Published in Proc Natl Acad Sci U S A on January 27, 2003
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A (2004) 7.42
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res (2007) 7.34
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci U S A (2007) 4.54
Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res (2007) 4.52
The evolution of mammalian gene families. PLoS One (2006) 3.04
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res (2004) 2.94
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol (2007) 2.34
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol (2008) 2.33
Comparative genomics of major histocompatibility complexes. Immunogenetics (2004) 2.31
Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues. J Exp Med (2005) 2.23
Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc Natl Acad Sci U S A (2005) 2.18
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res (2004) 2.17
Why primate models matter. Am J Primatol (2014) 2.05
Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res (2004) 2.01
An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci (2007) 1.98
Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Philos Trans R Soc Lond B Biol Sci (2004) 1.96
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc Natl Acad Sci U S A (2006) 1.95
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 1.94
Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals. Proc Natl Acad Sci U S A (2005) 1.88
Filoviruses are ancient and integrated into mammalian genomes. BMC Evol Biol (2010) 1.87
Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci U S A (2007) 1.86
Comparative genomics of natural killer cell receptor gene clusters. PLoS Genet (2005) 1.85
Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proc Natl Acad Sci U S A (2003) 1.83
Varying environments can speed up evolution. Proc Natl Acad Sci U S A (2007) 1.81
Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans. BMC Evol Biol (2004) 1.75
Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals. PLoS One (2013) 1.75
Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol (2005) 1.75
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res (2004) 1.73
Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci U S A (2007) 1.72
Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res (2004) 1.72
Coadaptation in mother and infant regulated by a paternally expressed imprinted gene. Proc Biol Sci (2004) 1.72
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res (2011) 1.70
Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res (2004) 1.70
Evolutionary history of lagomorphs in response to global environmental change. PLoS One (2013) 1.68
New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primates. Proc Natl Acad Sci U S A (2007) 1.63
Accelerated rate of gene gain and loss in primates. Genetics (2007) 1.62
Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence. Proc Natl Acad Sci U S A (2004) 1.62
Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol (2012) 1.57
Origin and evolution of new exons in rodents. Genome Res (2005) 1.57
Characterization of intron loss events in mammals. Genome Res (2006) 1.56
Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates. Genome Res (2005) 1.56
Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet (2006) 1.55
Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res (2008) 1.54
Hotspots of mutation and breakage in dog and human chromosomes. Genome Res (2005) 1.54
A comparative view of face perception. J Comp Psychol (2010) 1.52
Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet (2009) 1.52
Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc Natl Acad Sci U S A (2009) 1.52
A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence. BMC Evol Biol (2007) 1.50
Robust time estimation reconciles views of the antiquity of placental mammals. PLoS One (2007) 1.49
The scaling of frontal cortex in primates and carnivores. Proc Natl Acad Sci U S A (2004) 1.48
A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res (2004) 1.48
Indel-based evolutionary distance and mouse-human divergence. Genome Res (2004) 1.47
Distribution of living Cupressaceae reflects the breakup of Pangea. Proc Natl Acad Sci U S A (2012) 1.44
The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res (2004) 1.41
Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol (2008) 1.41
Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium. PLoS One (2015) 1.41
Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution. BMC Evol Biol (2009) 1.40
Accelerated FoxP2 evolution in echolocating bats. PLoS One (2007) 1.34
The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews). Proc Natl Acad Sci U S A (2003) 1.33
An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genet (2008) 1.29
Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics (2005) 1.29
Evolution and survival on eutherian sex chromosomes. PLoS Genet (2009) 1.29
Computational challenges in the analysis of ancient DNA. Genome Biol (2010) 1.27
Positive Darwinian selection and the birth of an olfactory receptor clade in teleosts. Proc Natl Acad Sci U S A (2009) 1.27
The uncoupling protein 1 gene (UCP1) is disrupted in the pig lineage: a genetic explanation for poor thermoregulation in piglets. PLoS Genet (2006) 1.26
Loss of teeth and enamel in tetrapods: fossil record, genetic data and morphological adaptations. J Anat (2009) 1.26
The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philos Trans R Soc Lond B Biol Sci (2011) 1.24
The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. J Mol Evol (2007) 1.23
A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics (2006) 1.23
Loss of LINE-1 activity in the megabats. Genetics (2008) 1.21
A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India. Proc Natl Acad Sci U S A (2011) 1.21
Elephants and human color-blind deuteranopes have identical sets of visual pigments. Genetics (2005) 1.18
Integrating reptilian herpesviruses into the family herpesviridae. J Virol (2005) 1.18
The rise of army ants and their relatives: diversification of specialized predatory doryline ants. BMC Evol Biol (2014) 1.17
Social intelligence in the spotted hyena (Crocuta crocuta). Philos Trans R Soc Lond B Biol Sci (2007) 1.17
Comparison of predicted and actual consequences of missense mutations. Proc Natl Acad Sci U S A (2015) 1.17
Structural and functional annotation of the porcine immunome. BMC Genomics (2013) 1.16
Complex signatures of selection and gene conversion in the duplicated globin genes of house mice. Genetics (2007) 1.16
Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination. J Virol (2011) 1.16
The historical biogeography of Mammalia. Philos Trans R Soc Lond B Biol Sci (2011) 1.15
Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs. Genome Biol (2006) 1.13
Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora. Proc Biol Sci (2004) 1.13
Early Eocene lagomorph (Mammalia) from Western India and the early diversification of Lagomorpha. Proc Biol Sci (2008) 1.13
Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals. Syst Biol (2011) 1.12
Coexpression of linked genes in Mammalian genomes is generally disadvantageous. Mol Biol Evol (2008) 1.12
Parasite resistance and the adaptive significance of sleep. BMC Evol Biol (2009) 1.12
A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection. BMC Genomics (2006) 1.12
The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome Res (2004) 1.11
The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J Mol Evol (2008) 1.10
Additional remains of Wadilemur elegans, a primitive stem galagid from the late Eocene of Egypt. Proc Natl Acad Sci U S A (2005) 1.10
Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments. BMC Evol Biol (2008) 1.10
Optimizing culture conditions of a porcine epithelial cell line IPEC-J2 through a histological and physiological characterization. Cytotechnology (2011) 1.10
Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates. J Mol Evol (2006) 1.09
Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade. Proc Biol Sci (2007) 1.09
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett (2014) 1.08
Adaptive diversification of vomeronasal receptor 1 genes in rodents. J Mol Evol (2005) 1.07
Coordinated postnatal down-regulation of multiple growth-promoting genes: evidence for a genetic program limiting organ growth. FASEB J (2010) 1.07
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Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol (1998) 10.28
Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science (2001) 8.68
Molecular phylogenetics and the origins of placental mammals. Nature (2001) 8.42
Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol (2001) 6.69
Parallel adaptive radiations in two major clades of placental mammals. Nature (2001) 4.65
A compound poisson process for relaxing the molecular clock. Genetics (2000) 4.37
Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci U S A (2002) 3.38
Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol Evol (2002) 3.12
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Endemic African mammals shake the phylogenetic tree. Nature (1997) 2.30
A phylogenetic foundation for comparative mammalian genomics. Genome Inform (2001) 2.16
Molecular dating and biogeography of the early placental mammal radiation. J Hered (2001) 2.13
Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature (2002) 1.97
Integrated fossil and molecular data reconstruct bat echolocation. Proc Natl Acad Sci U S A (2001) 1.95
Molecular evidence regarding the origin of echolocation and flight in bats. Nature (2000) 1.94
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Sequence gaps join mice and men: phylogenetic evidence from deletions in two proteins. Mol Biol Evol (2002) 1.33
Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc Natl Acad Sci U S A (2002) 1.32
Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Syst Biol (1999) 1.19
Methods for high-density admixture mapping of disease genes. Am J Hum Genet (2004) 12.02
A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet (2004) 10.87
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HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection. Science (2004) 8.22
The influence of HLA genotype on AIDS. Annu Rev Med (2001) 7.77
Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat Genet (2002) 7.58
Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1. Nat Genet (2007) 6.83
A molecular phylogeny for bats illuminates biogeography and the fossil record. Science (2005) 6.47
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
A molecular phylogeny of living primates. PLoS Genet (2011) 5.61
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction. Nat Genet (2005) 4.45
Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nat Rev Genet (2005) 4.04
Common genetic variation and the control of HIV-1 in humans. PLoS Genet (2009) 3.68
Immunobiology of allogeneic hematopoietic stem cell transplantation. Annu Rev Immunol (2007) 3.65
Genetic restoration of the Florida panther. Science (2010) 3.59
Advances in graft-versus-host disease biology and therapy. Nat Rev Immunol (2012) 3.50
The late Miocene radiation of modern Felidae: a genetic assessment. Science (2006) 3.35
Mammalian phylogenomics comes of age. Trends Genet (2004) 3.31
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol (2008) 3.21
Coexpression of Tim-3 and PD-1 identifies a CD8+ T-cell exhaustion phenotype in mice with disseminated acute myelogenous leukemia. Blood (2011) 3.18
Molecules consolidate the placental mammal tree. Trends Ecol Evol (2004) 3.02
AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis. Nat Med (2005) 2.97
'Unlicensed' natural killer cells dominate the response to cytomegalovirus infection. Nat Immunol (2010) 2.57
Public stem cell banks: considerations of justice in stem cell research and therapy. Hastings Cent Rep (2004) 2.53
Donor B-cell alloantibody deposition and germinal center formation are required for the development of murine chronic GVHD and bronchiolitis obliterans. Blood (2011) 2.33
Defining the critical hurdles in cancer immunotherapy. J Transl Med (2011) 2.32
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res (2009) 2.30
Molecular and genomic data identify the closest living relative of primates. Science (2007) 2.26
Strong influence of human leukocyte antigen (HLA)-DP gene variants on development of persistent chronic hepatitis B virus carriers in the Han Chinese population. Hepatology (2011) 2.24
IFN-gamma mediates CD4+ T-cell loss and impairs secondary antitumor responses after successful initial immunotherapy. Nat Med (2007) 2.23
Aging predisposes to acute inflammatory induced pathology after tumor immunotherapy. J Exp Med (2013) 2.18
Molecular genetics and evolution of melanism in the cat family. Curr Biol (2003) 2.16
Cytonuclear genomic dissociation in African elephant species. Nat Genet (2004) 2.16
KIR/HLA pleiotropism: protection against both HIV and opportunistic infections. PLoS Pathog (2006) 2.06
Americans hear as well or better today compared with 40 years ago: hearing threshold levels in the unscreened adult population of the United States, 1959-1962 and 1999-2004. Ear Hear (2010) 2.04
The adequacy of morphology for reconstructing the early history of placental mammals. Syst Biol (2007) 2.03
APOBEC3G genetic variants and their influence on the progression to AIDS. J Virol (2004) 1.97
Elevated male European and female African contributions to the genomes of African American individuals. Hum Genet (2006) 1.97
The proteasome inhibitor PS-341 sensitizes neoplastic cells to TRAIL-mediated apoptosis by reducing levels of c-FLIP. Blood (2003) 1.97
Revision anterior cruciate ligament reconstruction: etiology of failures and clinical results. J Knee Surg (2004) 1.96
From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci U S A (2009) 1.95
Balanced polymorphism selected by genetic versus infectious human disease. Annu Rev Genomics Hum Genet (2002) 1.93
