Published in Proc Int Conf Intell Syst Mol Biol on January 01, 1994
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46
Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol (2008) 10.29
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci (1999) 9.82
Major facilitator superfamily. Microbiol Mol Biol Rev (1998) 9.77
Natural RNA circles function as efficient microRNA sponges. Nature (2013) 8.93
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell (2011) 6.83
An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell (2010) 6.76
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics (2004) 5.90
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res (2004) 5.66
Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev (1998) 5.16
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev (2006) 4.97
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol (2005) 4.86
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res (2010) 4.77
Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63
Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol (2007) 4.40
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34
Predicting effective microRNA target sites in mammalian mRNAs. Elife (2015) 4.30
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res (2001) 4.29
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell (2013) 4.28
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol (2002) 4.24
Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol (2008) 4.10
Comparative epigenomic analysis of murine and human adipogenesis. Cell (2010) 4.08
Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol (2004) 4.03
Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell (2011) 3.94
A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res (2010) 3.89
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85
Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell (2003) 3.80
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol (2004) 3.66
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev (2007) 3.56
The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53
Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol (2006) 3.52
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics (2010) 3.47
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc Natl Acad Sci U S A (2004) 3.37
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.27
A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25
Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol (2009) 3.24
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics (2005) 3.23
Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol (2009) 3.20
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol (2011) 3.18
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res (2008) 3.09
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell (2007) 3.01
Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci U S A (2009) 2.95
Genomic analysis of the unfolded protein response in Arabidopsis shows its connection to important cellular processes. Plant Cell (2003) 2.94
A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res (2007) 2.93
Genomewide characterization of non-polyadenylated RNAs. Genome Biol (2011) 2.92
Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol (2011) 2.85
The COOH-terminal domain of Myo2p, a yeast myosin V, has a direct role in secretory vesicle targeting. J Cell Biol (1999) 2.84
Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell (2004) 2.84
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
Enhancer transcripts mark active estrogen receptor binding sites. Genome Res (2013) 2.82
Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. Nucleic Acids Res (2010) 2.80
Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol (2010) 2.80
An alternative mode of microRNA target recognition. Nat Struct Mol Biol (2012) 2.77
cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res (2006) 2.75
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res (2011) 2.73
Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors. Plant Cell (2005) 2.70
Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity (2010) 2.70
Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol (2003) 2.67
Genome-wide identification of TAL1's functional targets: insights into its mechanisms of action in primary erythroid cells. Genome Res (2010) 2.64
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol (2007) 2.59
Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev (2009) 2.58
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res (2005) 2.58
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol (2014) 2.57
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
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
DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet (2009) 2.56
A phosphate transporter from Medicago truncatula involved in the acquisition of phosphate released by arbuscular mycorrhizal fungi. Plant Cell (2002) 2.56
Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol (2006) 2.56
Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily. Mol Microbiol (2003) 2.53
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol (2003) 2.50
Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46
Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium. Nucleic Acids Res (2014) 2.41
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38
The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J (2002) 2.37
The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol (1995) 7.31
Access to genetic sequence data. Science (1992) 0.75