Published in J Biomed Inform on August 17, 2010
From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med (2011) 4.05
A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
EliXR: an approach to eligibility criteria extraction and representation. J Am Med Inform Assoc (2011) 2.26
Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88
PharmGKB: the Pharmacogenomics Knowledge Base. Methods Mol Biol (2013) 1.81
Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet (2012) 1.68
Discovery and explanation of drug-drug interactions via text mining. Pac Symp Biocomput (2012) 1.53
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinformatics (2015) 1.44
Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semantics (2011) 1.29
Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness. J Biomed Semantics (2013) 1.22
A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text. J Biomed Inform (2012) 1.19
Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature. J Biomed Inform (2014) 1.18
Semantically enabling pharmacogenomic data for the realization of personalized medicine. Pharmacogenomics (2012) 1.05
Systematic identification of pharmacogenomics information from clinical trials. J Biomed Inform (2012) 1.03
Mining the pharmacogenomics literature--a survey of the state of the art. Brief Bioinform (2012) 1.02
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PLoS One (2014) 0.94
Databases in the area of pharmacogenetics. Hum Mutat (2011) 0.91
Connecting the dots between PubMed abstracts. PLoS One (2012) 0.91
A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. J Biomed Inform (2013) 0.90
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. J Biomed Inform (2012) 0.90
Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics (2013) 0.88
Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation. Pac Symp Biocomput (2012) 0.86
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. Brief Bioinform (2016) 0.86
A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform (2012) 0.83
Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. AMIA Annu Symp Proc (2013) 0.80
Trends in computational biology—2010. Nat Biotechnol (2011) 0.79
Combining position weight matrices and document-term matrix for efficient extraction of associations of methylated genes and diseases from free text. PLoS One (2013) 0.79
Automating case definitions using literature-based reasoning. Appl Clin Inform (2013) 0.78
Formalizing biomedical concepts from textual definitions. J Biomed Semantics (2015) 0.75
Learning the Structure of Biomedical Relationships from Unstructured Text. PLoS Comput Biol (2015) 0.75
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics (2001) 6.05
Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J (2001) 5.94
RelEx--relation extraction using dependency parse trees. Bioinformatics (2006) 4.81
Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol (1999) 4.55
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol (2008) 3.54
Extraction of regulatory gene/protein networks from Medline. Bioinformatics (2005) 3.43
Extracting semantic predications from Medline citations for pharmacogenomics. Pac Symp Biocomput (2007) 3.04
OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics (2008) 2.81
Empirical distributional semantics: methods and biomedical applications. J Biomed Inform (2009) 2.45
Semantic relations asserting the etiology of genetic diseases. AMIA Annu Symp Proc (2003) 2.32
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics (2009) 2.15
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol (2009) 1.90
Unsupervised method for automatic construction of a disease dictionary from a large free text collection. AMIA Annu Symp Proc (2008) 1.78
Towards pharmacogenomics knowledge discovery with the semantic web. Brief Bioinform (2009) 1.24
Querying parse tree database of Medline text to synthesize user-specific biomolecular networks. Pac Symp Biocomput (2009) 0.98
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res (2009) 10.58
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
The incidentalome: a threat to genomic medicine. JAMA (2006) 7.24
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res (2011) 6.59
Genetics. Genomic research and human subject privacy. Science (2004) 6.56
PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res (2002) 6.40
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
Development of large-scale functional brain networks in children. PLoS Biol (2009) 5.25
Network analysis of intrinsic functional brain connectivity in Alzheimer's disease. PLoS Comput Biol (2008) 5.15
Biomedical ontologies: a functional perspective. Brief Bioinform (2007) 4.67
The open biomedical annotator. Summit on Translat Bioinforma (2009) 4.19
From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med (2011) 4.05
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics (2003) 3.97
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res (2002) 3.77
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Health-information altruists--a potentially critical resource. N Engl J Med (2005) 3.61
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine. Circulation (2013) 3.45
Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc (2002) 3.32
Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. Lancet (2013) 3.21
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Data-driven prediction of drug effects and interactions. Sci Transl Med (2012) 2.93
Challenges in the clinical application of whole-genome sequencing. Lancet (2010) 2.92
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet (2007) 2.65
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
The National Center for Biomedical Ontology. J Am Med Inform Assoc (2011) 2.55
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J Am Med Inform Assoc (2011) 2.53
Clinical implementation of pharmacogenomics: overcoming genetic exceptionalism. Lancet Oncol (2010) 2.52
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res (2007) 2.45
The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation. Clin Pharmacol Ther (2013) 2.39
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
Time to organize the bioinformatics resourceome. PLoS Comput Biol (2005) 2.25
MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics (2008) 2.24
Using binning to maintain confidentiality of medical data. Proc AMIA Symp (2002) 2.23
Web-scale pharmacovigilance: listening to signals from the crowd. J Am Med Inform Assoc (2013) 2.19
iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics (2009) 2.15
PharmGKB: understanding the effects of individual genetic variants. Drug Metab Rev (2008) 2.09
GAPSCORE: finding gene and protein names one word at a time. Bioinformatics (2004) 2.05
The Stanford Tissue Microarray Database. Nucleic Acids Res (2007) 1.96
Pharmacogenomics: challenges and opportunities. Ann Intern Med (2006) 1.96
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res (2004) 1.92
Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics (2010) 1.91
Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88
Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. J Biomed Semantics (2012) 1.83
Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput (2002) 1.81
In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat (2010) 1.81
PharmGKB: the Pharmacogenomics Knowledge Base. Methods Mol Biol (2013) 1.81
PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol (2005) 1.80
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res (2008) 1.78
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J Am Med Inform Assoc (2012) 1.73
Using text analysis to identify functionally coherent gene groups. Genome Res (2002) 1.71
Comparison of ontology-based semantic-similarity measures. AMIA Annu Symp Proc (2008) 1.69
A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. AMIA Annu Symp Proc (2010) 1.68
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics (2008) 1.64
Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet (2004) 1.61
Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions. J Am Med Inform Assoc (2012) 1.60
MutDB: annotating human variation with functionally relevant data. Bioinformatics (2003) 1.54
BioPortal: ontologies and data resources with the click of a mouse. AMIA Annu Symp Proc (2008) 1.54
Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A (2008) 1.54
Doxorubicin pathways: pharmacodynamics and adverse effects. Pharmacogenet Genomics (2011) 1.53
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc (2004) 1.53
Building a biomedical ontology recommender web service. J Biomed Semantics (2010) 1.53
Discovery and explanation of drug-drug interactions via text mining. Pac Symp Biocomput (2012) 1.53
The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res (2003) 1.44
Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform (2010) 1.39
Mining clinical text for signals of adverse drug-drug interactions. J Am Med Inform Assoc (2013) 1.38
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol (2006) 1.38
Metformin pathways: pharmacokinetics and pharmacodynamics. Pharmacogenet Genomics (2012) 1.38
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc (2004) 1.37
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res (2003) 1.35
A literature-based method for assessing the functional coherence of a gene group. Bioinformatics (2003) 1.33
A call for the creation of personalized medicine databases. Nat Rev Drug Discov (2006) 1.30
Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics (2004) 1.30
Using ODIN for a PharmGKB revalidation experiment. Database (Oxford) (2012) 1.29
Using temporal patterns in medical records to discern adverse drug events from indications. AMIA Jt Summits Transl Sci Proc (2012) 1.29
Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semantics (2011) 1.29
The coming age of data-driven medicine: translational bioinformatics' next frontier. J Am Med Inform Assoc (2012) 1.29
Biomedical term mapping databases. Nucleic Acids Res (2005) 1.29
Very important pharmacogene summary: ABCB1 (MDR1, P-glycoprotein). Pharmacogenet Genomics (2011) 1.29
Informatics confronts drug-drug interactions. Trends Pharmacol Sci (2013) 1.28
Turning limited experimental information into 3D models of RNA. RNA (2010) 1.27
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc (2008) 1.27
Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes. PLoS One (2013) 1.27
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Web Semant (2011) 1.27
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics (2011) 1.27
PharmGKB summary: methotrexate pathway. Pharmacogenet Genomics (2011) 1.27
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci U S A (2007) 1.26