Published in Nucleic Acids Res on August 12, 2010
Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. BMC Genomics (2014) 0.75
Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol (2011) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res (2002) 47.62
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
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
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol (1997) 17.52
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
AmiGO: online access to ontology and annotation data. Bioinformatics (2008) 10.77
Using Dirichlet mixture priors to derive hidden Markov models for protein families. Proc Int Conf Intell Syst Mol Biol (1993) 10.73
Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics (2001) 9.11
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
A comparison of scoring functions for protein sequence profile alignment. Bioinformatics (2004) 6.44
A gene network for navigating the literature. Nat Genet (2004) 6.43
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc Int Conf Intell Syst Mol Biol (1998) 5.54
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics (2002) 4.49
Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A (2002) 4.44
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res (2006) 4.32
The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol (2000) 4.21
An overview of the structures of protein-DNA complexes. Genome Biol (2000) 3.90
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics (2002) 3.79
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol (2007) 3.37
What determines the specificity of action of Drosophila homeodomain proteins? Cell (1990) 3.34
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07
Classification and nomenclature of all human homeobox genes. BMC Biol (2007) 2.61
The genesis and evolution of homeobox gene clusters. Nat Rev Genet (2005) 2.56
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res (2009) 2.34
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol (2006) 2.27
Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27
Automated protein subfamily identification and classification. PLoS Comput Biol (2007) 1.89
Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol Biol Evol (2001) 1.57
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics (2009) 1.44
Semi-supervised protein classification using cluster kernels. Bioinformatics (2005) 1.42
Functional specificity of the Antennapedia homeodomain. Proc Natl Acad Sci U S A (1993) 1.39
Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38
HomeoDB: a database of homeobox gene diversity. Evol Dev (2008) 1.26
Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer. J Mol Biol (2008) 1.19
A rational nomenclature for vertebrate homeobox (HOX) genes. Nucleic Acids Res (1993) 1.10
Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. Dev Genes Evol (2008) 1.05
Determining functional specificity from protein sequences. Bioinformatics (2005) 0.95
Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins. Proteins (2004) 0.92
Graph-based clustering for finding distant relationships in a large set of protein sequences. Bioinformatics (2004) 0.87
Efficient functional clustering of protein sequences using the Dirichlet process. Bioinformatics (2008) 0.85
PartiGeneDB--collating partial genomes. Nucleic Acids Res (2005) 0.80
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics (2003) 12.00
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell (2007) 8.43
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. J Clin Oncol (2011) 8.37
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol (2013) 7.97
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell (2006) 5.72
STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell (2010) 5.67
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2003) 5.60
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell (2003) 5.57
ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res (2004) 5.44
High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov (2011) 5.30
Unique features of a highly pathogenic Campylobacter jejuni strain. Infect Immun (2006) 5.21
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
DNA-binding specificities of human transcription factors. Cell (2013) 5.14
High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91
Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet (2002) 4.68
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell (2004) 4.18
Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell (2006) 4.03
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res (2002) 3.93
A census of human soluble protein complexes. Cell (2012) 3.90
Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell (2006) 3.86
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol (2004) 3.72
Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res (2008) 3.69
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc (2009) 3.48
Identification of a bacterial type III effector family with G protein mimicry functions. Cell (2006) 3.47
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44
The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res (2004) 3.39
Using expression profiling data to identify human microRNA targets. Nat Methods (2007) 3.37
Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins (2003) 3.21
A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11
Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A (2008) 3.10
The synthetic genetic interaction spectrum of essential genes. Nat Genet (2005) 3.06
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics (2009) 3.05
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell (2011) 2.89
Conservation of core gene expression in vertebrate tissues. J Biol (2009) 2.84
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A (2004) 2.80
Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science (2011) 2.78
Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol (2008) 2.73
Why are there still over 1000 uncharacterized yeast genes? Genetics (2007) 2.71
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol (2009) 2.65
SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. Dev Cell (2007) 2.64
Systematic identification of mammalian regulatory motifs' target genes and functions. Nat Methods (2008) 2.58
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins (2005) 2.52
Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins (2007) 2.48
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) (2010) 2.47
High nucleosome occupancy is encoded at human regulatory sequences. PLoS One (2010) 2.43
Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell (2010) 2.43
RBPDB: a database of RNA-binding specificities. Nucleic Acids Res (2010) 2.42
RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesis. Mol Biol Cell (2003) 2.40
Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A (2006) 2.39
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34