Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

(2016) Sara J.C. Gosline et al.   Cell Reports

Identification of a PEAK1/ZEB1 signaling axis during TGFβ/fibronectin-induced EMT in breast cancer

(2015) Megan Agajanian et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Statistics requantitates the central dogma

(2015) J. J. Li et al.   SCIENCE

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

(2014) Nicolas Alcaraz et al.   BMC Systems Biology

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network

(2014) D. Chasman et al.   Molecular Systems Biology

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

EGFR and c-Met Cross Talk in Glioblastoma and Its Regulation by Human Cord Blood Stem Cells

(2014) Kiran Kumar Velpula et al.   Translational Oncology

Identifying proteins controlling key disease signaling pathways

(2013) Anthony Gitter et al.   BIOINFORMATICS

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

(2013) Nurcan Tuncbag et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

STITCH 4: integration of protein–chemical interactions with user data

(2013) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Extensive changes in DNA methylation are associated with expression of mutant huntingtin

(2013) C. W. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

(2013) Shao-shan Carol Huang et al.   PLoS Computational Biology

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

(2013) Ashwini Patil et al.   PLoS Computational Biology

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

(2012) A. Gitter et al.   GENOME RESEARCH

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets

(2012) Sara J. C. Gosline et al.   Integrative Biology

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

(2011) A. Lan et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

A systems view of epithelial–mesenchymal transition signaling states

(2010) Stuart Thomson et al.   CLINICAL & EXPERIMENTAL METASTASIS

The output of Hedgehog signaling is controlled by the dynamic association between Suppressor of Fused and the Gli proteins

(2010) E. W. Humke et al.   GENES & DEVELOPMENT

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Discovering pathways by orienting edges in protein interaction networks

(2010) Anthony Gitter et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Suppression of TGFβ-Induced Epithelial-Mesenchymal Transition Like Phenotype by a PIAS1 Regulated Sumoylation Pathway in NMuMG Epithelial Cells

(2010) Stuart J. Netherton et al.   PLoS One

Finding undetected protein associations in cell signaling by belief propagation

(2010) M. Bailly-Bechet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying functional modules using expression profiles and confidence-scored protein interactions

(2009) Igor Ulitsky et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY