Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk

(2010) Chandra A. Reynolds et al.   HUMAN MOLECULAR GENETICS

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease

(2010) Mun-Gwan Hong et al.   JOURNAL OF HUMAN GENETICS

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

(2010) Andrey Alexeyenko et al.   PLoS One

How and when should interactome-derived clusters be used to predict functional modules and protein function?

(2009) Jimin Song et al.   BIOINFORMATICS

Comparative study of gene set enrichment methods

(2009) Luca Abatangelo et al.   BMC BIOINFORMATICS

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure

(2009) A Annibale et al.   Journal of Physics A-Mathematical and Theoretical

Network-based Identification of Novel Cancer Genes

(2009) Gabriel Östlund et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimized Null Model for Protein Structure Networks

(2009) Tijana Milenković et al.   PLoS One

Geometric De-noising of Protein-Protein Interaction Networks

(2009) Oleksii Kuchaiev et al.   PLoS Computational Biology

A global pathway crosstalk network

(2008) Yong Li et al.   BIOINFORMATICS

The Notch pathway in prostate development and cancer

(2008) Kevin G. Leong et al.   DIFFERENTIATION

Estrogen-Dependent Signaling in a Molecularly Distinct Subclass of Aggressive Prostate Cancer

(2008) Sunita R. Setlur et al.   JNCI-Journal of the National Cancer Institute

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

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