Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

(2011) Luca Beltrame et al.   BIOINFORMATICS

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

(2011) Rosemary Braun et al.   PLoS Genetics

Complexity in signal transduction

(2010) Jameel Iqbal et al.   Annals of the New York Academy of Sciences

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Deconvoluting Post-Transplant Immunity: Cell Subset-Specific Mapping Reveals Pathways for Activation and Expansion of Memory T, Monocytes and B Cells

(2010) Yevgeniy A. Grigoryev et al.   PLoS One

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

(2009) Galina V. Glazko et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Analysis of Gene Sets Based on the Underlying Regulatory Network

(2009) Ali Shojaie et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Use and misuse of the gene ontology annotations

(2008) Seung Yon Rhee et al.   NATURE REVIEWS GENETICS

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

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

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