Published in Proc Natl Acad Sci U S A on January 31, 2005
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol (2005) 2.50
Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A (2007) 2.40
Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol (2006) 2.04
Sporulation in the budding yeast Saccharomyces cerevisiae. Genetics (2011) 1.88
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res (2007) 1.50
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol (2011) 1.39
Gene expression from random libraries of yeast promoters. Genetics (2006) 1.34
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst Biol (2007) 1.34
Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics (2005) 1.26
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.19
Role of Ndt80p in sterol metabolism regulation and azole resistance in Candida albicans. Eukaryot Cell (2009) 1.17
Cell type-specific transcriptome analysis reveals a major role for Zeb1 and miR-200b in mouse inner ear morphogenesis. PLoS Genet (2011) 1.16
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res (2009) 1.15
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol (2008) 1.12
The Sum1/Ndt80 transcriptional switch and commitment to meiosis in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (2012) 1.07
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics (2005) 1.05
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3. BMC Genomics (2008) 1.05
A topology-based metric for measuring term similarity in the gene ontology. Adv Bioinformatics (2012) 1.04
fREDUCE: detection of degenerate regulatory elements using correlation with expression. BMC Bioinformatics (2007) 1.01
The Ime2 protein kinase enhances the disassociation of the Sum1 repressor from middle meiotic promoters. Mol Cell Biol (2009) 1.00
A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol (2009) 1.00
Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics (2010) 0.93
Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius. Am J Physiol Regul Integr Comp Physiol (2008) 0.93
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol (2010) 0.92
Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci (2006) 0.89
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. Genome Biol (2007) 0.88
Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. BMC Syst Biol (2011) 0.88
Bayesian Joint Modeling of Multiple Gene Networks and Diverse Genomic Data to Identify Target Genes of a Transcription Factor. Ann Appl Stat (2012) 0.86
Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics (2010) 0.86
Identification of temporal association rules from time-series microarray data sets. BMC Bioinformatics (2009) 0.85
Bladder inflammatory transcriptome in response to tachykinins: neurokinin 1 receptor-dependent genes and transcription regulatory elements. BMC Urol (2007) 0.85
Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. PLoS One (2008) 0.81
Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal. Nucleic Acids Res (2013) 0.80
Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation. BMC Syst Biol (2010) 0.80
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs. BMC Bioinformatics (2007) 0.79
GBNet: deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. BMC Bioinformatics (2008) 0.79
Embedding mRNA stability in correlation analysis of time-series gene expression data. PLoS Comput Biol (2008) 0.79
Reconstructing transcriptional regulatory networks through genomics data. Stat Methods Med Res (2009) 0.77
An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol (2014) 0.77
An overview of the importance of conformational flexibility in gene regulation by the transcription factors. J Biophys (2010) 0.76
Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. Int J Comput Biol Drug Des (2009) 0.75
Transcriptional Network Architecture of Breast Cancer Molecular Subtypes. Front Physiol (2016) 0.75
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst Biol (2015) 0.75
Dissecting genetic architecture of startle response in Drosophila melanogaster using multi-omics information. Sci Rep (2017) 0.75
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
The transcriptional program of sporulation in budding yeast. Science (1998) 37.23
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res (2001) 16.22
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92
Predicting gene expression from sequence. Cell (2004) 8.12
SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics (1999) 6.79
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A (2003) 6.02
The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol (1985) 5.79
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell (2000) 4.17
Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J (1999) 3.65
Defining transcription modules using large-scale gene expression data. Bioinformatics (2004) 3.33
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics (2004) 3.31
Transcriptional regulation of meiosis in budding yeast. Int Rev Cytol (2003) 1.95
Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol Cell Biol (2003) 1.90
Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response. Proc Natl Acad Sci U S A (2001) 1.87
A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae. Proc Natl Acad Sci U S A (2002) 1.70
Transcriptional regulation of meiosis in yeast. Curr Opin Cell Biol (2000) 1.64
Regulation of the premiddle and middle phases of expression of the NDT80 gene during sporulation of Saccharomyces cerevisiae. Mol Cell Biol (2002) 1.43
Dissecting the transcription networks of a cell using computational genomics. Curr Opin Genet Dev (2003) 0.92
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature (2003) 14.49
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res (2002) 10.65
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03
Clopidogrel with aspirin in acute minor stroke or transient ischemic attack. N Engl J Med (2013) 8.76
Introductory science and mathematics education for 21st-Century biologists. Science (2004) 7.69
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98
Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med (2004) 6.91
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A (2005) 6.54
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res (2003) 5.69
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol (2002) 5.20
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 4.97
Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet (2004) 4.77
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell (2007) 4.27
Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A (2003) 3.98
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
CTLA-4 blockade enhances polyfunctional NY-ESO-1 specific T cell responses in metastatic melanoma patients with clinical benefit. Proc Natl Acad Sci U S A (2008) 3.80
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell (2004) 3.73
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet (2008) 3.58
Evolution of alternative transcriptional circuits with identical logic. Nature (2006) 3.58
The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53
Saccharomyces genome database: underlying principles and organisation. Brief Bioinform (2004) 3.46
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res (2005) 3.43
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38
Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (2006) 3.32
Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res (2006) 3.31
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A (2002) 3.28
Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem (2002) 3.26
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet (2007) 3.24
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A (2003) 3.14
Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell (2004) 3.02
Cell- and gene-specific regulation of primary target genes by the androgen receptor. Genes Dev (2007) 2.96
A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95
A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90
Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A (2003) 2.87
Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression. Nat Cell Biol (2008) 2.68
Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci U S A (2006) 2.68
The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Mol Biol Cell (2003) 2.56
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
Saccharomyces Genome Database. Methods Enzymol (2002) 2.47
Ammonium toxicity and potassium limitation in yeast. PLoS Biol (2006) 2.39
Variation in gene expression patterns in human gastric cancers. Mol Biol Cell (2003) 2.39
Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell (2005) 2.30
The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci U S A (2009) 2.28
Comparing whole genomes using DNA microarrays. Nat Rev Genet (2008) 2.27
Evolution of eukaryotic transcription circuits. Science (2008) 2.24
Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Mol Biol Cell (2003) 2.18
Dynamic XML-based exchange of relational data: application to the Human Brain Project. AMIA Annu Symp Proc (2003) 2.16
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell (2004) 2.15
Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci U S A (2002) 2.14
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol (2010) 2.05
Universal Reference RNA as a standard for microarray experiments. BMC Genomics (2004) 2.00
Genetic variations and treatments that affect the lifespan of the NPC1 mouse. J Lipid Res (2007) 1.99
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
New mutant phenotype data curation system in the Saccharomyces Genome Database. Database (Oxford) (2009) 1.95
Genome-wide diversity and selective pressure in the human rhinovirus. Virol J (2007) 1.94
Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell (2009) 1.92
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) (2012) 1.92
Diabetes and poor outcomes within 6 months after acute ischemic stroke: the China National Stroke Registry. Stroke (2011) 1.91
The China National Stroke Registry for patients with acute cerebrovascular events: design, rationale, and baseline patient characteristics. Int J Stroke (2011) 1.90
Antibody-based targeting of FGFR3 in bladder carcinoma and t(4;14)-positive multiple myeloma in mice. J Clin Invest (2009) 1.89
Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol (2008) 1.86
Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast (2006) 1.85
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS One (2007) 1.83
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proc Natl Acad Sci U S A (2002) 1.81
Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One (2007) 1.80
Indole- and indolizine-glyoxylamides displaying cytotoxicity against multidrug resistant cancer cell lines. Bioorg Med Chem Lett (2008) 1.80
Genetic variation and the fate of beneficial mutations in asexual populations. Genetics (2011) 1.77
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet (2007) 1.77
GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics (2004) 1.75