The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes.

PubWeight™: 0.78‹?›

🔗 View Article (PMC 2806350)

Published in BMC Genomics on December 18, 2009

Authors

Fernando Cruz1, Julien Roux, Marc Robinson-Rechavi

Author Affiliations

1: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland. Fernando.CruzRodriguez@unil.ch

Articles cited by this

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57

PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68

Ensembl 2009. Nucleic Acids Res (2008) 25.38

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33

BioMart--biological queries made easy. BMC Genomics (2009) 11.06

Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics (1990) 9.41

Transcription regulation and animal diversity. Nature (2003) 9.22

Microsatellites: simple sequences with complex evolution. Nat Rev Genet (2004) 8.64

Coding-sequence determinants of gene expression in Escherichia coli. Science (2009) 8.38

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91

Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci U S A (2004) 4.75

Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69

Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet (2000) 3.79

Microsatellite instability generates diversity in brain and sociobehavioral traits. Science (2005) 3.43

Simple sequence repeats as advantageous mutators in evolution. Trends Genet (2006) 3.12

Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci U S A (1998) 3.02

Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol (1995) 2.42

Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature (1995) 2.29

Amino acid runs in eukaryotic proteomes and disease associations. Proc Natl Acad Sci U S A (2002) 2.17

Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res (2007) 2.09

Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res (2006) 1.87

Comparative analysis of amino acid repeats in rodents and humans. Genome Res (2004) 1.78

OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol Biol (2007) 1.65

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet (2008) 1.54

Evolution of microsatellites in the yeast Saccharomyces cerevisiae: role of length and number of repeated units. J Mol Evol (1999) 1.46

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45

Cis-acting modifiers of expanded CAG/CTG triplet repeat expandability: associations with flanking GC content and proximity to CpG islands. Hum Mol Genet (1999) 1.25

A role for selection in regulating the evolutionary emergence of disease-causing and other coding CAG repeats in humans and mice. Mol Biol Evol (2001) 1.25

Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol (2009) 1.21

Conservation of polyglutamine tract size between mice and humans depends on codon interruption. Mol Biol Evol (1999) 1.17

Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol (2005) 1.16

Microsatellite polymorphism in natural populations of wild emmer wheat, Triticum dicoccoides, in Israel. Theor Appl Genet (2002) 1.11

Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics (2006) 1.09

DNA sequences shaped by selection for stability. PLoS Genet (2006) 1.06

Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species. Mol Biol Evol (2007) 1.05

Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors. Mol Biol Evol (1997) 1.01

The CAG/polyglutamine tract diseases: gene products and molecular pathogenesis. Brain Pathol (1997) 0.97

Elevated basal slippage mutation rates among the Canidae. J Hered (2007) 0.97

Sequence polymorphism of candidate behavioural genes in Drosophila melanogaster flies from 'Evolution canyon'. Mol Ecol (2005) 0.96

Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biol (2006) 0.91

Simple repeat evolution includes dramatic primary sequence changes that conserve folding potential. Biochem Biophys Res Commun (2007) 0.88

Hypothermic preservation effect on mammalian cells of type III antifreeze proteins from notched-fin eelpout. Cryobiology (2008) 0.86

Interactions between homopolymeric amino acids (HPAAs). Protein Sci (2007) 0.84

Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR. Mol Biol Evol (2008) 0.83

Articles by these authors

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03

The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19

The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol (2006) 2.30

How confident can we be that orthologs are similar, but paralogs differ? Trends Genet (2009) 2.21

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput Biol (2012) 1.65

Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol (2004) 1.58

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45

Developmental constraints on vertebrate genome evolution. PLoS Genet (2008) 1.43

The genomic impact of 100 million years of social evolution in seven ant species. Trends Genet (2011) 1.25

Evidence for polygenic adaptation to pathogens in the human genome. Mol Biol Evol (2013) 1.16

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Brief Bioinform (2011) 1.15

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol (2013) 1.14

Brain-derived neurotrophic factor/tropomyosin-related kinase receptor type B signaling is a downstream effector of the brainstem melanocortin system in food intake control. Endocrinology (2009) 1.11

An ontology to clarify homology-related concepts. Trends Genet (2010) 1.10

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics (2012) 1.10

NUREBASE: database of nuclear hormone receptors. Nucleic Acids Res (2002) 1.08

When orthologs diverge between human and mouse. Brief Bioinform (2011) 1.07

vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics (2012) 1.07

Neofunctionalization in vertebrates: the example of retinoic acid receptors. PLoS Genet (2006) 1.05

Community-wide plasmid gene mobilization and selection. ISME J (2013) 1.03

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res (2010) 1.03

Selectome: a database of positive selection. Nucleic Acids Res (2008) 1.02

Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evol Dev (2010) 1.01

Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Negl Trop Dis (2010) 1.00

The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PLoS Genet (2013) 0.97

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics (2010) 0.95

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst Biol (2007) 0.94

Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res (2013) 0.93

Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol Cell Proteomics (2010) 0.92

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res (2012) 0.92

Central inflammation and sickness-like behavior induced by the food contaminant deoxynivalenol: a PGE2-independent mechanism. Toxicol Sci (2011) 0.91

Advances in deoxynivalenol toxicity mechanisms: the brain as a target. Toxins (Basel) (2012) 0.90

Update of NUREBASE: nuclear hormone receptor functional genomics. Nucleic Acids Res (2004) 0.89

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford) (2012) 0.89

Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR. Mol Biol Evol (2003) 0.89

Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY. J Mol Evol (2003) 0.88

The food-contaminant deoxynivalenol modifies eating by targeting anorexigenic neurocircuitry. PLoS One (2011) 0.88

Nuclear receptors are markers of animal genome evolution. J Struct Funct Genomics (2003) 0.87

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Mol Biol Evol (2010) 0.87

Evidence for an episodic model of protein sequence evolution. Biochem Soc Trans (2009) 0.84

How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics (2012) 0.84

Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair. BMC Syst Biol (2011) 0.84

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environ Microbiol (2014) 0.83

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport. Physiol Genomics (2011) 0.82

The challenge of modeling nuclear receptor regulatory networks in mammalian cells. Mol Cell Endocrinol (2010) 0.82

Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis. Mol Biochem Parasitol (2007) 0.82

gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution. Stud Health Technol Inform (2012) 0.80

Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects. Mol Biol Evol (2009) 0.79

Uncovering hidden duplicated content in public transcriptomics data. Database (Oxford) (2013) 0.79

Phylogenetic code in the cloud - can it meet the expectations? Stud Health Technol Inform (2010) 0.79

Acute oral metformin enhances satiation and activates brainstem nesfatinergic neurons. Obesity (Silver Spring) (2014) 0.79

A benchmark of gene expression tissue-specificity metrics. Brief Bioinform (2017) 0.78

Comparative modular analysis of gene expression in vertebrate organs. BMC Genomics (2012) 0.78

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics (2016) 0.77

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics (2014) 0.76

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database (Oxford) (2013) 0.75

Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals. Mol Cell Endocrinol (2008) 0.75

The central question of type 2 diabetes. Pharm Pat Anal (2013) 0.75