Published in Nucleic Acids Res on June 04, 2008
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
Microbial interactions: from networks to models. Nat Rev Microbiol (2012) 3.28
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res (2009) 1.44
Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics (2010) 1.32
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res (2014) 1.29
jClust: a clustering and visualization toolbox. Bioinformatics (2009) 1.20
Bioinformatics resources for the study of gene regulation in bacteria. J Bacteriol (2008) 1.16
Network-based modeling of the human gut microbiome. Chem Biodivers (2010) 1.02
Linking proteins to signaling pathways for experiment design and evaluation. PLoS One (2012) 0.98
Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res (2011) 0.96
A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution. BMC Evol Biol (2010) 0.89
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res (2012) 0.89
The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics (2012) 0.88
Comprehensive Map of Molecules Implicated in Obesity. PLoS One (2016) 0.88
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. Mob DNA (2012) 0.83
MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnol J (2016) 0.81
A binary matrix factorization algorithm for protein complex prediction. Proteome Sci (2011) 0.77
Endothelial cell dysfunction and cardiac hypertrophy in the STOX1 model of preeclampsia. Sci Rep (2016) 0.77
Reconstruction of the temporal signaling network in Salmonella-infected human cells. Front Microbiol (2015) 0.76
Antiviral innate immunity through the lens of systems biology. Virus Res (2015) 0.75
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. BMC Syst Biol (2012) 0.75
Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC). PLoS One (2015) 0.75
No3CoGP: non-conserved and conserved coexpressed gene pairs. BMC Res Notes (2014) 0.75
Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis. Mol Cell Proteomics (2016) 0.75
An overview of bioinformatics methods for modeling biological pathways in yeast. Brief Funct Genomics (2015) 0.75
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. BMC Res Notes (2017) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
Lethality and centrality in protein networks. Nature (2001) 29.64
The large-scale organization of metabolic networks. Nature (2000) 27.57
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
The Gene Ontology project in 2008. Nucleic Acids Res (2007) 11.71
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03
MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res (2004) 8.58
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85
Functional and topological characterization of protein interaction networks. Proteomics (2004) 4.57
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Protein complex prediction via cost-based clustering. Bioinformatics (2004) 4.30
Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol (2005) 4.16
How reliable are experimental protein-protein interaction data? J Mol Biol (2003) 3.59
Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics (2003) 3.24
Detection of functional modules from protein interaction networks. Proteins (2004) 3.08
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol (2008) 1.92
Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol (2006) 1.81
Knowledge representation of signal transduction pathways. Bioinformatics (2001) 1.63
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics (2004) 1.56
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics (2007) 1.48
Graphs in molecular biology. BMC Bioinformatics (2007) 1.38
GraphCrunch: a tool for large network analyses. BMC Bioinformatics (2008) 1.35
Graph-based analysis of metabolic networks. Ernst Schering Res Found Workshop (2002) 1.35
Inferring meaningful pathways in weighted metabolic networks. J Mol Biol (2005) 1.28
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics (2008) 1.22
Hierarchical analysis of dependency in metabolic networks. Bioinformatics (2003) 1.20
Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res (2005) 1.19
An overview of data models for the analysis of biochemical pathways. Brief Bioinform (2003) 1.06
GeneMCL in microarray analysis. Comput Biol Chem (2005) 0.88
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85
RSAT: regulatory sequence analysis tools. Nucleic Acids Res (2008) 3.93
The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res (2004) 3.39
RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res (2011) 2.82
The EMBRACE web service collection. Nucleic Acids Res (2010) 2.26
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc (2008) 2.17
ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res (2009) 2.07
Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02
Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome. PLoS One (2010) 1.99
The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood (2009) 1.97
KLHL3 mutations cause familial hyperkalemic hypertension by impairing ion transport in the distal nephron. Nat Genet (2012) 1.93
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res (2011) 1.79
Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res (2010) 1.59
Alteration of the microRNA network during the progression of Alzheimer's disease. EMBO Mol Med (2013) 1.54
Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol Cell Biol (2007) 1.50
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids Res (2010) 1.47
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res (2012) 1.45
Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc (2008) 1.40
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol (2013) 1.35
Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics (2010) 1.32
The powerful law of the power law and other myths in network biology. Mol Biosyst (2009) 1.29
Inferring meaningful pathways in weighted metabolic networks. J Mol Biol (2005) 1.28
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J (2013) 1.26
Whole-exome sequencing and high throughput genotyping identified KCNJ11 as the thirteenth MODY gene. PLoS One (2012) 1.24
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics (2008) 1.22
Transcriptional regulation of protein complexes in yeast. Genome Biol (2004) 1.20
Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res (2005) 1.19
Highly sensitive diagnosis of 43 monogenic forms of diabetes or obesity through one-step PCR-based enrichment in combination with next-generation sequencing. Diabetes Care (2013) 1.18
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc (2008) 1.17
Metabolic pathfinding using RPAIR annotation. J Mol Biol (2009) 1.13
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc (2012) 1.07
Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl Environ Microbiol (2009) 1.06
An overview of data models for the analysis of biochemical pathways. Brief Bioinform (2003) 1.06
Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. Methods Mol Biol (2007) 1.03
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics (2009) 1.02
Clusters of conserved beta cell marker genes for assessment of beta cell phenotype. PLoS One (2011) 1.01
Discovery of motifs in promoters of coregulated genes. Methods Mol Biol (2007) 1.00
A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol Rev (2006) 1.00
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics (2009) 0.99
Modularity of the transcriptional response of protein complexes in yeast. J Mol Biol (2006) 0.98
Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res (2011) 0.96
Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS One (2011) 0.95
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PLoS One (2007) 0.95
PhiGO, a phage ontology associated with the ACLAME database. Res Microbiol (2007) 0.93
In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis. Plant Physiol (2003) 0.92
Soil microbiome responses to the short-term effects of Amazonian deforestation. Mol Ecol (2015) 0.92
Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data. Nat Protoc (2008) 0.91
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics (2005) 0.90
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics (2007) 0.87
p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle (2014) 0.84
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. Mob DNA (2012) 0.83
Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae. BMC Proc (2008) 0.82
Predicting metabolic pathways by sub-network extraction. Methods Mol Biol (2012) 0.79
Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems (2011) 0.79
Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. BMC Genomics (2013) 0.78
Novel LEPR mutations in obese Pakistani children identified by PCR-based enrichment and next generation sequencing. Obesity (Silver Spring) (2013) 0.76
In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics (2009) 0.76
Multi-class protein fold classification using a new ensemble machine learning approach. Genome Inform (2003) 0.75
Erratum: Genetic variants in LEP, LEPR, and MC4R explain 30% of severe obesity in children from a consanguineous population. Obesity (Silver Spring) (2017) 0.75