Published in Proc Natl Acad Sci U S A on August 21, 2003
Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A (2005) 8.65
High-content flow cytometry and temporal data analysis for defining a cellular signature of graft-versus-host disease. Biol Blood Marrow Transplant (2007) 4.14
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
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
Extracting binary signals from microarray time-course data. Nucleic Acids Res (2007) 1.67
Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol (2011) 1.65
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinformatics (2009) 1.43
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. J Comput Biol (2010) 1.41
Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. BMC Bioinformatics (2005) 1.19
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
A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression. BMC Bioinformatics (2011) 1.08
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. BMC Bioinformatics (2008) 1.06
Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput Biol (2012) 1.01
Dynamics of the microbiota in response to host infection. PLoS One (2014) 0.98
Time series expression analyses using RNA-seq: a statistical approach. Biomed Res Int (2013) 0.98
Functional assessment of time course microarray data. BMC Bioinformatics (2009) 0.97
A statistical framework for biomarker discovery in metabolomic time course data. Bioinformatics (2011) 0.96
In search of functional association from time-series microarray data based on the change trend and level of gene expression. BMC Bioinformatics (2006) 0.93
More powerful significant testing for time course gene expression data using functional principal component analysis approaches. BMC Bioinformatics (2013) 0.90
Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster. BMC Bioinformatics (2008) 0.86
The wavelet-based cluster analysis for temporal gene expression data. EURASIP J Bioinform Syst Biol (2007) 0.86
Pathway Analysis: State of the Art. Front Physiol (2015) 0.86
Time warping of evolutionary distant temporal gene expression data based on noise suppression. BMC Bioinformatics (2009) 0.85
Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. BMC Syst Biol (2010) 0.82
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biol (2016) 0.80
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genomics (2012) 0.79
Frequency-based time-series gene expression recomposition using PRIISM. BMC Syst Biol (2012) 0.79
A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. BMC Bioinformatics (2014) 0.78
timeClip: pathway analysis for time course data without replicates. BMC Bioinformatics (2014) 0.78
A growth curve model with fractional polynomials for analysing incomplete time-course data in microarray gene expression studies. Adv Bioinformatics (2011) 0.77
Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments. Cell Syst (2016) 0.75
Selecting the most appropriate time points to profile in high-throughput studies. Elife (2017) 0.75
Early response index: a statistic to discover potential early stage disease biomarkers. BMC Bioinformatics (2017) 0.75
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. Bioinformatics (2016) 0.75
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Functional discovery via a compendium of expression profiles. Cell (2000) 31.39
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) 7.99
The plasticity of dendritic cell responses to pathogens and their components. Science (2001) 5.58
Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci U S A (2002) 5.18
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A (2002) 3.83
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Dynamic modeling of gene expression data. Proc Natl Acad Sci U S A (2001) 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
Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput (1999) 3.07
Aligning gene expression time series with time warping algorithms. Bioinformatics (2001) 2.82
Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature (2000) 2.74
Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A (2001) 2.55
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
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol (2001) 2.03
Forkhead genes in transcriptional silencing, cell morphology and the cell cycle. Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae. Genetics (2000) 1.82
A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Hum Mol Genet (2002) 1.43
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet (2006) 10.47
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12
Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol (2009) 3.96
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell (2004) 3.74
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15
Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput (2002) 3.05
Genotype to phenotype: a complex problem. Science (2010) 2.92
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (2005) 2.52
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A (2009) 2.36
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
Global organization of replication time zones of the mouse genome. Genome Res (2008) 2.11
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
Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U S A (2006) 1.96
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
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
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
Global gene deletion analysis exploring yeast filamentous growth. Science (2012) 1.67
Control of transcription by cell size. PLoS Biol (2010) 1.61
Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly. EMBO J (2003) 1.59
K-ary clustering with optimal leaf ordering for gene expression data. Bioinformatics (2003) 1.53
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
Differentiated human stem cells resemble fetal, not adult, β cells. Proc Natl Acad Sci U S A (2014) 1.44
Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron (2010) 1.41
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
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol (2008) 1.29
Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol (2009) 1.27
Genome-wide analysis of the replication program in mammals. Chromosome Res (2010) 1.23
Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods (2011) 1.20
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol (2011) 1.19
Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol (2007) 1.18
Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines. Cancer Res (2008) 1.16
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Rapid haplotype inference for nuclear families. Genome Biol (2010) 1.03
High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics (2012) 1.01
DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics (2011) 0.98
The short isoform of the CEACAM1 receptor in intestinal T cells regulates mucosal immunity and homeostasis via Tfh cell induction. Immunity (2012) 0.97
An analysis of intra array repeats: the good, the bad and the non informative. BMC Genomics (2006) 0.95
Competition between small RNAs: a quantitative view. Biophys J (2012) 0.95
Tamoxifen induces heparanase expression in estrogen receptor-positive breast cancer. Clin Cancer Res (2007) 0.92
DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med (2010) 0.91
Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast. Genetics (2010) 0.89
Molecular characteristics of liver metastases from uveal melanoma. Invest Ophthalmol Vis Sci (2007) 0.89
A combined expression-interaction model for inferring the temporal activity of transcription factors. J Comput Biol (2009) 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
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics (2006) 0.86
Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization. PLoS One (2012) 0.84
Continuous hidden process model for time series expression experiments. Bioinformatics (2007) 0.84
Genome-wide analysis of androgen receptor targets reveals COUP-TF1 as a novel player in human prostate cancer. PLoS One (2012) 0.80
Integrative analysis of methylome and transcriptome reveals the importance of unmethylated CpGs in non-CpG island gene activation. Biomed Res Int (2013) 0.79
ReadDB provides efficient storage for mapped short reads. BMC Bioinformatics (2011) 0.75
Antibiotic effects on gut microbiota and metabolism are host dependent. J Clin Invest (2016) 0.75
A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Res (2012) 0.75
Ruler arrays reveal haploid genomic structural variation. PLoS One (2012) 0.75