Published in Bioinformatics on September 27, 2005
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics (2009) 1.96
MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res (2010) 1.79
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res (2007) 1.76
A survey of visualization tools for biological network analysis. BioData Min (2008) 1.76
Genes and (common) pathways underlying drug addiction. PLoS Comput Biol (2007) 1.57
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol (2007) 1.53
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. Genome Biol (2008) 1.49
Arena3D: visualization of biological networks in 3D. BMC Syst Biol (2008) 1.45
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet (2006) 1.31
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res (2010) 1.26
jClust: a clustering and visualization toolbox. Bioinformatics (2009) 1.20
AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics (2009) 1.17
Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells. Cell Stress Chaperones (2010) 1.10
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res (2009) 1.09
PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics (2009) 1.07
GTPase-mediated regulation of the unfolded protein response in Caenorhabditis elegans is dependent on the AAA+ ATPase CDC-48. Mol Cell Biol (2008) 1.06
Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol (2009) 1.05
FunSimMat update: new features for exploring functional similarity. Nucleic Acids Res (2009) 1.04
Analysis of human and mouse reprogramming of somatic cells to induced pluripotent stem cells. What is in the plate? PLoS One (2010) 1.02
LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics (2010) 1.00
Role of pro-oncogenic protein disulfide isomerase (PDI) family member anterior gradient 2 (AGR2) in the control of endoplasmic reticulum homeostasis. J Biol Chem (2011) 0.98
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98
Construction and analysis of protein-protein interaction networks. Autom Exp (2010) 0.94
Visualization of protein interaction networks: problems and solutions. BMC Bioinformatics (2013) 0.92
Medusa: A tool for exploring and clustering biological networks. BMC Res Notes (2011) 0.91
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics (2011) 0.90
Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD. Behav Brain Funct (2007) 0.89
CFL1 expression levels as a prognostic and drug resistance marker in nonsmall cell lung cancer. Cancer (2010) 0.89
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Res (2010) 0.84
TVNViewer: an interactive visualization tool for exploring networks that change over time or space. Bioinformatics (2011) 0.84
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database (Oxford) (2010) 0.84
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. J R Soc Interface (2008) 0.83
Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Res (2008) 0.83
Systems biology elucidates common pathogenic mechanisms between nonalcoholic and alcoholic-fatty liver disease. PLoS One (2013) 0.83
Altered expression of Alzheimer's disease-related genes in the cerebellum of autistic patients: a model for disrupted brain connectome and therapy. Cell Death Dis (2014) 0.83
Systems pharmacology of mifepristone (RU486) reveals its 47 hub targets and network: comprehensive analysis and pharmacological focus on FAK-Src-Paxillin complex. Sci Rep (2015) 0.82
Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens. PLoS One (2013) 0.82
Major components of energy drinks (caffeine, taurine, and guarana) exert cytotoxic effects on human neuronal SH-SY5Y cells by decreasing reactive oxygen species production. Oxid Med Cell Longev (2013) 0.82
Evolutionary plasticity determination by orthologous groups distribution. Biol Direct (2011) 0.82
Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes. J Proteome Res (2014) 0.81
Impaired expression of NER gene network in sporadic solid tumors. Nucleic Acids Res (2007) 0.80
Secretome of the biocontrol agent metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection. J Proteome Res (2014) 0.79
Constructing the HBV-human protein interaction network to understand the relationship between HBV and hepatocellular carcinoma. J Exp Clin Cancer Res (2010) 0.78
Comparative transcriptome profiling of two Brassica napus cultivars under chromium toxicity and its alleviation by reduced glutathione. BMC Genomics (2016) 0.77
Pregnancy-induced gingivitis and OMICS in dentistry: in silico modeling and in vivo prospective validation of estradiol-modulated inflammatory biomarkers. OMICS (2014) 0.77
The gene expression profiles of induced pluripotent stem cells (iPSCs) generated by a non-integrating method are more similar to embryonic stem cells than those of iPSCs generated by an integrating method. Genet Mol Biol (2012) 0.77
Snazer: the simulations and networks analyzer. BMC Syst Biol (2010) 0.77
Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease. Sci Rep (2015) 0.77
Dspp mutations disrupt mineralization homeostasis during odontoblast differentiation. Am J Transl Res (2015) 0.76
Cellular Metabolic Network Analysis: Discovering Important Reactions in Treponema pallidum. Biomed Res Int (2015) 0.76
Proteomic analysis of effluents from perfused human heart for transplantation: identification of potential biomarkers for ischemic heart damage. Proteome Sci (2012) 0.75
Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae. Int J Proteomics (2016) 0.75
Sequencing and bioinformatics analysis of the differentially expressed genes in herniated discs with or without calcification. Int J Mol Med (2016) 0.75
Physiological Mechanisms Only Tell Half Story: Multiple Biological Processes are involved in Regulating Freezing Tolerance of Imbibed Lactuca sativa Seeds. Sci Rep (2017) 0.75
WebGIVI: a web-based gene enrichment analysis and visualization tool. BMC Bioinformatics (2017) 0.75
Infection with Plasmodium berghei ookinetes alters protein expression in the brain of Anopheles albimanus mosquitoes. Parasit Vectors (2016) 0.75
Plant toxin β-ODAP activates integrin β1 and focal adhesion: A critical pathway to cause neurolathyrism. Sci Rep (2017) 0.75
An integrated approach of predicted miR-34a targets identifies a signature for gastric cancer. Oncol Lett (2015) 0.75
RNA-Seq Profiling of Intact and Enucleated Oocyte SCNT Embryos Reveals the Role of Pig Oocyte Nucleus in Somatic Reprogramming. PLoS One (2016) 0.75
Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human. PLoS One (2016) 0.75
3DProIN: Protein-Protein Interaction Networks and Structure Visualization. Am J Bioinform Comput Biol (2014) 0.75
Genome scale modeling in systems biology: algorithms and resources. Curr Genomics (2014) 0.75
Comparative proteomic analysis of proteins expression changes in the mammary tissue of cows infected with Escherichia coli mastitis. J Vet Sci (2014) 0.75
MicroRNA profile comparison of the corneal endothelia of young and old mice: implications for senescence of the corneal endothelium. Mol Vis (2013) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Comparative metagenomics of microbial communities. Science (2005) 25.88
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res (2002) 25.06
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Enterotypes of the human gut microbiome. Nature (2011) 24.36
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 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Drug target identification using side-effect similarity. Science (2008) 9.24
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
Bioinformatics in the post-sequence era. Nat Genet (2003) 8.83
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev (2006) 8.78
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res (2007) 4.84
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Res (2003) 4.42
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
A genome-wide survey of human pseudogenes. Genome Res (2003) 4.34
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol (2008) 3.95
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev (2007) 3.92
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Prediction of effective genome size in metagenomic samples. Genome Biol (2007) 3.73
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J (2003) 3.68
Systematic identification of novel protein domain families associated with nuclear functions. Genome Res (2002) 3.50
SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics (2010) 3.48
Function prediction and protein networks. Curr Opin Cell Biol (2003) 3.46
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Extraction of regulatory gene/protein networks from Medline. Bioinformatics (2005) 3.43
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Dev Cell (2006) 3.29
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
The DNA sequence of human chromosome 7. Nature (2003) 3.18
Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol (2007) 3.15
Accurate and universal delineation of prokaryotic species. Nat Methods (2013) 3.14
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06
Environments shape the nucleotide composition of genomes. EMBO Rep (2005) 2.96
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A (2009) 2.89
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol (2004) 2.83
SHOT: a web server for the construction of genome phylogenies. Trends Genet (2002) 2.79
ASTD: The Alternative Splicing and Transcript Diversity database. Genomics (2008) 2.72
A holistic approach to marine eco-systems biology. PLoS Biol (2011) 2.71
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. Genomics (2003) 2.69
NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res (2007) 2.69
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Information extraction from full text scientific articles: where are the keywords? BMC Bioinformatics (2003) 2.64
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA (2005) 2.59
The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci U S A (2002) 2.59
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
iPath2.0: interactive pathway explorer. Nucleic Acids Res (2011) 2.50