Empirical comparison of structure-based pathway methods

On the selection of appropriate distances for gene expression data clustering

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ArrayExpress update—simplifying data submissions

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A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methods and approaches in the topology-based analysis of biological pathways

(2013) Cristina Mitrea et al.   Frontiers in Physiology

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes

(2012) Zuguang Gu et al.   BMC Systems Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

The Integration of Biological Pathway Knowledge in Cancer Genomics: A review of existing computational approaches

(2011) Vinay Varadan et al.   IEEE SIGNAL PROCESSING MAGAZINE

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets

(2009) Laura L. Elo et al.   BRIEFINGS IN BIOINFORMATICS

Analysis of Gene Sets Based on the Underlying Regulatory Network

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

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

(2009) Da Wei Huang et al.   Nature Protocols

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies

(2008) L.L. Elo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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