Behavioral risk exposure and host genetics of susceptibility to HIV-1 infection. J Infect Dis (2005) 1.89
Guidelines for naming nonprimate APOBEC3 genes and proteins. J Virol (2008) 1.86
Every genome sequence needs a good map. Genome Res (2009) 1.85
Inhibition of acute graft-versus-host disease with retention of graft-versus-tumor effects by the proteasome inhibitor bortezomib. Proc Natl Acad Sci U S A (2004) 1.85
Genome-wide scans for footprints of natural selection. Philos Trans R Soc Lond B Biol Sci (2010) 1.84
mAbs to Bacillus anthracis capsular antigen for immunoprotection in anthrax and detection of antigenemia. Proc Natl Acad Sci U S A (2004) 1.83
HLA-Cw*04 and hepatitis C virus persistence. J Virol (2002) 1.83
TLR agonists regulate alloresponses and uncover a critical role for donor APCs in allogeneic bone marrow rejection. Blood (2008) 1.82
CCL3L1 and HIV/AIDS susceptibility. Nat Med (2009) 1.73
Accounting for multiple comparisons in a genome-wide association study (GWAS). BMC Genomics (2010) 1.71
Natural killer cell subsets differentially reject embryonic stem cells based on licensing. Transplantation (2014) 1.70
The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics (2008) 1.69
Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples. Mol Ecol (2008) 1.68
Mouse Ly49G2+ NK cells dominate early responses during both immune reconstitution and activation independently of MHC. Blood (2011) 1.68
Mesozoic origin for West Indian insectivores. Nature (2004) 1.67
Patterns of molecular genetic variation among African elephant populations. Mol Ecol (2002) 1.64
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes. Genome Biol (2008) 1.63
A family matter: conclusive resolution of the taxonomic position of the long-fingered bats, miniopterus. Mol Biol Evol (2007) 1.62
Modulating influence on HIV/AIDS by interacting RANTES gene variants. Proc Natl Acad Sci U S A (2002) 1.61
Phylogeography and genetic ancestry of tigers (Panthera tigris). PLoS Biol (2004) 1.60
Using mutual information to measure the impact of multiple genetic factors on AIDS. J Acquir Immune Defic Syndr (2006) 1.59
Effects of human TRIM5alpha polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection. Virology (2006) 1.59
Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res (2009) 1.59
Genomics and conservation genetics. Trends Ecol Evol (2006) 1.57
Sensitization of tumor cells to NK cell-mediated killing by proteasome inhibition. J Immunol (2008) 1.57
Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS One (2008) 1.54
Comprehensive analysis of class I and class II HLA antigens and chronic hepatitis B virus infection. J Virol (2003) 1.52
Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet (2009) 1.52
Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One (2012) 1.52
Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange. Mol Phylogenet Evol (2006) 1.50
Suppression of natural killer cell-mediated bone marrow cell rejection by CD4+CD25+ regulatory T cells. Proc Natl Acad Sci U S A (2006) 1.47
Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species. J Virol (2005) 1.47
Inherited motor neuron disease in domestic cats: a model of spinal muscular atrophy. Pediatr Res (2005) 1.46
Mutation in CEP290 discovered for cat model of human retinal degeneration. J Hered (2007) 1.46
Arthroscopic release of the long head of the biceps tendon: functional outcome and clinical results. Am J Sports Med (2005) 1.46
Host programmed death ligand 1 is dominant over programmed death ligand 2 expression in regulating graft-versus-host disease lethality. Blood (2013) 1.44
Restoring tigers to the Caspian region. Science (2011) 1.43
Molecular evidence for species-level distinctions in clouded leopards. Curr Biol (2006) 1.41
IL-10 and TGF-beta induce alloreactive CD4+CD25- T cells to acquire regulatory cell function. Blood (2003) 1.40
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res (2005) 1.40
Tissue sampling methods and standards for vertebrate genomics. Gigascience (2012) 1.39
Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals". Science (2013) 1.39
Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol Phylogenet Evol (2010) 1.39
NCI First International Workshop on The Biology, Prevention, and Treatment of Relapse After Allogeneic Hematopoietic Stem Cell Transplantation: Report from the Committee on the Biology Underlying Recurrence of Malignant Disease following Allogeneic HSCT: Graft-versus-Tumor/Leukemia Reaction. Biol Blood Marrow Transplant (2010) 1.38
Ibrutinib treatment ameliorates murine chronic graft-versus-host disease. J Clin Invest (2014) 1.38