Published in Genome Biol Evol on January 01, 2012
Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data. PLoS Genet (2013) 1.03
Hand before foot? Cortical somatotopy suggests manual dexterity is primitive and evolved independently of bipedalism. Philos Trans R Soc Lond B Biol Sci (2013) 0.77
The role of DNA insertions in phenotypic differentiation between humans and other primates. Genome Biol Evol (2015) 0.76
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
A fine-scale map of recombination rates and hotspots across the human genome. Science (2005) 26.82
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67
Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform (2008) 22.07
Evolution at two levels in humans and chimpanzees. Science (1975) 21.07
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
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Simple methods for testing the molecular evolutionary clock hypothesis. Genetics (1993) 11.26
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet (2001) 9.35
Variation in genome-wide mutation rates within and between human families. Nat Genet (2011) 8.84
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci U S A (2010) 7.07
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Genetic evidence for complex speciation of humans and chimpanzees. Nature (2006) 6.66
Fast and flexible simulation of DNA sequence data. Genome Res (2008) 4.45
Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol (1995) 4.31
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J Mol Evol (1984) 4.04
Isolation with migration models for more than two populations. Mol Biol Evol (2009) 4.01
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Immunological time scale for hominid evolution. Science (1967) 3.76
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet (2006) 3.53
Variation in the mutation rate across mammalian genomes. Nat Rev Genet (2011) 3.09
Late Miocene hominids from the Middle Awash, Ethiopia. Nature (2001) 3.03
Genes and speciation. Nat Rev Genet (2004) 2.94
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol (2008) 2.90
Primate molecular divergence dates. Mol Phylogenet Evol (2006) 2.77
Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia. Nature (1994) 2.52
A new species of great ape from the late Miocene epoch in Ethiopia. Nature (2007) 2.46
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics (2002) 2.41
Genetics and the making of Homo sapiens. Nature (2003) 2.20
Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci U S A (1997) 2.13
X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content. Genome Res (1997) 2.06
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res (2011) 1.88
New material of the earliest hominid from the Upper Miocene of Chad. Nature (2005) 1.66
Variable molecular clocks in hominoids. Proc Natl Acad Sci U S A (2006) 1.66
On the estimation of ancestral population sizes of modern humans. Genet Res (1997) 1.58
Ancestral population genomics: the coalescent hidden Markov model approach. Genetics (2009) 1.54
A physical map of human chromosome 7: an integrated YAC contig map with average STS spacing of 79 kb. Genome Res (1997) 1.53
A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans. Proc Natl Acad Sci U S A (2007) 1.38
Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput Biol (2008) 1.35
The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol Biol Evol (2006) 1.31
Inferring the mode of speciation from genomic data: a study of the great apes. Genetics (2005) 1.27
Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. J Mol Evol (2004) 1.12
Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution. Proc Natl Acad Sci U S A (2012) 1.12
Anthropology. Apes among the tangled branches of human origins. Science (2010) 1.02
Timing of replication is a determinant of neutral substitution rates but does not explain slow Y chromosome evolution in rodents. Mol Biol Evol (2009) 1.02
A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol Evol (2010) 1.01
Colloquium paper: reconstructing human evolution: achievements, challenges, and opportunities. Proc Natl Acad Sci U S A (2010) 0.97
Generation time and effective population size in Polar Eskimos. Proc Biol Sci (2008) 0.96
A web tool for comparative genomics: G-compass. Gene (2005) 0.94
Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates. Genome Biol Evol (2009) 0.88
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. Bioinformatics (2009) 0.86
An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Mol Biol Evol (2011) 0.83
Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes. BMC Evol Biol (2011) 0.79
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet (2006) 3.76
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res (2006) 2.90
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc Natl Acad Sci U S A (2002) 2.00
Loss of urate oxidase activity in hominoids and its evolutionary implications. Mol Biol Evol (2002) 2.00
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc Natl Acad Sci U S A (2003) 1.64
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A (2003) 1.43
Coevolution of the S-locus genes SRK, SLG and SP11/SCR in Brassica oleracea and B. rapa. Genetics (2002) 1.42
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res (2005) 1.39
Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Hum Mol Genet (2005) 1.36
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res (2006) 1.34
A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol (2005) 1.34
Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution. Genetics (2005) 1.34
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res (2007) 1.32
Lineage-specific loss of function of bitter taste receptor genes in humans and nonhuman primates. Genetics (2005) 1.31
Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene (2005) 1.27
Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene (2006) 1.26
Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system. Gene (2005) 1.26
The dominance of alleles controlling self-incompatibility in Brassica pollen is regulated at the RNA level. Plant Cell (2002) 1.26
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
The origin and genetic variation of domestic chickens with special reference to junglefowls Gallus g. gallus and G. varius. PLoS One (2010) 1.20
H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Res (2006) 1.20
Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol Biol Evol (2002) 1.18
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res (2009) 1.16
Origins of mouse inbred strains deduced from whole-genome scanning by polymorphic microsatellite loci. Mamm Genome (2005) 1.12
The origin and evolution of human ampliconic gene families and ampliconic structure. Genome Res (2006) 1.03
The evolutionary relationship between gene duplication and alternative splicing. Gene (2008) 1.02
Preservation of a pseudogene by gene conversion and diversifying selection. Genetics (2008) 1.01
H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic Acids Res (2009) 1.00
Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene (2006) 1.00
Persistence of Mhc heterozygosity in homozygous clonal killifish, Rivulus marmoratus: implications for the origin of hermaphroditism. Genetics (2002) 0.99
Distribution and effects of nonsense polymorphisms in human genes. PLoS One (2008) 0.99
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Res (2008) 0.98
Evolutionary history of the cancer immunity antigen MAGE gene family. PLoS One (2011) 0.98
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Res (2008) 0.97
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res (2012) 0.97
A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evol Biol (2007) 0.96
Natural selection in the TLR-related genes in the course of primate evolution. Immunogenetics (2008) 0.95
Phylogenetic analyses of Zostera species based on rbcL and matK nucleotide sequences: implications for the origin and diversification of seagrasses in Japanese waters. Genes Genet Syst (2003) 0.95
A web tool for comparative genomics: G-compass. Gene (2005) 0.94
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. BMC Syst Biol (2012) 0.94
Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study. Proteins (2007) 0.93
Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals. Genetics (2006) 0.90
Gene flow between species of Lake Victoria haplochromine fishes. Mol Biol Evol (2007) 0.90
Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evol Biol (2010) 0.90
Divergence, demography and gene loss along the human lineage. Philos Trans R Soc Lond B Biol Sci (2010) 0.89
[H-Invitational Database: integrated database of human genes]. Tanpakushitsu Kakusan Koso (2004) 0.87
Evolution of the CYP2D gene cluster in humans and four non-human primates. Genes Genet Syst (2011) 0.87
Frequent segmental sequence exchanges and rapid gene duplication characterize the MHC class I genes in lemurs. Immunogenetics (2003) 0.87
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. Nucleic Acids Res (2006) 0.86
Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome. Gene (2007) 0.86
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. Bioinformatics (2009) 0.86
Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains. Gene (2005) 0.85
Mhc-DRB genes evolution in lemurs. Immunogenetics (2002) 0.85
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. Nucleic Acids Res (2010) 0.84
Current perspectives on the intensity of natural selection of MHC loci. Immunogenetics (2013) 0.84
Evolutionary relationships of major histocompatibility complex class I genes in simian primates. Genetics (2004) 0.84
Comparative analysis of the S-intergenic region in class-II S haplotypes of self-incompatible Brassica rapa (syn. campestris). Genes Genet Syst (2006) 0.83
Estimation of the highest chromosome number of eukaryotes based on the minimum interaction theory. J Theor Biol (2002) 0.83
Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans. Genetics (2008) 0.83
No evidence for a second evolutionary stratum during the early evolution of mammalian sex chromosomes. PLoS One (2012) 0.82
In vivo function and evolution of the eutherian-specific pluripotency marker UTF1. PLoS One (2013) 0.81
Evolutionary growth process of highly conserved sequences in vertebrate genomes. Gene (2012) 0.80
MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus. BMC Evol Biol (2012) 0.80
The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes. Gene (2009) 0.79
Evolution of genomic structures on Mammalian sex chromosomes. Curr Genomics (2012) 0.79
A prioritization analysis of disease association by data-mining of functional annotation of human genes. Genomics (2011) 0.79
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. BMC Genomics (2008) 0.79
A human-specific allelic group of the MHC DRB1 gene in primates. J Physiol Anthropol (2014) 0.79
Identification of CTL epitopes in hepatitis C virus by a genome-wide computational scanning and a rational design of peptide vaccine. Immunogenetics (2007) 0.79
Novel algorithm for automated genotyping of microsatellites. Nucleic Acids Res (2004) 0.79
Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes. BMC Evol Biol (2011) 0.79
Prediction of protein-destabilizing polymorphisms by manual curation with protein structure. PLoS One (2012) 0.78
Evolutionary history of sex-linked mammalian amelogenin genes. Cells Tissues Organs (2007) 0.78
A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evol Biol (2010) 0.78
On the origin and function of an insertion element VPaI-1 specific to post-1995 pandemic Vibrio parahaemolyticus strains. Genes Genet Syst (2008) 0.77
Evolutionary origin of peptidoglycan recognition proteins in vertebrate innate immune system. BMC Evol Biol (2011) 0.77
RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations. Database (Oxford) (2013) 0.77
Biological implication for loss of function at major histocompatibility complex loci. Immunogenetics (2008) 0.77
Characteristic beta-globin gene cluster haplotypes of Evenkis and Oroqens in north China. Hum Biol (2004) 0.77
Characteristics of the beta-globin gene cluster haplotypes of three Han Chinese populations at Beijing, Xi'an, and Kunming as compared with those of other Asian populations. Biochem Genet (2008) 0.77
Computational analysis and functional expression of ancestral copepod luciferase. Gene (2013) 0.76
Genomic structure and evolution of multigene families: "flowers" on the human genome. Int J Evol Biol (2012) 0.76
[Human transcriptome]. Tanpakushitsu Kakusan Koso (2005) 0.75
[The origin and diversity of PGRP gene family]. Tanpakushitsu Kakusan Koso (2004) 0.75
Beta-globin gene cluster haplotype frequencies in Khalkhs and Buryats of Mongolia. Hum Biol (2006) 0.75