Biomedical discovery acceleration, with applications to craniofacial developmentGetting started in text miningThe International Society for Computational Biology 10th AnniversaryOpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expressionChanges to NIH Grant System May BackfireCurrent methodologies for translational bioinformaticsU-Compare: share and compare text mining tools with UIMAEDGAR: extraction of drugs, genes and relations from the biomedical literatureBiomedical language processing: what's beyond PubMed?Ontologies for programs, not people.A survey of computational tools for downstream analysis of proteomic and other omic datasetsGene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.KaBOB: ontology-based semantic integration of biomedical databases.Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parametersCombining heterogenous data for prediction of disease related and pharmacogenesU-Compare bio-event meta-service: compatible BioNLP event extraction servicesAn open-source framework for large-scale, flexible evaluation of biomedical text mining systems.The textual characteristics of traditional and Open Access scientific journals are similar.Concept annotation in the CRAFT corpus.Visual management of large scale data mining projects.Mining molecular binding terminology from biomedical text.Visual analysis of biological data-knowledge networksOntologies in biological data visualization.MutationFinder: a high-performance system for extracting point mutation mentions from text.The PhenoGen informatics website: tools for analyses of complex traits.GeneRIF quality assurance as summary revision.Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breedHIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.Empirical data on corpus design and usage in biomedical natural language processing.BioCreAtIvE task1A: entity identification with a stochastic tagger.Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.Finding GeneRIFs via gene ontology annotations.Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling.Improving protein function prediction methods with integrated literature data.Semantic role labeling for protein transport predicates.The topology of the bacterial co-conserved protein network and its implications for predicting protein function.Nominalization and alternations in biomedical language.Predicting protein linkages in bacteria: which method is best depends on task.Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins.
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