gravel
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 108:11983-8. 2011
  9. pmc Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:1251-5. 2007
  10. pmc Gene-based testing of interactions in association studies of quantitative traits
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 9:e1003321. 2013

Collaborators

Detail Information

Publications23

  1. pmc Recent explosive human population growth has resulted in an excess of rare genetic variants
    Alon Keinan
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Science 336:740-3. 2012
    ..Hence, the extreme recent human population growth needs to be taken into consideration in studying the genetics of complex diseases and traits...
  2. pmc Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing
    Srikanth Gottipati
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Genet 43:741-3. 2011
    ..This relative reduction is most parsimoniously explained by differences in demographic history without the need to invoke natural selection...
  3. pmc Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation
    Diana Chang
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Comput Biol 8:e1002600. 2012
    ..Finally, we find the variance in associated allele frequency to be a potential indicator of synthetic associations...
  4. pmc Human population differentiation is strongly correlated with local recombination rate
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1000886. 2010
    ....
  5. pmc Can a sex-biased human demography account for the reduced effective population size of chromosome X in non-Africans?
    Alon Keinan
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Mol Biol Evol 27:2312-21. 2010
    ....
  6. pmc Neutral genomic regions refine models of recent rapid human population growth
    Elodie Gazave
    Departments of Biological Statistics and Computational Biology and Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
    Proc Natl Acad Sci U S A 111:757-62. 2014
    ..This observation and results also shed light on the discrepancy in demographic estimates among recent studies. ..
  7. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001373. 2011
    ..For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas...
  8. pmc Demographic history and rare allele sharing among human populations
    Simon Gravel
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 108:11983-8. 2011
    ..Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence...
  9. pmc Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:1251-5. 2007
    ..Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians...
  10. pmc Gene-based testing of interactions in association studies of quantitative traits
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 9:e1003321. 2013
    ..We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies...
  11. pmc Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect
    Elodie Gazave
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853
    Genetics 195:969-78. 2013
    ..Combined, our results suggest that the genetic risk of complex diseases in growing populations might be distributed across a larger number of more weakly deleterious rare variants. ..
  12. pmc Detecting natural selection by empirical comparison to random regions of the genome
    Fuli Yu
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Hum Mol Genet 18:4853-67. 2009
    ..Our study also provides a prototype for how empirical scans for ancient selection can be carried out once many genomes are sequenced...
  13. pmc Accelerated genetic drift on chromosome X during the human dispersal out of Africa
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 41:66-70. 2009
    ..We conclude that a sex-biased process that reduced the female effective population size, or an episode of natural selection unusually affecting chromosome X, was associated with the founding of non-African populations...
  14. pmc Rare LPL gene variants attenuate triglyceride reduction and HDL cholesterol increase in response to fenofibric acid therapy in individuals with mixed dyslipidemia
    Feng Gao
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
    Atherosclerosis 234:249-53. 2014
    ..We sought to identify rare genetic variants (frequency ≤ 1%) in genes involved in TG and HDL-C metabolism that affect the response to fenofibric acid (FA) therapy...
  15. pmc Genome-wide inference of natural selection on human transcription factor binding sites
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
    Nat Genet 45:723-9. 2013
    ..Overall, regulatory elements seem to contribute substantially to both adaptive substitutions and deleterious polymorphisms with key implications for human evolution and disease. ..
  16. ncbi Contrasting X-Linked and Autosomal Diversity across 14 Human Populations
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Am J Hum Genet 94:827-44. 2014
    ..Further reductions can be predicted by more extreme demographic events in excess of those captured by the latest studies but, in the absence of these, also by historical sex-biased demographic events or other processes. ..
  17. pmc Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation
    Jeffrey M Kidd
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Am J Hum Genet 91:660-71. 2012
    ....
  18. pmc Analysis of multiple association studies provides evidence of an expression QTL hub in gene-gene interaction network affecting HDL cholesterol levels
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 9:e92469. 2014
    ....
  19. pmc Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants
    George Ayodo
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 81:234-42. 2007
    ..This empirically demonstrates that combining association analysis with evidence of natural selection can increase power to detect risk variants by orders of magnitude--up to P=.000018 for HBB and P=.00043 for CD36...
  20. pmc NRE: a tool for exploring neutral loci in the human genome
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, 102 Weill Hall, Ithaca 14853, USA
    BMC Bioinformatics 13:301. 2012
    ..Several recent studies in humans have stressed the large effect of natural selection at linked neutral sites and have shown that the choice of putatively neutral regions can have a marked effect on estimates of demographic history...
  21. pmc Interaction between SNPs in the RXRA and near ANGPTL3 gene region inhibits apoB reduction after statin-fenofibric acid therapy in individuals with mixed dyslipidemia
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
    J Lipid Res 53:2425-8. 2012
    ..Further study is required to examine the clinical applicability of this genetic interaction and its effect on coronary events...
  22. pmc Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 8:e1002714. 2012
    ..In conclusion, based on a knowledge-driven analysis of epistasis, together with a new locus-based validation method, we successfully identified and validated an interaction affecting a complex trait in multi-ethnic populations...
  23. pmc Mapping copy number variation by population-scale genome sequencing
    Ryan E Mills
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nature 470:59-65. 2011
    ..Our analytical framework and SV map serves as a resource for sequencing-based association studies...