Published in BMC Genomics on May 24, 2010
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol (2000) 13.01
Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol (2002) 9.31
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
The rapid evolution of reproductive proteins. Nat Rev Genet (2002) 6.88
RNA exosome depletion reveals transcription upstream of active human promoters. Science (2008) 6.80
Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet (2003) 6.60
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics (2006) 6.50
The antisense transcriptomes of human cells. Science (2008) 6.29
A coalescent estimator of the population recombination rate. Genetics (1997) 6.05
An abundance of bidirectional promoters in the human genome. Genome Res (2004) 5.90
The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet (2004) 5.79
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A (1999) 5.04
Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet (2006) 4.29
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15
Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci U S A (2001) 4.15
Sequence features in regions of weak and strong linkage disequilibrium. Genome Res (2005) 3.74
Bidirectional gene organization: a common architectural feature of the human genome. Cell (2002) 3.47
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol (2005) 2.80
Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol (2002) 2.79
Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A (2007) 2.56
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A (2001) 2.50
Evolution of protein-coding genes in Drosophila. Trends Genet (2008) 2.36
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Nucleic Acids Res (2008) 2.33
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res (2006) 2.21
Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics (2002) 2.20
Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics (2007) 1.88
FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res (2007) 1.75
Mammalian overlapping genes: the comparative perspective. Genome Res (2004) 1.74
Cross-species comparison of Drosophila male accessory gland protein genes. Genetics (2005) 1.71
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Using protein complexes to predict phenotypic effects of gene mutation. Genome Biol (2007) 1.57
Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Mol Biol Evol (2008) 1.54
The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci (2003) 1.51
Non-African populations of Drosophila melanogaster have a unique origin. Mol Biol Evol (2004) 1.50
Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet (2002) 1.39
Human antisense genes have unusually short introns: evidence for selection for rapid transcription. Trends Genet (2005) 1.35
Protein evolution in the context of Drosophila development. J Mol Evol (2005) 1.29
Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol (2008) 1.22
An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC Plant Biol (2008) 1.20
Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster. Nucleic Acids Res (2005) 1.18
Origin of gene overlap: the case of TCP1 and ACAT2. Genetics (1999) 1.06
Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol (2008) 0.96
Adaptive protein evolution and regulatory divergence in Drosophila. Mol Biol Evol (2006) 0.94
Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PLoS One (2008) 0.86
Decoupled differentiation of gene expression and coding sequence among Drosophila populations. Genes Genet Syst (2008) 0.85
Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Curr Biol (2011) 2.48
Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races. Mol Biol Evol (2006) 1.55
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res (2007) 1.50
Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques. Mol Ecol (2009) 1.21
A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in root growth vigor. Proc Natl Acad Sci U S A (2010) 0.87
Vitamin K epoxide reductase complex subunit 1 (Vkorc1) haplotype diversity in mouse priority strains. BMC Res Notes (2008) 0.85
Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system. BMC Genomics (2007) 0.85
Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup. BMC Genet (2010) 0.81
Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast. Genomics (2010) 0.80
Effects of Tamm-Horsfall protein on the protection of MCDK cells from oxalate induced free radical injury. Urol Res (2003) 0.76
Annotating ebony on the fly. Mol Ecol (2007) 0.75
Vkorc1 variation in house mice during warfarin and difenacoum field trials. Pest Manag Sci (2012) 0.75