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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol. 2024 ;42(1):139-147.
. Levels of the genealogical hierarchy and the problem of hominoid phylogeny. Am J Phys Anthropol. 1994 ;94(1):81-8.
. A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. Curr Biol. 2015 ;25(5):613-20.
. Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci U S A. 2002 ;99(22):14292-7.
. Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration. Nat Commun. 2019 ;10(1):5121.
. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms. In Silico Biol. 2007 ;7(2):195-200.
. P450 redox enzymes in the white rot fungus Phanerochaete chrysosporium: gene transcription, heterologous expression, and activity analysis on the purified proteins. Curr Microbiol. 2010 ;61(4):306-14.
. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res. 2006 ;16(11):1334-8.
. Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene. 2009 ;448(2):242-9.
. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol. 2004 ;11(5):1001-21.
. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol. 2020 ;18(12):e3000954.
. Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 2005 ;15(7):914-27.
. Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A. 2006 ;103(47):17626-31.
. Reorganization and expansion of the nidoviral family Arteriviridae. Arch Virol. 2016 ;161(3):755-68.
. Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nat Commun. 2018 ;9(1):859.
. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 ;344(6188):1168-1173.
. Simian T-lymphotropic virus type 1 (STLV-1) infection in wild yellow baboons (Papio hamadryas cynocephalus) from Mikumi National Park, Tanzania. Virology. 1997 ;228(2):350-9.
. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proc Natl Acad Sci U S A. 2010 ;107(50):21242-7.
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Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies. PLoS Genet. 2019 ;15(9):e1008208.
. 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.
. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol. 2020 ;20(1):33.
. Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol Biol Evol. 2003 ;20(9):1463-79.
. Variability of dopamine D4 receptor (DRD4) gene sequence within and among nonhuman primate species. Proc Natl Acad Sci U S A. 1995 ;92(2):427-31.
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