Published in Mol Biol Evol on February 12, 2004
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
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67
The influence of recombination on human genetic diversity. PLoS Genet (2006) 4.04
Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32
The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet (2008) 3.16
Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res (2007) 3.16
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res (2010) 2.37
Why do human diversity levels vary at a megabase scale? Genome Res (2005) 2.33
The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res (2010) 2.26
The scale of mutational variation in the murid genome. Genome Res (2005) 1.95
Hotspots of biased nucleotide substitutions in human genes. PLoS Biol (2009) 1.89
Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res (2004) 1.73
Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res (2007) 1.72
The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res (2010) 1.72
Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Res (2005) 1.70
Variable molecular clocks in hominoids. Proc Natl Acad Sci U S A (2006) 1.66
A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics (2012) 1.65
Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res (2011) 1.62
Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc Biol Sci (2006) 1.62
Heterogeneous genomic molecular clocks in primates. PLoS Genet (2006) 1.55
Mammalian GC content is very close to mutational equilibrium. J Mol Evol (2005) 1.55
Hotspots of mutation and breakage in dog and human chromosomes. Genome Res (2005) 1.54
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res (2010) 1.52
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol (2008) 1.41
The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. BMC Evol Biol (2015) 1.41
GC-biased segregation of noncoding polymorphisms in Drosophila. Genetics (2005) 1.40
Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol (2011) 1.36
Stable recombination hotspots in birds. Science (2015) 1.36
Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput Biol (2008) 1.35
The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics (2008) 1.33
CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol (2008) 1.30
Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res (2005) 1.27
Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci (2010) 1.25
Recombination is associated with the evolution of genome structure and worker behavior in honey bees. Proc Natl Acad Sci U S A (2012) 1.22
Recombination drives vertebrate genome contraction. PLoS Genet (2012) 1.20
Genomic and proteomic adaptations to growth at high temperature. Genome Biol (2004) 1.20
CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res (2008) 1.19
Evolution of heterochromatic genes of Drosophila. Proc Natl Acad Sci U S A (2005) 1.19
Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol (2011) 1.17
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res (2008) 1.16
Recombination rate variation in closely related species. Heredity (Edinb) (2011) 1.16
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res (2004) 1.14
Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A (2005) 1.13
Molecular evolution of genes in avian genomes. Genome Biol (2010) 1.12
Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biol (2004) 1.11
Recombination spot identification Based on gapped k-mers. Sci Rep (2016) 1.09
The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol (2011) 1.08
Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics (2012) 1.07
Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction. PLoS Genet (2012) 1.04
Patterns and evolution of nucleotide landscapes in seed plants. Plant Cell (2012) 1.04
The influence of genomic context on mutation patterns in the human genome inferred from rare variants. Genome Res (2013) 1.04
Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome. Genetics (2012) 1.02
Both selective and neutral processes drive GC content evolution in the human genome. BMC Evol Biol (2008) 1.02
Statistical signals in bioinformatics. Proc Natl Acad Sci U S A (2005) 1.01
Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol (2012) 1.00
Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome. Genome Biol Evol (2012) 0.99
Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol (2011) 0.99
The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol (2011) 0.98
Codon usage is associated with the evolutionary age of genes in metazoan genomes. BMC Evol Biol (2009) 0.98
Evolutionary rate variation in Old World monkeys. Biol Lett (2009) 0.97
Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype. Mol Biol Evol (2013) 0.97
Evolution of gene sequence in response to chromosomal location. Genetics (2007) 0.97
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics (2006) 0.97
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol (2013) 0.95
Biased distributions and decay of long interspersed nuclear elements in the chicken genome. Genetics (2007) 0.95
Surprising fitness consequences of GC-biased gene conversion: I. Mutation load and inbreeding depression. Genetics (2010) 0.94
GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome. Genetics (2009) 0.94
Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events. BMC Evol Biol (2005) 0.94
The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model. J Mol Evol (2006) 0.94
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol (2005) 0.93
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J Mol Evol (2006) 0.93
Phase distribution of spliceosomal introns: implications for intron origin. BMC Evol Biol (2006) 0.92
Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics (2009) 0.92
Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes. BMC Evol Biol (2010) 0.92
Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biol (2007) 0.89
GC-biased evolution near human accelerated regions. PLoS Genet (2010) 0.89
