Published in Genome Biol on September 01, 2008
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc (2011) 3.14
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
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics (2009) 2.78
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 2.69
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics (2008) 2.32
Overview of the BioCreative III Workshop. BMC Bioinformatics (2011) 2.31
Integrating text mining into the MGI biocuration workflow. Database (Oxford) (2009) 2.21
Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res (2008) 2.09
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J Cheminform (2015) 1.96
Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biol (2008) 1.83
OntoGene in BioCreative II. Genome Biol (2008) 1.65
For I dipped into the future. EMBO Rep (2010) 1.59
Biomedical text mining and its applications. PLoS Comput Biol (2009) 1.46
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J Biomed Semantics (2011) 1.43
Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics (2010) 1.33
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
Automated recognition of brain region mentions in neuroscience literature. Front Neuroinform (2009) 1.00
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics (2011) 0.99
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics (2011) 0.99
Exploring species-based strategies for gene normalization. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.97
Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. J Biomed Biotechnol (2010) 0.97
tmBioC: improving interoperability of text-mining tools with BioC. Database (Oxford) (2014) 0.87
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. BMC Bioinformatics (2011) 0.81
Integrated bio-entity network: a system for biological knowledge discovery. PLoS One (2011) 0.80
BioDEAL: community generation of biological annotations. BMC Med Inform Decis Mak (2009) 0.75
The distributed annotation system. BMC Bioinformatics (2001) 42.98
A survey of current work in biomedical text mining. Brief Bioinform (2005) 7.64
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics (2005) 6.92
A gene network for navigating the literature. Nat Genet (2004) 6.43
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
Web services at the European bioinformatics institute. Nucleic Acids Res (2007) 4.48
Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics (2005) 3.85
Text-mining and information-retrieval services for molecular biology. Genome Biol (2005) 3.54
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol (2008) 3.54
Term identification in the biomedical literature. J Biomed Inform (2004) 3.22
Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics (2005) 3.01
AliBaba: PubMed as a graph. Bioinformatics (2006) 2.82
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinformatics (2006) 2.74
iHOP web services. Nucleic Acids Res (2007) 2.65
Data-poor categorization and passage retrieval for gene ontology annotation in Swiss-Prot. BMC Bioinformatics (2005) 2.14
BioCreAtIvE task1A: entity identification with a stochastic tagger. BMC Bioinformatics (2005) 2.05
Structure prediction meta server. Bioinformatics (2001) 2.02
Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol (2008) 1.93
Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biol (2008) 1.83
Finding the evidence for protein-protein interactions from PubMed abstracts. Bioinformatics (2006) 1.56
Rule-based human gene normalization in biomedical text with confidence estimation. Comput Syst Bioinformatics Conf (2007) 1.51
Automating curation using a natural language processing pipeline. Genome Biol (2008) 1.17
GPSDB: a new database for synonyms expansion of gene and protein names. Bioinformatics (2004) 1.01
Meta, Meta(N) and cyber servers. Bioinformatics (2003) 0.84
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics (2005) 14.50
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell (2006) 11.98
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet (2011) 6.43
A gene network for navigating the literature. Nat Genet (2004) 6.43
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics (2005) 6.02
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res (2006) 5.60
Relation between microRNA expression and progression and prognosis of gastric cancer: a microRNA expression analysis. Lancet Oncol (2009) 5.56
Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet (2009) 5.31
In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell (2011) 5.19
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
MicroRNA profiling of the murine hematopoietic system. Genome Biol (2005) 4.94
Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (2003) 4.88
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform (2004) 4.57
PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Pigment Cell Melanoma Res (2010) 4.50
Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev (2009) 4.43
Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol (2008) 4.36
Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun (2013) 4.35
Functional copy-number alterations in cancer. PLoS One (2008) 4.27
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (2007) 4.16
Event extraction with complex event classification using rich features. J Bioinform Comput Biol (2010) 4.09
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
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
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
Mesenchymal stem cell implantation in a swine myocardial infarct model: engraftment and functional effects. Ann Thorac Surg (2002) 3.62
A series of PDB related databases for everyday needs. Nucleic Acids Res (2010) 3.60
Text-mining and information-retrieval services for molecular biology. Genome Biol (2005) 3.54
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol (2008) 3.54
Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol (2007) 3.46
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet (2011) 3.41
Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol (2010) 3.37
Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron (2009) 3.27
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet (2012) 3.08
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