Published in Nucleic Acids Res on April 14, 2008
Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res (2011) 0.81
Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol (1961) 65.10
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Stochastic gene expression in a single cell. Science (2002) 34.54
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol (1998) 8.34
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Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res (2006) 2.82
Standards for systems biology. Nat Rev Genet (2006) 1.77
Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol (2006) 1.61
gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation. Metab Eng (2005) 1.60
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res (2004) 1.45
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data. BMC Bioinformatics (2006) 0.97
Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol (2006) 0.87
Modeling gene expression control using Omes Law. Mol Syst Biol (2006) 0.78
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics (2005) 3.98
Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol (2005) 3.62
Gene sequence-based criteria for identification of new rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov. J Clin Microbiol (2003) 3.59
The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet (2011) 3.57
Why do hubs tend to be essential in protein networks? PLoS Genet (2006) 3.29
Gene losses during human origins. PLoS Biol (2006) 3.17
RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet (2010) 2.71
Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A (2008) 2.60
Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet (2012) 2.32
Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol (2006) 2.22
Genomic patterns of pleiotropy and the evolution of complexity. Proc Natl Acad Sci U S A (2010) 2.19
Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nat Genet (2010) 2.16
Mouse duplicate genes are as essential as singletons. Trends Genet (2007) 2.12
More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci U S A (2007) 2.00
Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol (2006) 1.97
Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals. Proc Natl Acad Sci U S A (2005) 1.88
Toward a molecular understanding of pleiotropy. Genetics (2006) 1.88
Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land. Genome Res (2007) 1.85
Adaptive diversification of bitter taste receptor genes in Mammalian evolution. Mol Biol Evol (2003) 1.82
Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes. Mol Biol Evol (2005) 1.77
Expression of hiwi gene in human gastric cancer was associated with proliferation of cancer cells. Int J Cancer (2006) 1.76
The hearing gene Prestin unites echolocating bats and whales. Curr Biol (2010) 1.62
Higher duplicability of less important genes in yeast genomes. Mol Biol Evol (2005) 1.57
Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo. Mol Biol Evol (2010) 1.53
Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet (2010) 1.51
Composition and evolution of the V2r vomeronasal receptor gene repertoire in mice and rats. Genomics (2005) 1.47
Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci U S A (2011) 1.46
The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories. Genomics (2005) 1.43
Sex-specific splicing of the honeybee doublesex gene reveals 300 million years of evolution at the bottom of the insect sex-determination pathway. Genetics (2007) 1.43
Gene complexity and gene duplicability. Curr Biol (2005) 1.42
Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes. Hum Mol Genet (2004) 1.38
In search of the biological significance of modular structures in protein networks. PLoS Comput Biol (2007) 1.38
The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast. Cell Rep (2012) 1.36
Evolution of the sweet taste receptor gene Tas1r2 in bats. Mol Biol Evol (2010) 1.36
Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol Syst Biol (2010) 1.35
Origin of the genetic components of the vomeronasal system in the common ancestor of all extant vertebrates. Mol Biol Evol (2008) 1.33
Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A (2011) 1.32
MicroRNA let-7c inhibits migration and invasion of human non-small cell lung cancer by targeting ITGB3 and MAP4K3. Cancer Lett (2013) 1.31
Positive selection for elevated gene expression noise in yeast. Mol Syst Biol (2009) 1.30
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci U S A (2012) 1.29
Genomic and genetic evidence for the loss of umami taste in bats. Genome Biol Evol (2011) 1.27
Did brain-specific genes evolve faster in humans than in chimpanzees? Trends Genet (2006) 1.26
Positive selection on protein-length in the evolution of a primate sperm ion channel. Proc Natl Acad Sci U S A (2003) 1.26
Gene dosage and gene duplicability. Genetics (2008) 1.23
Abundant indispensable redundancies in cellular metabolic networks. Genome Biol Evol (2009) 1.23
Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation. Proc Natl Acad Sci U S A (2012) 1.22
Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats. Gene (2004) 1.21
p37 from Mycoplasma hyorhinis promotes cancer cell invasiveness and metastasis through activation of MMP-2 and followed by phosphorylation of EGFR. Mol Cancer Ther (2008) 1.21
Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Rep (2012) 1.19
Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus. Mol Biol Evol (2007) 1.19
Why are some human disease-associated mutations fixed in mice? Trends Genet (2003) 1.19
Why is the correlation between gene importance and gene evolutionary rate so weak? PLoS Genet (2009) 1.16
On the definition and measurement of pleiotropy. Trends Genet (2013) 1.14
Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis. Mol Biol Evol (2008) 1.13
No gene-specific optimization of mutation rate in Escherichia coli. Mol Biol Evol (2013) 1.13
Coexpression of linked genes in Mammalian genomes is generally disadvantageous. Mol Biol Evol (2008) 1.12
Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol Biol Evol (2004) 1.11
Neuronal protein synuclein gamma predicts poor clinical outcome in breast cancer. Int J Cancer (2007) 1.10
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2013) 1.09
Diet shapes the evolution of the vertebrate bitter taste receptor gene repertoire. Mol Biol Evol (2013) 1.08
Positive selection for indel substitutions in the rodent sperm protein catsper1. Mol Biol Evol (2005) 1.07
Contrasting genetic paths to morphological and physiological evolution. Proc Natl Acad Sci U S A (2010) 1.05
Evolution of the complementary sex-determination gene of honey bees: balancing selection and trans-species polymorphisms. Genome Res (2006) 1.04
Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biol Evol (2010) 1.02
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PLoS Comput Biol (2012) 1.02
Generation of novel monoclonal antibodies and their application for detecting ARD1 expression in colorectal cancer. Cancer Lett (2008) 1.02
High expression hampers horizontal gene transfer. Genome Biol Evol (2012) 1.01
Evaluation of transovarial transmission and transmissibility of Ehrlichia chaffeensis (Rickettsiales: Anaplasmataceae) in Amblyomma americanum (Acari: Ixodidae). J Med Entomol (2003) 1.01
Suppression of tumor growth and metastasis by a VEGFR-1 antagonizing peptide identified from a phage display library. Int J Cancer (2004) 1.01
Evolutionary dynamics of nematode operons: easy come, slow go. Genome Res (2008) 1.00
Remarkable expansions of an X-linked reproductive homeobox gene cluster in rodent evolution. Genomics (2006) 1.00
Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes. Genome Biol Evol (2009) 0.99
Human coding RNA editing is generally nonadaptive. Proc Natl Acad Sci U S A (2014) 0.96
Zebrafish ribonucleases are bactericidal: implications for the origin of the vertebrate RNase A superfamily. Mol Biol Evol (2007) 0.95
Rapid evolution of mammalian X-linked testis-expressed homeobox genes. Genetics (2004) 0.93
Evidence for escape from adaptive conflict? Nature (2009) 0.91
Diagnosis of gastric cancer using decision tree classification of mass spectral data. Cancer Sci (2007) 0.90
Origin and evolution of the vertebrate vomeronasal system viewed through system-specific genes. Bioessays (2006) 0.90
A big world inside small-world networks. PLoS One (2009) 0.90
Widespread losses of vomeronasal signal transduction in bats. Mol Biol Evol (2010) 0.89
Processed pseudogenes: the 'fossilized footprints' of past gene expression. Trends Genet (2009) 0.89
Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals. Gene (2006) 0.88
Mismatches between feeding ecology and taste receptor evolution: an inconvenient truth. Proc Natl Acad Sci U S A (2012) 0.85
Genetic evidence for the coexistence of pheromone perception and full trichromatic vision in howler monkeys. Mol Biol Evol (2004) 0.85
Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon? Genetics (2005) 0.84
Obligate intracellular bacterium Ehrlichia inhibiting mitochondrial activity. Microbes Infect (2010) 0.84
Elevated maspin expression is associated with better overall survival in esophageal squamous cell carcinoma (ESCC). PLoS One (2013) 0.84
Genome-wide evolutionary conservation of N-glycosylation sites. Mol Biol Evol (2011) 0.84
Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents. J Mol Evol (2004) 0.83
Positive selection, not negative selection, in the pseudogenization of rcsA in Yersinia pestis. Proc Natl Acad Sci U S A (2008) 0.83
Rapid evolution of primate ESX1, an X-linked placenta- and testis-expressed homeobox gene. Hum Mol Genet (2007) 0.82
IL1 receptor antagonist gene IL1-RN variable number of tandem repeats polymorphism and cancer risk: a literature review and meta-analysis. PLoS One (2012) 0.82
Preparation and characterization of monoclonal antibodies against nucleostemin, a protein that controls cell proliferation in stem cells and cancer cells. Hybridoma (Larchmt) (2005) 0.81
Accelerated evolution and loss of a domain of the sperm-egg-binding protein SED1 in ancestral primates. Mol Biol Evol (2006) 0.80
Why are genes encoded on the lagging strand of the bacterial genome? Genome Biol Evol (2013) 0.79
Phylogenetic evidence for parallel adaptive origins of digestive RNases in Asian and African leaf monkeys: a response to Xu et al. (2009). Mol Phylogenet Evol (2009) 0.79
On the growth of scientific knowledge: yeast biology as a case study. PLoS Comput Biol (2009) 0.78
Toward genome-wide identification of Bateson-Dobzhansky-Muller incompatibilities in yeast: a simulation study. Genome Biol Evol (2013) 0.78
The microevolution of V1r vomeronasal receptor genes in mice. Genome Biol Evol (2011) 0.77
A panorama of mammalian gene expression evolution. Mol Syst Biol (2011) 0.76