Published in Nucleic Acids Res on July 01, 2006
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res (2007) 2.22
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana. BMC Syst Biol (2011) 1.02
CoMoDis: composite motif discovery in mammalian genomes. Nucleic Acids Res (2006) 0.83
Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae. BMC Mol Biol (2008) 0.78
TAFFEL: Independent Enrichment Analysis of gene sets. BMC Bioinformatics (2011) 0.76
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
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
Learning the parts of objects by non-negative matrix factorization. Nature (1999) 21.77
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res (2003) 18.69
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30
Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res (1999) 13.02
Ensembl 2006. Nucleic Acids Res (2006) 11.66
Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell (1997) 11.61
Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Evaluation of gene structure prediction programs. Genomics (1996) 8.57
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol (1998) 8.34
The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol (2003) 7.72
Regulatory sequence analysis tools. Nucleic Acids Res (2003) 5.72
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res (2005) 4.52
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res (2006) 4.32
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics (2001) 4.29
Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol Plant Microbe Interact (2005) 4.21
Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res (2003) 3.68
Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res (2002) 3.30
Induction of protein secretory pathway is required for systemic acquired resistance. Science (2005) 3.18
Arabidopsis local resistance to Botrytis cinerea involves salicylic acid and camalexin and requires EDS4 and PAD2, but not SID2, EDS5 or PAD4. Plant J (2003) 2.56
Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J (2003) 2.45
T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res (2005) 1.93
Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics (2005) 1.77
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol (2005) 1.58
Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant Physiol (2004) 1.38
POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res (2004) 1.25
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. Nucleic Acids Res (2005) 0.87
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
Exhaustive enumeration of protein domain families. J Mol Biol (2003) 4.95
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol (2009) 4.17
ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res (2005) 2.65
The global trace graph, a novel paradigm for searching protein sequence databases. Bioinformatics (2007) 2.52
PairsDB atlas of protein sequence space. Nucleic Acids Res (2007) 2.42
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins. Bioinformatics (2003) 1.99
PIAS proteins: pleiotropic interactors associated with SUMO. Cell Mol Life Sci (2009) 1.94
Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol (2003) 1.93
Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics (2005) 1.77
Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alpha-synuclein. J Neurochem (2003) 1.70
Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinformatics (2006) 1.51
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics (2005) 1.42
Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy. Nucleic Acids Res (2011) 1.38
POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res (2004) 1.25
Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics (2005) 1.23
Analysis and visualization of gene expression data using self-organizing maps. Neural Netw (2002) 1.22
Antipsychotic drug treatment induces differential gene expression in the rat cortex. J Neurochem (2002) 1.14
Regulation of TRKB surface expression by brain-derived neurotrophic factor and truncated TRKB isoforms. J Biol Chem (2002) 1.14
Microarray analysis of nonhuman primates: validation of experimental models in neurological disorders. FASEB J (2003) 1.13
SKN-1/Nrf2 inhibits dopamine neuron degeneration in a Caenorhabditis elegans model of methylmercury toxicity. Toxicol Sci (2010) 1.11
Evolution of the GDNF family ligands and receptors. Brain Behav Evol (2006) 1.09
Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis. New Phytol (2013) 1.07
Response of rainbow trout transcriptome to model chemical contaminants. Biochem Biophys Res Commun (2004) 1.06
The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle. Genetics (2013) 1.04
Automated detection of remote homology. Curr Opin Struct Biol (2002) 1.02
Global microRNA expression profiling of Caenorhabditis elegans Parkinson's disease models. J Mol Neurosci (2010) 1.01
Oligomerization of hantavirus nucleocapsid protein: analysis of the N-terminal coiled-coil domain. J Virol (2006) 0.99
Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. PLoS Pathog (2012) 0.98
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinformatics (2009) 0.98
Changes in gene expression in atherosclerotic plaques analyzed using DNA array. Atherosclerosis (2002) 0.97
Selective sensitivity of Caenorhabditis elegans neurons to RNA interference. Neuroreport (2005) 0.97
MPEA--metabolite pathway enrichment analysis. Bioinformatics (2011) 0.96
Identification of gene expression changes in transgenic C. elegans overexpressing human alpha-synuclein. Neurobiol Dis (2006) 0.96
Trustworthiness and metrics in visualizing similarity of gene expression. BMC Bioinformatics (2003) 0.96
Generation of Gene Ontology benchmark datasets with various types of positive signal. BMC Bioinformatics (2009) 0.96
Towards structured output prediction of enzyme function. BMC Proc (2008) 0.95
Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants. FEBS Lett (2007) 0.94
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. BMC Bioinformatics (2012) 0.94
Accurate detection of very sparse sequence motifs. J Comput Biol (2004) 0.91
Genome sequence of Lactobacillus crispatus ST1. J Bacteriol (2010) 0.91
Chronic antipsychotic drug treatment induces long-lasting expression of fos and jun family genes and activator protein 1 complex in the rat prefrontal cortex. Neuropsychopharmacology (2002) 0.91
Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana. Nucleic Acids Res (2006) 0.91
Brain-derived neurotrophic factor signaling modifies hippocampal gene expression during epileptogenesis in transgenic mice. Eur J Neurosci (2004) 0.91
Mass-spectrometric identification of anandamide and 2-arachidonoylglycerol in nematodes. Chem Biodivers (2008) 0.91
FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data. BMC Syst Biol (2009) 0.90
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics (2012) 0.89
Identification of genes regulated by memantine and MK-801 in adult rat brain by cDNA microarray analysis. Neuropsychopharmacology (2004) 0.89
Loss of neurturin in frog--comparative genomics study of GDNF family ligand-receptor pairs. Mol Cell Neurosci (2006) 0.88
Evaluation of different domain-based methods in protein interaction prediction. Biochem Biophys Res Commun (2009) 0.88
Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map. Bioinformatics (2011) 0.87
A theoretical model for the regulation of Sex-lethal, a gene that controls sex determination and dosage compensation in Drosophila melanogaster. Genetics (2003) 0.87
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. Nucleic Acids Res (2005) 0.87
GOParGenPy: a high throughput method to generate gene ontology data matrices. BMC Bioinformatics (2013) 0.87
Varietas: a functional variation database portal. Database (Oxford) (2010) 0.87
Oligomerization of Uukuniemi virus nucleocapsid protein. Virol J (2010) 0.87
C. elegans as a genetic model system to identify Parkinson's disease-associated therapeutic targets. CNS Neurol Disord Drug Targets (2012) 0.86
Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. BMC Genomics (2014) 0.86
Dynamics of 1α,25-dihydroxyvitamin D3-dependent chromatin accessibility of early vitamin D receptor target genes. Biochim Biophys Acta (2013) 0.86
Chronic ethanol exposure increases cytochrome P-450 and decreases activated in blocked unfolded protein response gene family transcripts in caenorhabditis elegans. J Biochem Mol Toxicol (2013) 0.86
Effects of antidepressant drug imipramine on gene expression in rat prefrontal cortex. Neurochem Res (2004) 0.85
The gene for the transcription factor BHLHE40/DEC1/stra13 is a dynamically regulated primary target of the vitamin D receptor. J Steroid Biochem Mol Biol (2012) 0.85
CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies. BMC Bioinformatics (2006) 0.84
Modeling the C. elegans nematode and its environment using a particle system. J Theor Biol (2008) 0.83
Determination of endocannabinoids in nematodes and human brain tissue by liquid chromatography electrospray ionization tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci (2011) 0.83
Fatty acid composition and gene expression profiles are altered in aryl hydrocarbon receptor-1 mutant Caenorhabditis elegans. Comp Biochem Physiol C Toxicol Pharmacol (2010) 0.82
Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans. BMC Genomics (2008) 0.82
LOCP--locating pilus operons in gram-positive bacteria. Bioinformatics (2009) 0.82
Caenorhabditis Elegans Mutants Predict Regulation of Fatty Acids and Endocannabinoids by the CYP-35A Gene Family. Front Pharmacol (2011) 0.81
Genes regulated in MPTP-treated macaques and human Parkinson's disease suggest a common signature in prefrontal cortex. Neurobiol Dis (2010) 0.80
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees. Bioinformatics (2010) 0.80
1H MR spectroscopic imaging of phospholipase-mediated membrane lipid release in apoptotic rat glioma in vivo. Magn Reson Med (2008) 0.80
Distinct gene expression profiles in adult rat brains after acute MK-801 and cocaine treatments. Eur Neuropsychopharmacol (2005) 0.79
Increased lifespan in transgenic Caenorhabditis elegans overexpressing human alpha-synuclein. Exp Gerontol (2006) 0.79
Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein. Virus Res (2012) 0.78
Construction and use of gene expression covariation matrix. BMC Bioinformatics (2009) 0.78
Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae. BMC Mol Biol (2008) 0.78
Genome sequence of Pectobacterium sp. strain SCC3193. J Bacteriol (2012) 0.78
Expression profiling to understand actions of NMDA/glutamate receptor antagonists in rat brain. Neurochem Res (2002) 0.78
Radiation-induced genomic instability in Caenorhabditis elegans. Mutat Res (2012) 0.78
Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans. Toxicol Lett (2013) 0.78
Analysis of microarray studies performed in the neurosciences. J Mol Neurosci (2005) 0.77
Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli. BMC Microbiol (2011) 0.77
Interspliced transcription chimeras: neglected pathological mechanism infiltrating gene accession queries? J Biomed Inform (2008) 0.77
Comprehensive comparison of graph based multiple protein sequence alignment strategies. BMC Bioinformatics (2012) 0.77
Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains. J Proteome Res (2014) 0.76