Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions: Fig. 1.

(2015) Gregory W. Gundersen et al.   BIOINFORMATICS

Dynamics of the discovery process of protein-protein interactions from low content studies

(2015) Zichen Wang et al.   BMC Systems Biology

Crowdsourcing in biomedicine: challenges and opportunities

(2015) Ritu Khare et al.   BRIEFINGS IN BIOINFORMATICS

Ranking Adverse Drug Reactions With Crowdsourcing

(2015) Assaf Gottlieb et al.   JOURNAL OF MEDICAL INTERNET RESEARCH

DISEASES: Text mining and data integration of disease–gene associations

(2015) Sune Pletscher-Frankild et al.   METHODS

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

(2015) Qian Zhu et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Scaling drug indication curation through crowdsourcing

(2015) Ritu Khare et al.   Database-The Journal of Biological Databases and Curation

Crowdsourcing the General Public for Large Scale Molecular Pathology Studies in Cancer

(2015) Francisco J. Candido dos Reis et al.   EBioMedicine

mirPub: a database for searching microRNA publications

(2014) Thanasis Vergoulis et al.   BIOINFORMATICS

The characteristic direction: a geometrical approach to identify differentially expressed genes

(2014) Neil R Clark et al.   BMC BIOINFORMATICS

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

(2014) Warren A. Kibbe et al.   NUCLEIC ACIDS RESEARCH

Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

(2014) John D. Burger et al.   Database-The Journal of Biological Databases and Curation

BeCAS: biomedical concept recognition services and visualization

(2013) T. Nunes et al.   BIOINFORMATICS

Crowdsourcing for bioinformatics

(2013) B. M. Good et al.   BIOINFORMATICS

Imatinib for Melanomas Harboring Mutationally Activated or Amplified KIT Arising on Mucosal, Acral, and Chronically Sun-Damaged Skin

(2013) F. Stephen Hodi et al.   JOURNAL OF CLINICAL ONCOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

ExpressionBlast: mining large, unstructured expression databases

(2013) Guy E Zinman et al.   NATURE METHODS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

A searchable cross-platform gene expression database reveals connections between drug treatments and disease

(2012) Gareth Williams   BMC GENOMICS

Insulin resistance: A significant risk factor of endometrial cancer

(2012) Nan Mu et al.   GYNECOLOGIC ONCOLOGY

Targeting Estrogen Receptor-α Reduces Adrenocortical Cancer (ACC) Cell Growthin Vitroandin Vivo: Potential Therapeutic Role of Selective Estrogen Receptor Modulators (SERMs) for ACC Treatment

(2012) Rosa Sirianni et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Understanding obesity and endometrial cancer risk: opportunities for prevention

(2011) Rosemarie E. Schmandt et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

(2011) Jesse M. Engreitz et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

SIGNATURE: A workbench for gene expression signature analysis

(2011) Jeffrey T Chang et al.   BMC BIOINFORMATICS

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

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

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

(2009) Chunlai Feng et al.   BMC GENOMICS

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

(2008) Michael J Boedigheimer et al.   BMC GENOMICS

Targeting CD24 for Treatment of Colorectal and Pancreatic Cancer by Monoclonal Antibodies or Small Interfering RNA

(2008) E. Sagiv et al.   CANCER RESEARCH

Reduced expression of low-density lipoprotein receptor in hepatocellular carcinoma with paraneoplastic hypercholesterolemia

(2007) Tetsuro Sohda et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY