Pathway reporter genes define molecular phenotypes of human cells

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation

(2014) Arianne C Richard et al.   BMC GENOMICS

Highly sensitive amplicon-based transcript quantification by semiconductor sequencing

(2014) Jitao Zhang et al.   BMC GENOMICS

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Data mining reveals a network of early-response genes as a consensus signature of drug-induced in vitro and in vivo toxicity

(2013) J D Zhang et al.   PHARMACOGENOMICS JOURNAL

A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects

(2013) Emőke-Ágnes Horvát et al.   PLoS One

Hypoxia perturbs aryl hydrocarbon receptor signaling and CYP1A1 expression induced by PCB 126 in human skin and liver-derived cell lines

(2013) Sabine U. Vorrink et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

Network information improves cancer outcome prediction

(2012) J. Roy et al.   BRIEFINGS IN BIOINFORMATICS

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery

(2012) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Zebrafish cardiac development requires a conserved secondary heart field

(2011) D. Hami et al.   DEVELOPMENT

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

Determination of the Human Cardiomyocyte mRNA and miRNA Differentiation Network by Fine-Scale Profiling

(2011) Joshua E. Babiarz et al.   STEM CELLS AND DEVELOPMENT

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases

(2011) Frank Emmert-Streib et al.   PLoS Computational Biology

DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks

(2010) Anna Bauer-Mehren et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Stat3 Directly Controls the Expression of Tbx5, Nkx2.5, and GATA4 and Is Essential for Cardiomyocyte Differentiation of P19CL6 Cells

(2010) Marylynn Snyder et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Neuregulin1/ErbB4 Signaling Induces Cardiomyocyte Proliferation and Repair of Heart Injury

(2009) Kevin Bersell et al.   CELL

Lipopolysaccharides can protect mesenchymal stem cells (MSCs) from oxidative stress-induced apoptosis and enhance proliferation of MSCs via Toll-like receptor(TLR)-4 and PI3K/Akt

(2009) Zhao-jun Wang et al.   CELL BIOLOGY INTERNATIONAL

Cellular Stress Response Pathway System as a Sentinel Ensemble in Toxicological Screening

(2009) Steven O. Simmons et al.   TOXICOLOGICAL SCIENCES

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Transcriptional and Functional Profiling of Human Embryonic Stem Cell-Derived Cardiomyocytes

(2008) Feng Cao et al.   PLoS One

Toxicity Testing in the 21st Century: Bringing the Vision to Life

(2008) Melvin E. Andersen et al.   TOXICOLOGICAL SCIENCES