Published in BMC Bioinformatics on February 01, 2010
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics (2011) 0.90
Biblio-MetReS: a bibliometric network reconstruction application and server. BMC Bioinformatics (2011) 0.89
Large-scale structure of a network of co-occurring MeSH terms: statistical analysis of macroscopic properties. PLoS One (2014) 0.83
Systems biology elucidates common pathogenic mechanisms between nonalcoholic and alcoholic-fatty liver disease. PLoS One (2013) 0.83
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PLoS One (2012) 0.83
Extracting rate changes in transcriptional regulation from MEDLINE abstracts. BMC Bioinformatics (2014) 0.80
Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics (2011) 0.79
Text Mining for Protein Docking. PLoS Comput Biol (2015) 0.78
A systems biological approach reveals multiple crosstalk mechanism between gram-positive and negative bacterial infections: an insight into core mechanism and unique molecular signatures. PLoS One (2014) 0.75
Database constraints applied to metabolic pathway reconstruction tools. ScientificWorldJournal (2014) 0.75
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspect Biol Med (1986) 5.94
Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot (2007) 5.80
Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol (2006) 5.21
Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol (1999) 4.55
Text mining and its potential applications in systems biology. Trends Biotechnol (2006) 3.91
Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics (2005) 3.85
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
Medusa: a simple tool for interaction graph analysis. Bioinformatics (2005) 3.74
Text-mining and information-retrieval services for molecular biology. Genome Biol (2005) 3.54
Extraction of regulatory gene/protein networks from Medline. Bioinformatics (2005) 3.43
Automated extraction of information in molecular biology. FEBS Lett (2000) 3.28
Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays (2004) 3.08
AliBaba: PubMed as a graph. Bioinformatics (2006) 2.82
Mining MEDLINE: abstracts, sentences, or phrases? Pac Symp Biocomput (2002) 2.82
Salicylic acid in plant defence--the players and protagonists. Curr Opin Plant Biol (2007) 2.64
Salicylic acid-independent plant defence pathways. Trends Plant Sci (1999) 2.47
Regulatory metabolic networks in drought stress responses. Curr Opin Plant Biol (2007) 2.39
Mechanisms of high salinity tolerance in plants. Methods Enzymol (2007) 2.17
The role of ethylene in host-pathogen interactions. Annu Rev Phytopathol (2006) 1.87
Distribution of information in biomedical abstracts and full-text publications. Bioinformatics (2004) 1.84
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics (2007) 1.79
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform (2001) 1.73
MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res (2009) 1.64
Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp (2002) 1.55
Arena3D: visualization of biological networks in 3D. BMC Syst Biol (2008) 1.45
Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics (2006) 1.38
Response and adaptation by plants to flooding stress. Ann Bot (2005) 1.37
The molecular biology of the low-temperature response in plants. Bioessays (2005) 1.19
NLProt: extracting protein names and sequences from papers. Nucleic Acids Res (2004) 1.02
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res (2009) 1.00
Querying parse tree database of Medline text to synthesize user-specific biomolecular networks. Pac Symp Biocomput (2009) 0.98
Salicylic acid-, jasmonic acid- and ethylene-mediated regulation of plant defense signaling. Genet Eng (N Y) (2007) 0.91
Exploiting the full potential of disease-resistance genes for agricultural use. Curr Opin Biotechnol (2000) 0.79
Extracting information from the literature by text mining. Anal Chem (2001) 0.77
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet (2009) 3.73
A series of PDB related databases for everyday needs. Nucleic Acids Res (2010) 3.60
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics (2011) 3.03
Reflect: augmented browsing for the life scientist. Nat Biotechnol (2009) 2.99
Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers. Curr Biol (2008) 2.67
Identification of LRRC8 heteromers as an essential component of the volume-regulated anion channel VRAC. Science (2014) 2.42
Aversion to nicotine is regulated by the balanced activity of β4 and α5 nicotinic receptor subunits in the medial habenula. Neuron (2011) 2.23
Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins (2011) 2.23
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17
The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. BMC Biochem (2007) 2.14
K2D2: estimation of protein secondary structure from circular dichroism spectra. BMC Struct Biol (2008) 2.12
Gene function in early mouse embryonic stem cell differentiation. BMC Genomics (2007) 1.96
A directed protein interaction network for investigating intracellular signal transduction. Sci Signal (2011) 1.95
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res (2006) 1.95
Status of text-mining techniques applied to biomedical text. Drug Discov Today (2006) 1.95
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
A survey of visualization tools for biological network analysis. BioData Min (2008) 1.76
MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res (2009) 1.64
Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb) (2008) 1.63
Src activation by β-adrenoreceptors is a key switch for tumour metastasis. Nat Commun (2013) 1.62
Using graph theory to analyze biological networks. BioData Min (2011) 1.54
Oct4 targets regulatory nodes to modulate stem cell function. PLoS One (2007) 1.52
Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners. Bioessays (2013) 1.48
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today (2005) 1.46
