Published in Bioinformatics on March 25, 2004
Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biol (2006) 1.78
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics (2006) 1.47
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics (2006) 1.41
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics (2005) 1.20
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.19
Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics (2008) 1.12
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics (2007) 1.09
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst Biol (2008) 1.07
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics (2005) 1.05
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. BMC Syst Biol (2009) 1.00
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. BMC Bioinformatics (2010) 0.93
Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. BMC Syst Biol (2009) 0.91
Identifying functional mechanisms of gene and protein regulatory networks in response to a broader range of environmental stresses. Comp Funct Genomics (2010) 0.90
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. BMC Bioinformatics (2010) 0.86
Underlying principles of natural selection in network evolution: systems biology approach. Evol Bioinform Online (2007) 0.85
An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference. Microarrays (Basel) (2015) 0.85
A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics (2007) 0.85
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One (2010) 0.83
A stochastic differential equation model for transcriptional regulatory networks. BMC Bioinformatics (2007) 0.82
Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations. PLoS One (2014) 0.81
Construction and clarification of dynamic gene regulatory network of cancer cell cycle via microarray data. Cancer Inform (2007) 0.81
Stochastic spatio-temporal dynamic model for gene/protein interaction network in early Drosophila development. Gene Regul Syst Bio (2009) 0.80
Gene regulatory networks modelling using a dynamic evolutionary hybrid. BMC Bioinformatics (2010) 0.80
Identifying a Transcription Factor's Regulatory Targets from its Binding Targets. Gene Regul Syst Bio (2010) 0.79
Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regul Syst Bio (2008) 0.79
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. Cells (2013) 0.78
Inference of gene regulation functions from dynamic transcriptome data. Elife (2016) 0.78
Reconstructing transcriptional regulatory networks through genomics data. Stat Methods Med Res (2009) 0.77
Systems level modeling of the cell cycle using budding yeast. Cancer Inform (2007) 0.76
Nonlinear dynamic trans/cis regulatory circuit for gene transcription via microarray data. Gene Regul Syst Bio (2007) 0.75
Variable Selection for Sparse High-Dimensional Nonlinear Regression Models by Combining Nonnegative Garrote and Sure Independence Screening. Stat Sin (2014) 0.75
Genetic and environmental factors affecting cryptic variations in gene regulatory networks. BMC Evol Biol (2013) 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
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
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
Authentication of medicinal herbs using PCR-amplified ITS2 with specific primers. Planta Med (2007) 1.23
Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol (2007) 1.23
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
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
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
Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics (2005) 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
A new measure of the robustness of biochemical networks. Bioinformatics (2005) 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
Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biol (2008) 1.09
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
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
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst Biol (2008) 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
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
Overlapping genes in the human and mouse genomes. BMC Genomics (2008) 1.03
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
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 network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics (2011) 1.01
ETOPE: Evolutionary test of predicted exons. Nucleic Acids Res (2003) 1.00
DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals. Ann N Y Acad Sci (2003) 0.98
Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A (2008) 0.98
Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol (2010) 0.98