Published in PLoS Genet on August 30, 2012
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol (2015) 2.19
Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet (2014) 1.72
Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations. Mol Ecol (2014) 1.61
A role for ultrasonic vocalisation in social communication and divergence of natural populations of the house mouse (Mus musculus domesticus). PLoS One (2014) 1.57
Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach. BMC Genomics (2016) 1.38
Computational approaches to species phylogeny inference and gene tree reconciliation. Trends Ecol Evol (2013) 1.10
Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome (2012) 1.08
Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Mol Biol Evol (2014) 1.05
Maximum likelihood inference of reticulate evolutionary histories. Proc Natl Acad Sci U S A (2014) 0.97
Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite. PLoS One (2014) 0.95
Hybridization reveals the evolving genomic architecture of speciation. Cell Rep (2013) 0.94
Incompatibility between Nuclear and Mitochondrial Genomes Contributes to an Interspecies Reproductive Barrier. Cell Metab (2016) 0.93
Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea. Mol Ecol (2014) 0.91
Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinformatics (2013) 0.89
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Mol Ecol (2016) 0.88
An HMM-based comparative genomic framework for detecting introgression in eukaryotes. PLoS Comput Biol (2014) 0.88
Interspecific introgressive origin of genomic diversity in the house mouse. Proc Natl Acad Sci U S A (2014) 0.88
Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Res (2015) 0.87
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. Elife (2014) 0.87
A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genomics (2015) 0.86
Insights into mammalian biology from the wild house mouse Mus musculus. Elife (2015) 0.85
Heterogeneity of genetic architecture of body size traits in a free-living population. Mol Ecol (2015) 0.84
Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus). Front Genet (2014) 0.84
R2d2 Drives Selfish Sweeps in the House Mouse. Mol Biol Evol (2016) 0.82
Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. Sci Data (2016) 0.81
Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot. BMC Evol Biol (2015) 0.81
Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet (2015) 0.81
Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. Evolution (2015) 0.80
Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus). Ecol Evol (2013) 0.80
Genomic copy number variation in Mus musculus. BMC Genomics (2015) 0.79
Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse. Mol Ecol (2015) 0.79
Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest. BMC Bioinformatics (2014) 0.78
Wild mice as bountiful resources of novel genetic variants for quantitative traits. Curr Genomics (2013) 0.78
Determining population structure and hybridization for two iris species. Ecol Evol (2014) 0.78
Introgression in the Drosophila subobscura--D. Madeirensis sister species: evidence of gene flow in nuclear genes despite mitochondrial differentiation. Evolution (2013) 0.78
Properties of different selection signature statistics and a new strategy for combining them. Heredity (Edinb) (2015) 0.78
Functional organization of the genome may shape the species boundary in the house mouse. Mol Biol Evol (2015) 0.77
Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953. BMC Evol Biol (2015) 0.77
A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. BMC Bioinformatics (2016) 0.76
Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach. Genome Biol Evol (2017) 0.76
Mistaken Identity: Another Bias in the Use of Relative Genetic Divergence Measures for Detecting Interspecies Introgression. PLoS One (2016) 0.75
Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus). BMC Evol Biol (2015) 0.75
Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution. PLoS One (2015) 0.75
High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep. Heredity (Edinb) (2015) 0.75
Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity (Edinb) (2016) 0.75
Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence. Mol Biol Evol (2014) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (2004) 125.23
Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics (2002) 34.50
A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet (2006) 28.32
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
A draft sequence of the Neandertal genome. Science (2010) 19.55
Positive natural selection in the human lineage. Science (2006) 12.55
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol (2010) 8.69
Diet and the evolution of human amylase gene copy number variation. Nat Genet (2007) 8.64
Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase. Nat Genet (2000) 7.83
Hybrid speciation. Nature (2007) 6.52
Germline mutations of the gene encoding bone morphogenetic protein receptor 1A in juvenile polyposis. Nat Genet (2001) 6.36
Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet (2009) 6.36
The signature of positive selection at randomly chosen loci. Genetics (2002) 6.06
Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res (2009) 5.88
A composite of multiple signals distinguishes causal variants in regions of positive selection. Science (2010) 5.61
The role of hybridization in evolution. Mol Ecol (2001) 5.46
A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol (2006) 4.57
Melanopsin (Opn4) requirement for normal light-induced circadian phase shifting. Science (2002) 4.24
Classic selective sweeps were rare in recent human evolution. Science (2011) 4.09
A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol (2007) 3.71
A customized and versatile high-density genotyping array for the mouse. Nat Methods (2009) 3.53
Individual recognition in mice mediated by major urinary proteins. Nature (2001) 3.09
Next generation software for functional trend analysis. Bioinformatics (2009) 3.01
Wild mice: an ever-increasing contribution to a popular mammalian model. Trends Genet (2003) 2.93
Genetics and the fitness of hybrids. Annu Rev Genet (2001) 2.56
Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics (2008) 2.53
Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Curr Biol (2011) 2.48
Genome-wide patterns of gene flow across a house mouse hybrid zone. Genome Res (2007) 2.47
Population differentiation as a test for selective sweeps. Genome Res (2010) 2.08
Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol (2008) 1.96
Genome-wide scans for footprints of natural selection. Philos Trans R Soc Lond B Biol Sci (2010) 1.84
Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genet (2009) 1.83
The cell cycle control gene ZAC/PLAGL1 is imprinted--a strong candidate gene for transient neonatal diabetes. Hum Mol Genet (2000) 1.76
Asymmetry and polymorphism of hybrid male sterility during the early stages of speciation in house mice. Evolution (2007) 1.74
An ancient evolutionary origin of genes associated with human genetic diseases. Mol Biol Evol (2008) 1.73
Reduced X-linked diversity in derived populations of house mice. Genetics (2007) 1.70
Linkage disequilibrium in wild mice. PLoS Genet (2007) 1.70
The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS Genet (2009) 1.63
An analysis of signatures of selective sweeps in natural populations of the house mouse. Mol Biol Evol (2006) 1.62
Zac1 (Lot1), a potential tumor suppressor gene, and the gene for epsilon-sarcoglycan are maternally imprinted genes: identification by a subtractive screen of novel uniparental fibroblast lines. Mol Cell Biol (2000) 1.61
Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.). Mol Ecol (2011) 1.58
Nucleotide variation in wild and inbred mice. Genetics (2007) 1.55
Understanding the onset of hybrid speciation. Trends Genet (2010) 1.50
Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol (2008) 1.44
Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe. Mol Ecol (2007) 1.42
Genetic evidence for hybrid trait speciation in heliconius butterflies. PLoS Genet (2010) 1.31
Evolution of the mouse t haplotype: recent and worldwide introgression to Mus musculus. Proc Natl Acad Sci U S A (1992) 1.10
Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans. Genetics (2008) 1.10
Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone. Mol Ecol (2011) 1.07
Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies. Genome Biol (2007) 1.00
Phactr2 and Parkinson's disease. Neurosci Lett (2009) 0.87
A test of the neutral model of expression change in natural populations of house mouse subspecies. Evolution (2009) 0.86
Impaired auditory-vestibular functions and behavioral abnormalities of Slitrk6-deficient mice. PLoS One (2011) 0.86
Evolutionary biology: a basic science for medicine in the 21st century. Perspect Biol Med (2011) 0.77
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Global diversity in the human salivary microbiome. Genome Res (2009) 5.16
Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A (2013) 5.03
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
DNA points the way ahead in taxonomy. Nature (2002) 3.86
Selection on codon bias. Annu Rev Genet (2008) 3.83
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (2010) 3.00
Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet (2010) 2.95
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science (2005) 2.56
An evolutionary analysis of orphan genes in Drosophila. Genome Res (2003) 2.52
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet (2010) 2.41
The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot (2005) 2.33
Parallel selection mapping using artificially selected mice reveals body weight control loci. Curr Biol (2012) 2.33
Modeling recent human evolution in mice by expression of a selected EDAR variant. Cell (2013) 2.17
A segmentation gene in tribolium produces a polycistronic mRNA that codes for multiple conserved peptides. Cell (2006) 2.06
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet (2007) 2.06
Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol (2004) 1.96
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics (2007) 1.89
Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol (2010) 1.87
Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A (2009) 1.78
Drosophila melanogaster recombination rate calculator. Gene (2010) 1.78
An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Front Zool (2007) 1.75
An ancient evolutionary origin of genes associated with human genetic diseases. Mol Biol Evol (2008) 1.73
Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol (2003) 1.72
General rules for optimal codon choice. PLoS Genet (2009) 1.71
Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philos Trans R Soc Lond B Biol Sci (2005) 1.70
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
An analysis of signatures of selective sweeps in natural populations of the house mouse. Mol Biol Evol (2006) 1.62
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol (2013) 1.60
Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.). Mol Ecol (2011) 1.58
Bis{μ-2,2'-[ethane-1,2-diylbis(nitrilo-methyl-idyne)]diphenolato}bis-[(thio-cyanato)manganese(III)]. Acta Crystallogr Sect E Struct Rep Online (2008) 1.57
Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One (2009) 1.53
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
Understanding the onset of hybrid speciation. Trends Genet (2010) 1.50
Emergence of a new gene from an intergenic region. Curr Biol (2009) 1.47
Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res (2006) 1.46
An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proc Biol Sci (2005) 1.45
Tris[2-(propyl-imino-meth-yl)phenolato-κN,O]cobalt(III). Acta Crystallogr Sect E Struct Rep Online (2008) 1.45
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
Reduced selection leads to accelerated gene loss in Shigella. Genome Biol (2007) 1.41
Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal Biochem (2009) 1.40
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet (2005) 1.39
Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci U S A (2013) 1.37
Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet (2013) 1.34
Identifying genes underlying skin pigmentation differences among human populations. Hum Genet (2006) 1.34
Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol (2003) 1.34
Heterozygote advantage as a natural consequence of adaptation in diploids. Proc Natl Acad Sci U S A (2011) 1.33
House mouse colonization patterns on the sub-Antarctic Kerguelen Archipelago suggest singular primary invasions and resilience against re-invasion. BMC Evol Biol (2010) 1.31
Next generation molecular ecology. Mol Ecol (2010) 1.30
Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One (2013) 1.30
Protein evolution in the context of Drosophila development. J Mol Evol (2005) 1.29
Correlated evolution of synonymous and nonsynonymous sites in Drosophila. J Mol Evol (2004) 1.27
Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Mol Ecol (2010) 1.26
Human infection with Candidatus Neoehrlichia mikurensis, China. Emerg Infect Dis (2012) 1.26
X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Genetics (2005) 1.26
Anterior and posterior waves of cyclic her1 gene expression are differentially regulated in the presomitic mesoderm of zebrafish. Development (2003) 1.25
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Res (2013) 1.25
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics (2013) 1.23
Oligonucleotide microarrays: widely applied--poorly understood. Brief Funct Genomic Proteomic (2007) 1.21
Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse. Genome Res (2006) 1.19
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS One (2012) 1.16
Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol (2007) 1.15
What we have also learned: adaptive speciation is theoretically plausible. Evolution (2005) 1.15
Positive selection on gene expression in the human brain. Curr Biol (2006) 1.14
The adaptive role of transposable elements in the Drosophila genome. Gene (2009) 1.14
Broker genes in human disease. Genome Biol Evol (2010) 1.13
An algorithm and program for finding sequence specific oligonucleotide probes for species identification. BMC Bioinformatics (2002) 1.13
Tracing early stages of species differentiation: ecological, morphological and genetic divergence of Galápagos sea lion populations. BMC Evol Biol (2008) 1.10
Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol Biol (2006) 1.10
Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans. Genetics (2008) 1.10
Origins and rates of aneuploidy in human blastomeres. Fertil Steril (2011) 1.10
The root of the East African cichlid radiations. BMC Evol Biol (2009) 1.10
Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome. J Mol Evol (2005) 1.09
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res (2010) 1.09
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Mol Biol Evol (2008) 1.04
A functional polymorphism within the MRP1 gene locus identified through its genomic signature of positive selection. Hum Mol Genet (2005) 1.04
Detecting genetic association of common human facial morphological variation using high density 3D image registration. PLoS Comput Biol (2013) 1.04
Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics (2004) 1.03
How intron splicing affects the deletion and insertion profile in Drosophila melanogaster. Genetics (2002) 1.03
SEGE: A database on 'intron less/single exonic' genes from eukaryotes. Bioinformatics (2002) 1.02
Evolutionary biology for the 21st century. PLoS Biol (2013) 1.01
Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Mol Biol Evol (2008) 1.01
Global patterns of genetic diversity and signals of natural selection for human ADME genes. Hum Mol Genet (2010) 1.01
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
Rapid sequence turnover at an intergenic locus in Drosophila. Mol Biol Evol (2004) 1.00