Published in Nucleic Acids Res on January 22, 2004
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
Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast. PLoS Genet (2008) 1.93
Circadian control of global gene expression patterns. Annu Rev Genet (2010) 1.85
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
Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges. Proc Natl Acad Sci U S A (2005) 1.52
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture. Proc Natl Acad Sci U S A (2009) 1.35
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics (2007) 1.24
Detecting periodic genes from irregularly sampled gene expressions: a comparison study. EURASIP J Bioinform Syst Biol (2008) 1.16
Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression. Mol Syst Biol (2014) 1.10
Bayesian detection of periodic mRNA time profiles without use of training examples. BMC Bioinformatics (2006) 1.05
Evolutionary and transcriptional analysis of karyopherin beta superfamily proteins. Mol Cell Proteomics (2008) 0.98
Spectral estimation in unevenly sampled space of periodically expressed microarray time series data. BMC Bioinformatics (2007) 0.95
A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments. BMC Bioinformatics (2007) 0.85
Extracting biologically significant patterns from short time series gene expression data. BMC Bioinformatics (2009) 0.85
Principal-oscillation-pattern analysis of gene expression. PLoS One (2012) 0.84
A branching process model for flow cytometry and budding index measurements in cell synchrony experiments. Ann Appl Stat (2009) 0.79
Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast. BMC Genomics (2009) 0.79
A temporal precedence based clustering method for gene expression microarray data. BMC Bioinformatics (2010) 0.78
Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge. EURASIP J Bioinform Syst Biol (2009) 0.76
Time-course analysis of cyanobacterium transcriptome: detecting oscillatory genes. PLoS One (2011) 0.75
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A (1999) 39.79
Systematic determination of genetic network architecture. Nat Genet (1999) 25.45
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) 7.99
Revealing modular organization in the yeast transcriptional network. Nat Genet (2002) 6.73
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
Aligning gene expression time series with time warping algorithms. Bioinformatics (2001) 2.82
Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A (2001) 2.55
Deciphering gene expression regulatory networks. Curr Opin Genet Dev (2002) 2.09
A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. Bioinformatics (2003) 1.86
Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proc Natl Acad Sci U S A (2002) 1.40
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Structures of the bacterial ribosome at 3.5 A resolution. Science (2005) 12.63
A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet (2006) 12.45
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01
The first metal-organic framework (MOF) of Imazethapyr and its SHG, piezoelectric and ferroelectric properties. Dalton Trans (2008) 8.86
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol (2007) 6.87
An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell (2010) 6.76
Hydrogen-bonded ferroelectrics based on metal-organic coordination. J Am Chem Soc (2009) 6.69
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Supramolecular bola-like ferroelectric: 4-methoxyanilinium tetrafluoroborate-18-crown-6. J Am Chem Soc (2011) 4.73
Bayesian inference of epistatic interactions in case-control studies. Nat Genet (2007) 4.31
Diisopropylammonium chloride: a ferroelectric organic salt with a high phase transition temperature and practical utilization level of spontaneous polarization. Adv Mater (2011) 4.30
The Spo0A regulon of Bacillus subtilis. Mol Microbiol (2003) 4.19
High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell (2004) 4.18
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Improved virological outcomes in British Columbia concomitant with decreasing incidence of HIV type 1 drug resistance detection. Clin Infect Dis (2010) 3.12
A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11
Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell (2012) 3.08
A multiferroic perdeutero metal-organic framework. Angew Chem Int Ed Engl (2011) 2.88
DAPK1 interaction with NMDA receptor NR2B subunits mediates brain damage in stroke. Cell (2010) 2.87
Net primary production of Chinese croplands from 1950 to 1999. Ecol Appl (2007) 2.61
The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. J Mol Biol (2003) 2.59
Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A (2006) 2.55
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol (2007) 2.54
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet (2005) 2.26
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics (2012) 2.21
De novo cis-regulatory module elicitation for eukaryotic genomes. Proc Natl Acad Sci U S A (2005) 2.20
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet (2005) 2.15
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A (2007) 2.09
Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J Invest Dermatol (2009) 2.06
Adenomatous polyposis coli (APC) differentially regulates beta-catenin phosphorylation and ubiquitination in colon cancer cells. J Biol Chem (2006) 1.86
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
IKK mediates ischemia-induced neuronal death. Nat Med (2005) 1.83
Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol (2007) 1.80
Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylation. J Biol Chem (2007) 1.78
HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics (2012) 1.77
The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl (2010) 1.76
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res (2004) 1.74
Vascular gene expression in nonneoplastic and malignant brain. Am J Pathol (2004) 1.71
Decoding human regulatory circuits. Genome Res (2004) 1.70
Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol (2014) 1.70
Information flow analysis of interactome networks. PLoS Comput Biol (2009) 1.68
Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways. Mol Cancer Res (2003) 1.67
On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res (2010) 1.67
Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol (2013) 1.66
A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. PLoS Comput Biol (2010) 1.66
Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Hum Genet (2004) 1.66
Azide-bridged one-dimensional Mn(III) polymers: effects of side group of Schiff base ligands on structure and magnetism. Inorg Chem (2007) 1.65
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res (2011) 1.63
Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics (2009) 1.61
Diisopropylammonium bromide is a high-temperature molecular ferroelectric crystal. Science (2013) 1.61
Specificity of Distalless repression and limb primordia development by abdominal Hox proteins. Dev Cell (2002) 1.61
Top-down proteomics on a chromatographic time scale using linear ion trap fourier transform hybrid mass spectrometers. Anal Chem (2007) 1.60
Nuclear factor-kappaB contributes to infarction after permanent focal ischemia. Stroke (2004) 1.58
Clustering analysis of SAGE data using a Poisson approach. Genome Biol (2004) 1.58
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci U S A (2003) 1.58
Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A (2010) 1.56
Polymorphism of antigen MPT64 in Mycobacterium tuberculosis strains. J Clin Microbiol (2013) 1.56
Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell (2007) 1.56
BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics (2004) 1.55
Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell (2006) 1.55
X-ray fluorescence microscopy reveals large-scale relocalization and extracellular translocation of cellular copper during angiogenesis. Proc Natl Acad Sci U S A (2007) 1.55
A boosting approach for motif modeling using ChIP-chip data. Bioinformatics (2005) 1.53
Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics (2005) 1.49
Clinical parameter and Th17 related to lymphocytes infiltrating degree of labial salivary gland in primary Sjögren's syndrome. Clin Rheumatol (2014) 1.47
Cooperation between Polycomb and androgen receptor during oncogenic transformation. Genome Res (2011) 1.47
KLF4 interacts with beta-catenin/TCF4 and blocks p300/CBP recruitment by beta-catenin. Mol Cell Biol (2009) 1.44
Major vascular involvement in Behçet's disease: a retrospective study of 796 patients. Clin Rheumatol (2013) 1.44
A systematic review of the effectiveness of oral health promotion activities among patients with cardiovascular disease. Int J Cardiol (2010) 1.43
Renal involvement and followup of 130 patients with primary Sjögren's syndrome. J Rheumatol (2007) 1.43
Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothorax. Genes Dev (2006) 1.42
Associations between salivary gland histopathologic diagnoses and phenotypic features of Sjögren's syndrome among 1,726 registry participants. Arthritis Rheum (2011) 1.42
Monitoring G-protein-coupled receptor signaling with DNA microarrays and real-time polymerase chain reaction. Methods Enzymol (2002) 1.41
Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res (2010) 1.41
Bim and Noxa are candidates to mediate the deleterious effect of the NF-kappa B subunit RelA in cerebral ischemia. J Neurosci (2006) 1.40
Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J Comput Biol (2004) 1.40
Development of gene silencing pyrrole-imidazole polyamide targeting the TGF-beta1 promoter for treatment of progressive renal diseases. J Am Soc Nephrol (2005) 1.39
Temporal analysis of Candida albicans gene expression during biofilm development. Microbiology (2007) 1.39
Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol (2003) 1.38
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 1.36
Bayesian inference of protein-protein interactions from biological literature. Bioinformatics (2009) 1.35