Published in Bioinformatics on February 24, 2005
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics (2009) 2.36
Quantifying global tolerance of biochemical systems: design implications for moiety-transfer cycles. PLoS Comput Biol (2009) 1.17
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
Alarin is a vasoactive peptide. Proc Natl Acad Sci U S A (2007) 0.97
On the adaptive design rules of biochemical networks in evolution. Evol Bioinform Online (2007) 0.92
On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach. Evol Bioinform Online (2011) 0.85
Underlying principles of natural selection in network evolution: systems biology approach. Evol Bioinform Online (2007) 0.85
A method for determining the robustness of bio-molecular oscillator models. BMC Syst Biol (2009) 0.84
Comparisons of robustness and sensitivity between cancer and normal cells by microarray data. Cancer Inform (2008) 0.83
Control design for signal transduction networks. Bioinform Biol Insights (2009) 0.81
Endobiogeny: a global approach to systems biology (part 1 of 2). Glob Adv Health Med (2013) 0.78
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. Cells (2013) 0.78
Robustness and Specificity in Signal Transduction via Physiologic Protein Interaction Networks. Clin Exp Pharmacol (2012) 0.76
A network characteristic that correlates environmental and genetic robustness. PLoS Comput Biol (2014) 0.76
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection. BMC Syst Biol (2014) 0.75
Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81
Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A (2007) 4.87
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell (2004) 4.59
Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol (2004) 4.08
Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol (2003) 3.33
Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature (2002) 3.23
Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol (2009) 2.98
The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res (2002) 2.84
Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol (2002) 2.73
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res (2007) 2.72
Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci U S A (2007) 2.67
Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res (2003) 2.60
Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Mol Biol Evol (2006) 2.55
Strong male-driven evolution of DNA sequences in humans and apes. Nature (2002) 2.53
Duplicate genes increase gene expression diversity within and between species. Nat Genet (2004) 2.40
Slow molecular clocks in Old World monkeys, apes, and humans. Mol Biol Evol (2002) 2.20
Low nucleotide diversity in chimpanzees and bonobos. Genetics (2003) 2.16
Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol (2003) 1.92
Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet (2007) 1.89
Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Mol Biol Evol (2004) 1.88
MicroRNA regulation of human protein protein interaction network. RNA (2007) 1.82
Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A (2005) 1.81
Concern Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet (2007) 1.80
Evolution of the yeast protein interaction network. Proc Natl Acad Sci U S A (2003) 1.78
Patterns of segmental duplication in the human genome. Mol Biol Evol (2004) 1.76
Molecular evolution meets the genomics revolution. Nat Genet (2003) 1.76
Organismal complexity, protein complexity, and gene duplicability. Proc Natl Acad Sci U S A (2003) 1.67
Natural selection on cis and trans regulation in yeasts. Genome Res (2010) 1.65
Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol (2005) 1.63
Larger genetic differences within africans than between Africans and Eurasians. Genetics (2002) 1.62
Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer. EMBO J (2011) 1.60
Lowly expressed human microRNA genes evolve rapidly. Mol Biol Evol (2009) 1.58
Multidimensional scaling for large genomic data sets. BMC Bioinformatics (2008) 1.54
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res (2007) 1.50
Coordinated histone modifications are associated with gene expression variation within and between species. Genome Res (2011) 1.49
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
Purification and characterization of enterovirus 71 viral particles produced from vero cells grown in a serum-free microcarrier bioreactor system. PLoS One (2011) 1.45
RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A (2008) 1.45
Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol (2005) 1.44
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol (2005) 1.44
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics (2004) 1.43
Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance. BMC Genomics (2010) 1.43
Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics (2006) 1.42
Rate of protein evolution versus fitness effect of gene deletion. Mol Biol Evol (2003) 1.41
DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat Commun (2012) 1.40
Signatures of domain shuffling in the human genome. Genome Res (2002) 1.39
Protein function, connectivity, and duplicability in yeast. Mol Biol Evol (2005) 1.39
Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biol (2006) 1.36
The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet (2012) 1.36
Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res (2006) 1.34
Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol (2005) 1.31
Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes". Science (2003) 1.30
CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol (2008) 1.30
Nucleotide diversity in gorillas. Genetics (2004) 1.28
Identification of transcription factor cooperativity via stochastic system model. Bioinformatics (2006) 1.25
Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics (2008) 1.25
Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A (2006) 1.24
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol (2007) 1.23
Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol Biol Evol (2005) 1.23
Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol (2007) 1.23
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Res (2010) 1.22
Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Res (2007) 1.21
News and views: the chimpanzee and us. Nature (2005) 1.21
Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol (2007) 1.20
Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiol (2012) 1.18
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics (2004) 1.17
Prediction of splice sites with dependency graphs and their expanded bayesian networks. Bioinformatics (2004) 1.17
Human adaptive evolution at Myostatin (GDF8), a regulator of muscle growth. Am J Hum Genet (2006) 1.16
Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Mol Biol Evol (2004) 1.16
Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen. J Mol Evol (2003) 1.14
External factors accelerate expression divergence between duplicate genes. Trends Genet (2007) 1.14
Effects of GC content and mutational pressure on the lengths of exons and coding sequences. J Mol Evol (2003) 1.13
How strong is the mutagenicity of recombination in mammals? Mol Biol Evol (2004) 1.13
The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. BMC Genomics (2010) 1.12
Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics (2008) 1.12
Evidence from opsin genes rejects nocturnality in ancestral primates. Proc Natl Acad Sci U S A (2005) 1.11
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogenet Evol (2002) 1.09
Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biol (2008) 1.09
The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol Biol Evol (2007) 1.07
Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (2004) 1.07
Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. Mol Biol Evol (2010) 1.06
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics (2005) 1.05
Thermosensitive liposomes entrapping iron oxide nanoparticles for controllable drug release. Nanotechnology (2009) 1.04
MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. BMC Syst Biol (2012) 1.04
Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biol Evol (2009) 1.04
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
Identification of protein functional surfaces by the concept of a split pocket. Proteins (2009) 1.03
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Res (2009) 1.03
Overlapping genes in the human and mouse genomes. BMC Genomics (2008) 1.03
Molecular evolution of bat color vision genes. Mol Biol Evol (2003) 1.02
Method for identifying transcription factor binding sites in yeast. Bioinformatics (2006) 1.02
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol (2014) 1.00
ETOPE: Evolutionary test of predicted exons. Nucleic Acids Res (2003) 1.00
Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A (2008) 0.98
DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals. Ann N Y Acad Sci (2003) 0.98
Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol (2010) 0.98
Clinicopathological features and prognostic factors of gastric cancer patients aged 40 years or younger. J Surg Oncol (2012) 0.97
Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol (2013) 0.97