Recombination in the human Pseudoautosomal region PAR1. PLoS Genet (2014) 0.89
Three tiers of genome evolution in reptiles. Integr Comp Biol (2008) 0.88
Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome. Genome Res (2010) 0.88
Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol Biol Evol (2013) 0.88
Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics (2011) 0.87
Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome. BMC Bioinformatics (2009) 0.87
Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics (2012) 0.87
Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. BMC Genomics (2011) 0.86
Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles. Genome Biol Evol (2013) 0.85
Long-range bidirectional strand asymmetries originate at CpG islands in the human genome. Genome Biol Evol (2009) 0.85
The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes. PLoS Genet (2014) 0.84
The evolution of transcription-associated biases of mutations across vertebrates. BMC Evol Biol (2010) 0.84
Substitution patterns are under different influences in primates and rodents. Genome Biol Evol (2011) 0.83
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet (2015) 0.82
The correlation between recombination rate and dinucleotide bias in Drosophila melanogaster. J Mol Evol (2008) 0.82
The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol (2012) 0.82
Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes. PLoS One (2008) 0.82
Quartet-based methods to reconstruct phylogenetic networks. BMC Syst Biol (2014) 0.82
NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations. PLoS One (2013) 0.82
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet (2010) 2.20
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet (2007) 2.18
Translational control of intron splicing in eukaryotes. Nature (2008) 2.15
Neutral effect of recombination on base composition in Drosophila. Genet Res (2003) 2.11
Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res (2002) 2.04
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun (2011) 2.03
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci U S A (2004) 1.98
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res (2013) 1.83
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet (2011) 1.63
Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol (2006) 1.62
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet (2008) 1.54
ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics (2004) 1.53
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet (2010) 1.53
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics (2011) 1.40
HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res (2005) 1.38
The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS Genet (2012) 1.38
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet (2004) 1.33
No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol Biol Evol (2005) 1.32
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies. Nucleic Acids Res (2007) 1.28
Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci (2010) 1.25
XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat Genet (2013) 1.20
Evidence that functional transcription units cover at least half of the human genome. Trends Genet (2004) 1.15
Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A (2005) 1.13
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics (2010) 1.12
Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res (2003) 1.11
Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation. Mol Biol Evol (2004) 1.09
Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J Mol Evol (2002) 1.06
Polymorphix: a sequence polymorphism database. Nucleic Acids Res (2005) 1.03
Placenta-specific INSL4 expression is mediated by a human endogenous retrovirus element. Biol Reprod (2002) 1.03
Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol (2009) 1.02
Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol (2012) 1.00
The relationship between DNA replication and human genome organization. Mol Biol Evol (2009) 1.00
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics (2004) 0.99
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol (2013) 0.99
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol (2013) 0.95
Unexpected observations after mapping LongSAGE tags to the human genome. BMC Bioinformatics (2007) 0.95
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J Mol Evol (2006) 0.93
Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Genetics (2003) 0.92
Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat (2011) 0.91
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis. Mol Cell Proteomics (2007) 0.89
Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet (2009) 0.89
Natural history of the ERVWE1 endogenous retroviral locus. Retrovirology (2005) 0.88
Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA. Cold Spring Harb Protoc (2010) 0.87
Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form. FEMS Microbiol Lett (2003) 0.87
Paramecium tetraurelia: the renaissance of an early unicellular model. Cold Spring Harb Protoc (2010) 0.86
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
Mass culture of Paramecium tetraurelia. Cold Spring Harb Protoc (2010) 0.81
Immunocytochemistry of Paramecium cytoskeletal structures. Cold Spring Harb Protoc (2010) 0.81
Maintaining clonal Paramecium tetraurelia cell lines of controlled age through daily reisolation. Cold Spring Harb Protoc (2010) 0.80
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome. Mol Biol Evol (2013) 0.78
DNA microinjection into the macronucleus of paramecium. Cold Spring Harb Protoc (2010) 0.78
Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region. Eur J Hum Genet (2004) 0.78
Optimization of multiplexed RADseq libraries using low-cost adaptors. Genetica (2015) 0.76
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition. Mol Biol Evol (2017) 0.75
Bioinformatics with a French accent. Genome Biol (2005) 0.75