Arena3D: visualization of biological networks in 3D. BMC Syst Biol (2008) 1.45
Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Res (2007) 1.42
Uncovering Earth's virome. Nature (2016) 1.40
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res (2012) 1.38
Recognition of 2'-O-methylated 3'-end of piRNA by the PAZ domain of a Piwi protein. Structure (2011) 1.37
Live coverage of scientific conferences using web technologies. PLoS Comput Biol (2010) 1.36
Integrating pathways of Parkinson's disease in a molecular interaction map. Mol Neurobiol (2013) 1.34
Evolving research trends in bioinformatics. Brief Bioinform (2006) 1.27
Taxonomic colouring of phylogenetic trees of protein sequences. BMC Bioinformatics (2006) 1.23
jClust: a clustering and visualization toolbox. Bioinformatics (2009) 1.20
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database (Oxford) (2014) 1.16
Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature (2010) 1.16
StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol Biol (2007) 1.15
Linking genes to diseases: it's all in the data. Genome Med (2009) 1.14
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol (2013) 1.10
Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res (2011) 1.10
Platinum nanoparticles and their cellular uptake and DNA platination at non-cytotoxic concentrations. Arch Toxicol (2011) 1.10
PU.1 level-directed chromatin structure remodeling at the Irf8 gene drives dendritic cell commitment. Cell Rep (2013) 1.09
Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput Biol (2009) 1.09
Microtubule-associated AIR9 recognizes the cortical division site at preprophase and cell-plate insertion. Curr Biol (2006) 1.09
A transcriptional roadmap to the induction of pluripotency in somatic cells. Stem Cell Rev (2010) 1.09
Nuclear calcium signaling in spinal neurons drives a genomic program required for persistent inflammatory pain. Neuron (2013) 1.09
Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics (2011) 1.07
Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network. PLoS One (2011) 1.06
Periostin shows increased evolutionary plasticity in its alternatively spliced region. BMC Evol Biol (2010) 1.06
Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie (2011) 1.05
Resident endothelial precursors in muscle, adipose, and dermis contribute to postnatal vasculogenesis. Stem Cells (2007) 1.05
Expression of protein elongation factor eEF1A2 predicts favorable outcome in breast cancer. Breast Cancer Res Treat (2006) 1.02
Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors. PLoS One (2013) 1.00
uORFdb--a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Res (2013) 0.99
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford) (2013) 0.99
Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition. PLoS One (2010) 0.99
Cellular uptake of platinum nanoparticles in human colon carcinoma cells and their impact on cellular redox systems and DNA integrity. Chem Res Toxicol (2009) 0.99
SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Res (2012) 0.98
CXCL5 limits macrophage foam cell formation in atherosclerosis. J Clin Invest (2013) 0.97
Live Coverage of Intelligent Systems for Molecular Biology/European Conference on computational biology (ISMB/ECCB) 2009. PLoS Comput Biol (2010) 0.97
Identification of gene 3' ends by automated EST cluster analysis. Proc Natl Acad Sci U S A (2008) 0.97
Toward silicon anodes for next-generation lithium ion batteries: a comparative performance study of various polymer binders and silicon nanopowders. ACS Appl Mater Interfaces (2013) 0.97
Using cited references to improve the retrieval of related biomedical documents. BMC Bioinformatics (2013) 0.96
Ultraviolet photoluminescence of ZnO quantum dots sputtered at room-temperature. Opt Express (2011) 0.96
From experimental setup to bioinformatics: an RNAi screening platform to identify host factors involved in HIV-1 replication. Biotechnol J (2010) 0.96
iAnn: an event sharing platform for the life sciences. Bioinformatics (2013) 0.96
ROMO1 is an essential redox-dependent regulator of mitochondrial dynamics. Sci Signal (2014) 0.96
Martini: using literature keywords to compare gene sets. Nucleic Acids Res (2009) 0.95
Molecular basis for pacemaker cells in epithelia. J Biol Chem (2002) 0.95
Implementation of an in vitro model system for investigation of reperfusion damage after renal ischemia. Cell Physiol Biochem (2009) 0.94
A role for GPx3 in activity of normal and leukemia stem cells. J Exp Med (2012) 0.94
Prediction of miRNA targets. Methods Mol Biol (2015) 0.93
Towards completion of the Earth's proteome. EMBO Rep (2007) 0.93
Cardiac alpha-myosin (MYH6) is the predominant sarcomeric disease gene for familial atrial septal defects. PLoS One (2011) 0.93
OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (2009) 0.92
Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni. Mem Inst Oswaldo Cruz (2006) 0.92
Mild therapeutic hypothermia after out-of-hospital cardiac arrest complicating ST-elevation myocardial infarction: long-term results in clinical practice. Clin Cardiol (2013) 0.92
Mitochondrial carriers and pores: key regulators of the mitochondrial apoptotic program? Apoptosis (2007) 0.92
Emergence and evolution of the renin-angiotensin-aldosterone system. J Mol Med (Berl) (2012) 0.91
Naïve adult stem cells from patients with Hutchinson-Gilford progeria syndrome express low levels of progerin in vivo. Biol Open (2012) 0.91
Medusa: A tool for exploring and clustering biological networks. BMC Res Notes (2011) 0.91
Which clustering algorithm is better for predicting protein complexes? BMC Res Notes (2011) 0.90
Facile preparation of water-soluble fluorescent gold nanoclusters for cellular imaging applications. Nanoscale (2011) 0.90
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics (2011) 0.90
Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLoS Genet (2012) 0.90
The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res (2004) 0.89