Network2Canvas: network visualization on a canvas with enrichment analysis

Sets2Networks: network inference from repeated observations of sets

(2012) Neil R Clark et al.   BMC Systems Biology

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

(2012) Jordi Barretina et al.   NATURE

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

(2011) Edward Y. Chen et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports

(2011) Nicholas P Tatonetti et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

(2011) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

GATE: software for the analysis and visualization of high-dimensional time series expression data

(2009) Ben D. MacArthur et al.   BIOINFORMATICS

KEA: kinase enrichment analysis

(2009) A. Lachmann et al.   BIOINFORMATICS

Direct reprogramming of human neural stem cells by OCT4

(2009) Jeong Beom Kim et al.   NATURE

GeneSigDB—a curated database of gene expression signatures

(2009) Aedín C. Culhane et al.   NUCLEIC ACIDS RESEARCH

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH