individual publications

• academic article

  • Balancing selection maintains a form of ERAP2 tat undergoes nonsense-mediated decay and affects antigen presentation.  PLoS Genetics.  6. 2010
  • Darwinian and demographic forces affecting human protein coding genes.  Genome Research.  19:838-849. 2009
  • Evolutionary processes acting on non‐coding DNA in humans inferred from patterns of polymorphism and divergence. PLoS Genetics .  PLoS Genetics.  5. 2009
  • Targets of balancing selection in the human genome.  Molecular Biology and Evolution.  26:2755-2764. 2009
  • Assessing the evolutionary impact of amino acid mutations in the human genome.  PLoS Genetics.  4. 2008
  • Patterns of positive selection in six mammalian genomes.  PLoS Genetics.  4. 2008
  • Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.  Genome Res.  18:1020-1029. 2008
  • Proportionally More Deleterious Variation in European than in African Populations.  Nature.  451:994-997. 2008
  • Genetic Variation Reveals Diametric Demographic Histories for Chinese and Indian Rhesus Macaques.  Science.  316:240-3. 2007
  • Genome-wide patterns of nucleotide polymorphism in domesticated Asian rice (Oryza sativa).  PLoS Genetics.  3:1745-56. 2007
  • Localizing recent adaptive evolution in the human genome.  PLoS Genetics.  3. 2007
  • Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila.  Molecular Biology and Evolution.  24:228-235. 2007
  • Patterns of Mutation and Selection at Synonymous Sites in Drosophila.  Molecular Biology and Evolution.  24:2687-2697. 2007
  • Recent and ongoing selection in the human genome.  Nat Rev Genet..  8:857-68. 2007
  • A novel method for same source cluster analysis in phylogenetic trees shows that Listeria monocytogenes contains niche-adapted clonal groups with distinct ecological preferences.  Journal of Clinical Microbiology.  44. 2006
  • CpG + CpNpG analysis of protein-coding sequences from tomato.  Molecular Biology and Evolution.  23:1318-1323. 2006
  • CpG plus CpNpG analysis of protein-coding sequences from tomato.  Molecular Biology and Evolution.  23:1318-1323. 2006
  • A scan for positively selected genes in the genomes of humans and chimpanzees.  PLoS Biology.  3. 2005
  • Ascertainment bias in studies of human genome-wide polymorphism.  Genome Research.  15:1496-1502. 2005
  • Bayesian and maximum likelihood estimation of genetic maps.  Genetical Research.  85:159-168. 2005
  • Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.  Theoretical and Applied Genetics.  112:72-84. 2005
  • Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.  Theoretical and Applied Genetics.  112:72-84. 2005
  • Comparative sequencing and analysis of Drosophila pseudoobscura.  Genome Res.  15:1-18. 2005
  • Detecting coevolving amino acid substitutions using Bayesian mutational mapping.  ISMB / Bioinformatics.  21 . 2005
  • Detecting site-specific physicochemical selective pressures: applications to the class-I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system.  Journal of Molecular Evolution.  60:315-326. 2005
  • Genomic scans for selective sweeps using SNP data.  Genome.  15:1566-75. 2005
  • Natural Selection on Protein-Coding Genes in the Human Genome.  Nature.  437:1153-7. 2005
  • Simultaneous inference of selection and population growth from patterns of variation in the human genome.  Proceedings of the National Academy of Sciences (PNAS).  102:7882-7. 2005
  • The population structure of African cultivated rice Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation.  Genetics.  169:1639-1647. 2005
  • Microsatellite mutation models:Insights from a comparison of humans and chimpanzees.  Genetics.  168:383-395. 2004
  • Reconstituting the frequency spectrum of ascertained SNP data.  Genetics.  168:2373-2382. 2004
  • Estimating effective paternity number in social insects and the effective number of alleles in a population.  Molecular Ecology.  12:3157-3164. 2003
  • Inferring non‐neutral evolution from human‐chimp‐mouse orthologous gene trios.  Science.  302:1960-1963. 2003
  • Linkage disequilibrium and inference of population‐level recombination at 538 sites across the human genome.  Amer. J. Human Genet.  73:285-300. 2003
  • Maximum Likelihood and Bayesian Methods for Estimating the Distribution of Selective Effects among Classes of Mutations Using DNA Polymorphism Data.  Theoretical Population Biology.  63:91-103. 2003
  • Positive selection in the human genome inferred from human‐chimp‐mouse orthologous gene alignments.  Cold Spr. Harbor Symp. Quant. Biol.  68:471-477. 2003
  • A Maximum Likelihood Method for Analyzing Pseudogene Evolution: Implications for Silent Site Evolution in Humans and Rodents.  Molecular Biology and Evolution.  19:110-7. 2002
  • The Cost of Inbreeding: Fixation of Deleterious Genes in Arabidopsis.  Nature.  416:531-534. 2002