John Novembre

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Human population structure and the adaptive response to pathogen-induced selection pressures
    John Novembre
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
    Philos Trans R Soc Lond B Biol Sci 367:878-86. 2012
  2. pmc Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays
    Arnd Gross
    Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16 18, 04107 Leipzig, Germany
    BMC Genet 12:67. 2011
  3. doi request reprint Perspectives on human population structure at the cusp of the sequencing era
    John Novembre
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA
    Annu Rev Genomics Hum Genet 12:245-74. 2011
  4. doi request reprint Spatial patterns of variation due to natural selection in humans
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095 1606, USA
    Nat Rev Genet 10:745-55. 2009
  5. doi request reprint Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Evolution 63:2914-25. 2009
  6. pmc Genes mirror geography within Europe
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 456:98-101. 2008
  7. pmc A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
    Bridgett M VonHoldt
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
    Genome Res 21:1294-305. 2011
  8. pmc Fast model-based estimation of ancestry in unrelated individuals
    David H Alexander
    Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA
    Genome Res 19:1655-64. 2009
  9. pmc Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data
    Darren Kessner
    Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
    Mol Biol Evol 30:1145-58. 2013
  10. pmc Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication
    Bridgett M VonHoldt
    Department of Ecology and Evolutionary Biology, 621 Charles E Young Drive South, University of California, Los Angeles, California 90095, USA
    Nature 464:898-902. 2010

Detail Information

Publications18

  1. pmc Human population structure and the adaptive response to pathogen-induced selection pressures
    John Novembre
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
    Philos Trans R Soc Lond B Biol Sci 367:878-86. 2012
    ....
  2. pmc Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays
    Arnd Gross
    Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16 18, 04107 Leipzig, Germany
    BMC Genet 12:67. 2011
    ..We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples...
  3. doi request reprint Perspectives on human population structure at the cusp of the sequencing era
    John Novembre
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA
    Annu Rev Genomics Hum Genet 12:245-74. 2011
    ..Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era...
  4. doi request reprint Spatial patterns of variation due to natural selection in humans
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095 1606, USA
    Nat Rev Genet 10:745-55. 2009
    ..Here, we review the challenges of these studies and emerging results, including how human population structure has influenced the response to novel selective pressures...
  5. doi request reprint Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Evolution 63:2914-25. 2009
    ..We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana...
  6. pmc Genes mirror geography within Europe
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 456:98-101. 2008
    ..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
  7. pmc A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
    Bridgett M VonHoldt
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
    Genome Res 21:1294-305. 2011
    ..Such admixture complicates decisions regarding endangered species restoration and protection...
  8. pmc Fast model-based estimation of ancestry in unrelated individuals
    David H Alexander
    Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA
    Genome Res 19:1655-64. 2009
    ....
  9. pmc Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data
    Darren Kessner
    Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
    Mol Biol Evol 30:1145-58. 2013
    ..Our method outperforms existing methods based on single-site allele frequencies, as well as simple approaches using sequence read data. We have implemented the method in a freely available open-source software tool...
  10. pmc Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication
    Bridgett M VonHoldt
    Department of Ecology and Evolutionary Biology, 621 Charles E Young Drive South, University of California, Los Angeles, California 90095, USA
    Nature 464:898-902. 2010
    ..More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity...
  11. pmc A model-based approach for analysis of spatial structure in genetic data
    Wen Yun Yang
    Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, USA
    Nat Genet 44:725-31. 2012
    ..These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B...
  12. ncbi request reprint Ascertainment bias in spatially structured populations: a case study in the eastern fence lizard
    Erica Bree Rosenblum
    Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
    J Hered 98:331-6. 2007
    ..Because bias correction methods performed well even when underlying assumptions were violated, our results suggest tools are currently available to analyze SNP data in structured populations...
  13. doi request reprint Recombination rates in admixed individuals identified by ancestry-based inference
    Daniel Wegmann
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
    Nat Genet 43:847-53. 2011
    ..These results suggest that outside of structurally variable regions, admixture does not substantially disrupt the factors controlling recombination rates in humans...
  14. pmc Finding haplotype block boundaries by using the minimum-description-length principle
    Eric C Anderson
    Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
    Am J Hum Genet 73:336-54. 2003
    ..than do other methods. These results suggest that our method may be useful for designing association-based mapping studies that exploit haplotype blocks...
  15. doi request reprint forqs: forward-in-time simulation of recombination, quantitative traits and selection
    Darren Kessner
    Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095 and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 30:576-7. 2014
    ..It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative traits...
  16. doi request reprint Characterizing bias in population genetic inferences from low-coverage sequencing data
    Eunjung Han
    Department of Biostatistics, University of California, Los Angeles
    Mol Biol Evol 31:723-35. 2014
    ..Thus, careful attention to the analysis pipeline and SFS estimation procedures is vital for population genetic inferences. ..
  17. pmc Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity
    Krishna R Veeramah
    Department of Eco and Evo Biol, Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, USA
    Eur J Hum Genet 19:995-1001. 2011
    ....
  18. ncbi request reprint Codon usage patterns in cytochrome oxidase I across multiple insect orders
    Joshua T Herbeck
    Division of Insect Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    J Mol Evol 56:691-701. 2003
    ..These shifts among codons in double-preference models are phylogenetically conservative...