Analyzing and interpreting genome data at the network level with ConsensusPathDB

High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry

(2016) Celi Sun et al.   NATURE GENETICS

Phospho-tyrosine dependent protein-protein interaction network

(2015) A. Grossmann et al.   Molecular Systems Biology

Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease

(2015) Alexander H Li et al.   NATURE GENETICS

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

(2014) Grégory Seumois et al.   NATURE IMMUNOLOGY

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

(2014) Margret R. Hoehe et al.   Nature Communications

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Gene set analysis methods: statistical models and methodological differences

(2013) H. Maciejewski   BRIEFINGS IN BIOINFORMATICS

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

STAT3 expression, activity and functional consequences of STAT3 inhibition in esophageal squamous cell carcinomas and Barrett’s adenocarcinomas

(2013) S Timme et al.   ONCOGENE

Cluster-based assessment of protein-protein interaction confidence

(2012) Atanas Kamburov et al.   BMC BIOINFORMATICS

Human pre-implantation embryo development

(2012) K. K. Niakan et al.   DEVELOPMENT

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

IntScore: a web tool for confidence scoring of biological interactions

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Effects of Uremic Toxins on Transport and Metabolism of Different Biopharmaceutics Drug Disposition Classification System Xenobiotics

(2011) Maribel Reyes et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

Human Embryonic Stem Cell Derived Hepatocyte-Like Cells as a Tool for In Vitro Hazard Assessment of Chemical Carcinogenicity

(2011) Reha Yildirimman et al.   TOXICOLOGICAL SCIENCES

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape

(2010) Konstantin Pentchev et al.   BIOINFORMATICS

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

Geometric De-noising of Protein-Protein Interaction Networks

(2009) Oleksii Kuchaiev et al.   PLoS Computational Biology

ConsensusPathDB—a database for integrating human functional interaction networks

(2008) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA