Published in BMC Biol on January 28, 2005
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Breakpoint graphs and ancestral genome reconstructions. Genome Res (2009) 2.78
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol (2009) 1.57
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res (2005) 1.54
A phylogenomic study of human, dog, and mouse. PLoS Comput Biol (2006) 1.49
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci (2007) 1.29
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics (2009) 1.08
Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features. BMC Bioinformatics (2007) 0.99
Two novel mouse genes mapped to chromosome Yp are expressed specifically in spermatids. Mamm Genome (2009) 0.99
Pyoverdine receptor: a case of positive Darwinian selection in Pseudomonas aeruginosa. J Bacteriol (2005) 0.91
Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genomics (2012) 0.91
PigGIS: Pig Genomic Informatics System. Nucleic Acids Res (2006) 0.87
The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes. Mol Phylogenet Evol (2007) 0.84
Neonatal colonisation expands a specific intestinal antigen-presenting cell subset prior to CD4 T-cell expansion, without altering T-cell repertoire. PLoS One (2012) 0.83
Phenotypic and functional analysis of monocyte populations in cattle peripheral blood identifies a subset with high endocytic and allogeneic T-cell stimulatory capacity. Vet Res (2015) 0.80
Up-regulated miR-145 expression inhibits porcine preadipocytes differentiation by targeting IRS1. Int J Biol Sci (2012) 0.79
Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution. PLoS One (2007) 0.79
How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome. PLoS One (2013) 0.79
Dissecting the role of milk components on gut microbiota composition. Gut Microbes (2012) 0.78
Towards the establishment of a porcine model to study human amebiasis. PLoS One (2011) 0.78
Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome. Evol Bioinform Online (2012) 0.78
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol (1985) 47.78
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40
A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol (1994) 19.91
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol (2001) 16.83
Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84
A molecular timescale for vertebrate evolution. Nature (1998) 13.92
Slightly deleterious mutant substitutions in evolution. Nature (1973) 13.79
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature (2003) 10.73
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol (1998) 8.74
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
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol (1994) 7.55
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res (2003) 7.21
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
Large-scale search for genes on which positive selection may operate. Mol Biol Evol (1996) 6.14
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol (2003) 6.04
Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylogenet Evol (1996) 3.97
Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. Proc Natl Acad Sci U S A (1990) 3.23
Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol (1995) 2.65
The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics (1990) 2.61
The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proc Natl Acad Sci U S A (1997) 2.40
Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci U S A (2000) 2.20
The marsupial mitochondrial genome and the evolution of placental mammals. Genetics (1994) 2.19
Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol (2003) 2.16
Molecular dating and biogeography of the early placental mammal radiation. J Hered (2001) 2.13
Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics (1999) 1.93
Inference of selection from multiple species alignments. Curr Opin Genet Dev (2002) 1.65
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Biol Evol (2004) 1.64
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci U S A (1993) 1.57
Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol Biol Evol (2003) 1.56
Frequent false detection of positive selection by the likelihood method with branch-site models. Mol Biol Evol (2004) 1.49
Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. Genetics (2001) 1.49
Molecular evidence for the early divergence of placental mammals. Bioessays (1999) 1.32
Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol (2003) 1.30
Rate constancy of globin gene evolution in placental mammals. Proc Natl Acad Sci U S A (1988) 1.16
Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol Phylogenet Evol (2003) 1.13
Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). Mol Biol Evol (2004) 1.12
Revisiting the Glires concept--phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol (2003) 1.11
Tests for positive selection on immune and reproductive genes in closely related species of the murine genus mus. J Mol Evol (2003) 1.08
The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. Proc Natl Acad Sci U S A (2003) 0.99
Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol Biol Evol (2003) 0.98
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One (2009) 5.26
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol (2009) 3.42
Great ape genetic diversity and population history. Nature (2013) 2.95
Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc (2009) 2.80
Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet (2008) 2.68
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res (2006) 2.68
Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet (2009) 2.68
Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A (2012) 2.59
Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR. BMC Mol Biol (2007) 2.55
The bonobo genome compared with the chimpanzee and human genomes. Nature (2012) 2.49
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet (2011) 2.24
Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science (2008) 2.19
Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci U S A (2012) 1.78
Ancestral population genomics: the coalescent hidden Markov model approach. Genetics (2009) 1.54
A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation. Genome Res (2005) 1.52
Threonine 53 in alpha-synuclein is conserved in long-living non-primate animals. Biochem Biophys Res Commun (2009) 1.48
Pig genome sequence--analysis and publication strategy. BMC Genomics (2010) 1.47
Copy number variation in the bovine genome. BMC Genomics (2010) 1.45
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet (2011) 1.37
A snapshot of CNVs in the pig genome. PLoS One (2008) 1.36
A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina. PLoS One (2012) 1.25
Extensive X-linked adaptive evolution in central chimpanzees. Proc Natl Acad Sci U S A (2012) 1.23
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet (2012) 1.23
Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun (2012) 1.20
Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc Natl Acad Sci U S A (2012) 1.16
LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs. Vet J (2011) 1.15
Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol (2007) 1.15
A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait. J Anim Sci (2013) 1.14
Homozygosity for a single base-pair mutation in the oocyte-specific GDF9 gene results in sterility in Thoka sheep. Reproduction (2009) 1.13
Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PLoS One (2013) 1.11
MicroRNA expression profiling of the porcine developing brain. PLoS One (2011) 1.10
Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics (2011) 1.09
Nuclear receptor corepressor-dependent repression of peroxisome-proliferator-activated receptor delta-mediated transactivation. Biochem J (2002) 1.08
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics (2009) 1.08
The minipig as a platform for new technologies in toxicology. J Pharmacol Toxicol Methods (2010) 1.08
Genetic and environmental influences of surfactant protein D serum levels. Am J Physiol Lung Cell Mol Physiol (2005) 1.06
An f2 pig resource population as a model for genetic studies of obesity and obesity-related diseases in humans: design and genetic parameters. Front Genet (2013) 1.05
Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds. BMC Genomics (2012) 1.03
A transcriptome map of perennial ryegrass (Lolium perenne L.). BMC Genomics (2012) 1.03
Advances in porcine genomics and proteomics--a toolbox for developing the pig as a model organism for molecular biomedical research. Brief Funct Genomics (2010) 1.02
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. BMC Med Genomics (2014) 1.02
Genome-wide association study in Dachshund: identification of a major locus affecting intervertebral disc calcification. J Hered (2011) 1.01
Characterization of the 2'-5'-oligoadenylate synthetase ubiquitin-like family. Nucleic Acids Res (2003) 1.01
Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera. Mol Biol Evol (2006) 0.99
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics (2007) 0.99
Gene expression profiles in testis of pigs with extreme high and low levels of androstenone. BMC Genomics (2007) 0.98
A form of albinism in cattle is caused by a tyrosinase frameshift mutation. Mamm Genome (2004) 0.98
Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics (2012) 0.96
Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues. PLoS One (2007) 0.95
The receptor locus for Escherichia coli F4ab/F4ac in the pig maps distal to the MUC4-LMLN region. Mamm Genome (2010) 0.94
Association between the porcine Escherichia coli F18 receptor genotype and phenotype and susceptibility to colonisation and postweaning diarrhoea caused by E. coli O138:F18. Vet Microbiol (2003) 0.94
Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II: meat quality traits. BMC Genet (2008) 0.93
Structured RNAs and synteny regions in the pig genome. BMC Genomics (2014) 0.92
Experimental infection with Escherichia coli O149:F4ac in weaned piglets. Vet Microbiol (2006) 0.92
Morphological variation of "complex vertebral malformation" in Holstein calves. J Vet Diagn Invest (2004) 0.92
On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics (2011) 0.92
Identification of 2 loci associated with development of myxomatous mitral valve disease in Cavalier King Charles Spaniels. J Hered (2011) 0.92
Genomic position mapping discrepancies of commercial SNP chips. PLoS One (2012) 0.91
Effects of bacterial colonization on the porcine intestinal proteome. J Proteome Res (2007) 0.91
Identification of a novel idiopathic epilepsy locus in Belgian Shepherd dogs. PLoS One (2012) 0.91
Gene expression profiles in liver of pigs with extreme high and low levels of androstenone. BMC Vet Res (2008) 0.91
Analysis of the real EADGENE data set: comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (open access publication). Genet Sel Evol (2007) 0.91
Prevalence and characteristics of epilepsy in the Belgian shepherd variants Groenendael and Tervueren born in Denmark 1995-2004. Acta Vet Scand (2008) 0.91
Association between SNPs within candidate genes and compounds related to boar taint and reproduction. BMC Genet (2009) 0.91
The genetic regulation of the terminating phase of liver regeneration. Comp Hepatol (2012) 0.91
DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae. PLoS Genet (2012) 0.90
CL-46, a novel collectin highly expressed in bovine thymus and liver. J Immunol (2002) 0.90
Enumeration of bifidobacteria in gastrointestinal samples from piglets. Appl Environ Microbiol (2003) 0.90
A robust linkage map of the porcine autosomes based on gene-associated SNPs. BMC Genomics (2009) 0.89
Depauperate genetic variability detected in the American and European bison using genomic techniques. Biol Direct (2009) 0.88
Mapping and expression studies of the mir17-92 cluster on pig chromosome 11. Mamm Genome (2005) 0.88
Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs. BMC Res Notes (2011) 0.87
UDP-glucose pyrophosphorylase is upregulated in carriers of the porcine RN- mutation in the AMP-activated protein kinase. Proteomics (2004) 0.87
A Gly98Val mutation in the N-Myc downstream regulated gene 1 (NDRG1) in Alaskan Malamutes with polyneuropathy. PLoS One (2013) 0.86
The EADGENE Microarray Data Analysis Workshop (open access publication). Genet Sel Evol (2007) 0.86
Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene. Neurogenetics (2009) 0.86
Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms. Genome Biol Evol (2012) 0.86
Expression profiles of miRNA-122 and its target CAT1 in minipigs (Sus scrofa) fed a high-cholesterol diet. Comp Med (2010) 0.86
Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics (2011) 0.86
How the RNA isolation method can affect microRNA microarray results. Acta Biochim Pol (2011) 0.85
A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. Genome Res (2013) 0.85