Publications
Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol Biol Evol. 2003 ;20(9):1463-79.
. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. Mol Phylogenet Evol. 2014 ;75:126-37.
. Unlocking the bovine genome. BMC Genomics. 2009 ;10:193.
. Treponema pallidum infection in the wild baboons of East Africa: distribution and genetic characterization of the strains responsible. PLoS One. 2012 ;7(12):e50882.
. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017 ;8:14061.
. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature. 2012 ;483(7387):82-6.
. Stress, genomes, and evolution. Cell Stress Chaperones. 2010 ;15(5):463-6.
. Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nat Commun. 2018 ;9(1):859.
. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res. 2009 ;19(2):167-77.
. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 ;432(7018):695-716.
Sequence analysis in reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res. 2020 ;30(12):1716-1726.
. Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS One. 2020 ;15(8):e0236285.
. Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A. 2006 ;103(47):17626-31.
. Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 2005 ;15(7):914-27.
. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res. 2016 ;26(12):1651-1662.
. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015 ;47(12):1435-42.
. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput. 2008 ;:102-13.
. P450ome of the white rot fungus Phanerochaete chrysosporium: structure, evolution and regulation of expression of genomic P450 clusters. Biochem Soc Trans. 2006 ;34(Pt 6):1165-9.
. Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. J Gen Virol. 2010 ;91(Pt 9):2203-15.
. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol. 2019 ;20(1):64.
. Mapping the -regulatory architecture of the human retina reveals noncoding genetic variation in disease. Proc Natl Acad Sci U S A. 2020 ;117(16):9001-9012.
. A map of human genome variation from population-scale sequencing. Nature. 2010 ;467(7319):1061-73.
. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014 ;508(7497):494-9.
. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 ;423(6942):825-37.
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