Published in Genome Biol on January 01, 2007
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
Circadian control of global gene expression patterns. Annu Rev Genet (2010) 1.85
Large scale comparison of global gene expression patterns in human and mouse. Genome Biol (2010) 1.77
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
Cross species analysis of microarray expression data. Bioinformatics (2009) 1.47
Mitotic exit and separation of mother and daughter cells. Genetics (2012) 1.10
Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell (2009) 1.09
Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics (2014) 1.03
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol (2008) 1.02
Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression. EMBO J (2014) 0.92
Scaling single-cell genomics from phenomenology to mechanism. Nature (2017) 0.89
Coordination of cell growth and division by the ubiquitin-proteasome system. Semin Cell Dev Biol (2012) 0.89
A novel method for cross-species gene expression analysis. BMC Bioinformatics (2013) 0.85
Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev (2011) 0.85
Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast. PLoS Genet (2013) 0.84
Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics. Ecotoxicology (2011) 0.83
Circular reasoning rather than cyclic expression. Genome Biol (2008) 0.81
Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast. BMC Genomics (2009) 0.79
Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res (2012) 0.77
Cross species expression analysis of innate immune response. J Comput Biol (2010) 0.77
Identifying novel cell cycle proteins in Apicomplexa parasites through co-expression decision analysis. PLoS One (2014) 0.76
Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet (2015) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev (2002) 10.06
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput (2001) 8.65
Targets of the cyclin-dependent kinase Cdk1. Nature (2003) 8.05
Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) 7.99
Cyclin A is required at two points in the human cell cycle. EMBO J (1992) 7.96
Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A (2005) 7.48
Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci (1990) 6.16
Periodic gene expression program of the fission yeast cell cycle. Nat Genet (2004) 5.60
STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics (2006) 5.21
Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell (1987) 5.12
A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Genes Dev (1995) 4.93
Global analysis of the genetic network controlling a bacterial cell cycle. Science (2000) 4.77
Similarities and differences in genome-wide expression data of six organisms. PLoS Biol (2003) 4.75
Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science (2000) 4.33
Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis. Annu Rev Genet (2001) 3.79
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development (2005) 2.97
A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90
The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol (2005) 2.86
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature (1993) 2.76
The ch-TOG/XMAP215 protein is essential for spindle pole organization in human somatic cells. Genes Dev (2003) 2.75
Relocation of Aurora B from centromeres to the central spindle at the metaphase to anaphase transition requires MKlp2. J Cell Biol (2004) 2.44
Comparative analysis of cytokinesis in budding yeast, fission yeast and animal cells. Curr Biol (2004) 2.37
Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol Cell Biol (1997) 2.36
Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell (2004) 2.34
Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A (2006) 2.31
Identification of cell cycle-regulated genes in fission yeast. Mol Biol Cell (2004) 2.29
Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet (2005) 2.21
Cell cycle-regulated gene expression in Arabidopsis. J Biol Chem (2002) 2.00
Fission yeast ch-TOG/XMAP215 homologue Alp14 connects mitotic spindles with the kinetochore and is a component of the Mad2-dependent spindle checkpoint. EMBO J (2001) 1.83
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res (2006) 1.73
Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis. Carcinogenesis (2006) 1.65
Global roles of Ste11p, cell type, and pheromone in the control of gene expression during early sexual differentiation in fission yeast. Proc Natl Acad Sci U S A (2006) 1.59
Fission yeast genes which disrupt mitotic chromosome segregation when overexpressed. Nucleic Acids Res (1996) 1.58
Cig2, a B-type cyclin, promotes the onset of S in Schizosaccharomyces pombe. Mol Cell Biol (1996) 1.52
pkl1(+)and klp2(+): Two kinesins of the Kar3 subfamily in fission yeast perform different functions in both mitosis and meiosis. Mol Biol Cell (2001) 1.50
The XMAP215 homologue Stu2 at yeast spindle pole bodies regulates microtubule dynamics and anchorage. EMBO J (2003) 1.39
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics (2005) 1.29
Transcription factor binding site identification using the self-organizing map. Bioinformatics (2005) 1.11
Plo1(+) regulates gene transcription at the M-G(1) interval during the fission yeast mitotic cell cycle. EMBO J (2002) 1.10
Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol (2005) 1.09
The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body. Biochim Biophys Acta (1998) 1.09
Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly. Proc Natl Acad Sci U S A (2006) 1.04
Identifying cycling genes by combining sequence homology and expression data. Bioinformatics (2006) 0.97
Comparative analysis of cell cycle regulated genes in eukaryotes. Genome Inform (2005) 0.90
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet (2006) 10.47
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics (2006) 5.21
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12
The sirtuin SIRT6 regulates lifespan in male mice. Nature (2012) 4.07
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol (2009) 3.96
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Clustering short time series gene expression data. Bioinformatics (2005) 3.48
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2010) 3.02
Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol (2007) 2.68
Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev (2002) 2.52
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One (2009) 2.29
Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci U S A (2013) 2.25
Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput (2005) 2.25
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
Global organization of replication time zones of the mouse genome. Genome Res (2008) 2.11
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A (2003) 2.10
The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell (2002) 2.10
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
A probabilistic generative model for GO enrichment analysis. Nucleic Acids Res (2008) 2.01
Modulation of the vitamin D3 response by cancer-associated mutant p53. Cancer Cell (2010) 1.95
Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res (2010) 1.84
Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83
MILANO--custom annotation of microarray results using automatic literature searches. BMC Bioinformatics (2005) 1.77
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol (2012) 1.76
Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. Am J Respir Crit Care Med (2014) 1.69
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife (2013) 1.64
A biological solution to a fundamental distributed computing problem. Science (2011) 1.62
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res (2011) 1.62
Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol (2008) 1.61
Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly. EMBO J (2003) 1.59
Vaccination deep into a pandemic wave potential mechanisms for a "third wave" and the impact of vaccination. Am J Prev Med (2010) 1.57
Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. Am J Respir Crit Care Med (2014) 1.54
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
Deconvolving cell cycle expression data with complementary information. Bioinformatics (2004) 1.51
Cross species analysis of microarray expression data. Bioinformatics (2009) 1.47
Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron (2010) 1.41
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol (2008) 1.40
ComiR: Combinatorial microRNA target prediction tool. Nucleic Acids Res (2013) 1.39
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity. Nat Neurosci (2013) 1.36
Discovering homotypic binding events at high spatial resolution. Bioinformatics (2010) 1.33
Discovering pathways by orienting edges in protein interaction networks. Nucleic Acids Res (2010) 1.32
Protein complex identification by supervised graph local clustering. Bioinformatics (2008) 1.32
Profibrotic role of miR-154 in pulmonary fibrosis. Am J Respir Cell Mol Biol (2012) 1.30
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics (2005) 1.29
Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol (2009) 1.27
Characterization of the ECB binding complex responsible for the M/G(1)-specific transcription of CLN3 and SWI4. Mol Cell Biol (2002) 1.25
A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics (2007) 1.24
Genome-wide analysis of the replication program in mammals. Chromosome Res (2010) 1.23
Alignment and classification of time series gene expression in clinical studies. Bioinformatics (2008) 1.22
Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods (2011) 1.20
FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations. BMC Public Health (2013) 1.18
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics (2009) 1.16
Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines. Cancer Res (2008) 1.16
Biological interaction networks are conserved at the module level. BMC Syst Biol (2011) 1.16
Extracting dynamics from static cancer expression data. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.14
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res (2012) 1.14
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.11
Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol (2005) 1.09
Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell (2009) 1.09
Retracted Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). PLoS One (2011) 1.09
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Genome Res (2005) 1.09
Probabilistic error correction for RNA sequencing. Nucleic Acids Res (2013) 1.08
Rad53 checkpoint kinase phosphorylation site preference identified in the Swi6 protein of Saccharomyces cerevisiae. Mol Cell Biol (2003) 1.03
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. PLoS One (2011) 1.02
Reconstructing dynamic microRNA-regulated interaction networks. Proc Natl Acad Sci U S A (2013) 1.01
Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics (2007) 1.01
MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis (2013) 1.00
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res (2005) 0.99
Key events during the transition from rapid growth to quiescence in budding yeast require posttranscriptional regulators. Mol Biol Cell (2013) 0.99
A patient-gene model for temporal expression profiles in clinical studies. J Comput Biol (2007) 0.98
DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics (2011) 0.98
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics (2013) 0.97
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 0.97
Identifying cycling genes by combining sequence homology and expression data. Bioinformatics (2006) 0.97
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol (2010) 0.97
Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol (2011) 0.96