Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

FNTM: a server for predicting functional networks of tissues in mouse

(2015) Jonathan Goya et al.   NUCLEIC ACIDS RESEARCH

Biological interpretation of genome-wide association studies using predicted gene functions

(2015) Tune H. Pers et al.   Nature Communications

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Precision Medicine Meets Public Health: Population Screening for BRCA1 and BRCA2

(2014) E. Levy-Lahad et al.   JNCI-Journal of the National Cancer Institute

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

(2014) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

(2014) Daniel Gusenleitner et al.   PLoS One

Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression Modules

(2014) Gregory J. Tawa et al.   PLoS One

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

tmVar: a text mining approach for extracting sequence variants in biomedical literature

(2013) C.-H. Wei et al.   BIOINFORMATICS

Biological network extraction from scientific literature: state of the art and challenges

(2013) C. Li et al.   BRIEFINGS IN BIOINFORMATICS

BRAFmutation testing algorithm for vemurafenib treatment in melanoma: recommendations from an expert panel

(2013) D. Gonzalez et al.   BRITISH JOURNAL OF DERMATOLOGY

Mode of action and dose–response framework analysis for receptor-mediated toxicity: The aryl hydrocarbon receptor as a case study

(2013) R. A. Budinsky et al.   CRITICAL REVIEWS IN TOXICOLOGY

Defining cell-type specificity at the transcriptional level in human disease

(2013) Wenjun Ju et al.   GENOME RESEARCH

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

Practice-Based Evidence: Profiling the Safety of Cilostazol by Text-Mining of Clinical Notes

(2013) Nicholas J. Leeper et al.   PLoS One

Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil

(2013) Magbubah Essack et al.   PLoS One

Progress in computational toxicology

(2013) Sean Ekins   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

(2013) Christopher Y. Park et al.   PLoS Computational Biology

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

(2012) Karin Verspoor et al.   BMC BIOINFORMATICS

Mining the pharmacogenomics literature--a survey of the state of the art

(2012) U. Hahn et al.   BRIEFINGS IN BIOINFORMATICS

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Text-mining solutions for biomedical research: enabling integrative biology

(2012) Dietrich Rebholz-Schuhmann et al.   NATURE REVIEWS GENETICS

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2012) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature

(2012) Rajesh Chowdhary et al.   PLoS One

Incorporating Biological, Chemical, and Toxicological Knowledge Into Predictive Models of Toxicity

(2012) David J. Dix et al.   TOXICOLOGICAL SCIENCES

A Comprehensive Statistical Analysis of Predicting In Vivo Hazard Using High-Throughput In Vitro Screening

(2012) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

The GNAT library for local and remote gene mention normalization

(2011) J. Hakenberg et al.   BIOINFORMATICS

The G protein-coupled receptors in the pufferfish Takifugu rubripes

(2011) Anita Sarkar et al.   BMC BIOINFORMATICS

PILGRM: an interactive data-driven discovery platform for expert biologists

(2011) C. S. Greene et al.   NUCLEIC ACIDS RESEARCH

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

(2011) P. L. Whetzel et al.   NUCLEIC ACIDS RESEARCH

Effect of Population Heterogenization on the Reproducibility of Mouse Behavior: A Multi-Laboratory Study

(2011) S. Helene Richter et al.   PLoS One

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

PubMed and beyond: a survey of web tools for searching biomedical literature

(2011) Z. Lu   Database-The Journal of Biological Databases and Curation

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

(2011) Dietrich Rebholz-Schuhmann et al.   Journal of Biomedical Semantics

LINNAEUS: A species name identification system for biomedical literature

(2010) Martin Gerner et al.   BMC BIOINFORMATICS

A guide to web tools to prioritize candidate genes

(2010) L.-C. Tranchevent et al.   BRIEFINGS IN BIOINFORMATICS

Predicting genetic modifier loci using functional gene networks

(2010) I. Lee et al.   GENOME RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Recent progress in automatically extracting information from the pharmacogenomic literature

(2010) Yael Garten et al.   PHARMACOGENOMICS

Event extraction for systems biology by text mining the literature

(2010) Sophia Ananiadou et al.   TRENDS IN BIOTECHNOLOGY

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

(2010) Raoul Frijters et al.   PLoS Computational Biology

High-performance gene name normalization with GENO

(2009) J. Wermter et al.   BIOINFORMATICS

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Overview of Developmental Heart Defects by Dioxins, PCBs, and Pesticides

(2009) PHILLIP G. KOPF et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART C-ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS

Rembrandt: Helping Personalized Medicine Become a Reality through Integrative Translational Research

(2009) S. Madhavan et al.   MOLECULAR CANCER RESEARCH

Environmental standardization: cure or cause of poor reproducibility in animal experiments?

(2009) S Helene Richter et al.   NATURE METHODS

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

(2009) Matthew A. Hibbs et al.   PLoS Computational Biology

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

(2009) David C. Hess et al.   PLoS Genetics

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inter-species normalization of gene mentions with GNAT

(2008) J. Hakenberg et al.   BIOINFORMATICS

A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model

(2008) Richard Judson et al.   BMC BIOINFORMATICS

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

(2008) Wei Yu et al.   BMC BIOINFORMATICS

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy

(2008) Xiangrong Kong et al.   BMC GENOMICS

PharmGKB: Understanding the Effects of Individual Genetic Variants

(2008) Katrin Sangkuhl et al.   DRUG METABOLISM REVIEWS

The Toxicity Data Landscape for Environmental Chemicals

(2008) Richard Judson et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

ENDEAVOUR update: a web resource for gene prioritization in multiple species

(2008) L.-C. Tranchevent et al.   NUCLEIC ACIDS RESEARCH

Getting Started in Text Mining

(2008) K. Bretonnel Cohen et al.   PLoS Computational Biology

A Genomewide Functional Network for the Laboratory Mouse

(2008) Yuanfang Guan et al.   PLoS Computational Biology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY