netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis

A comparative study of topology-based pathway enrichment analysis methods

(2019) Jing Ma et al.   BMC BIOINFORMATICS

PathBank: a comprehensive pathway database for model organisms

(2019) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Network-based pathway enrichment analysis with incomplete network information

(2016) Jing Ma et al.   BIOINFORMATICS

Systemic alterations in the metabolome of diabetic NOD mice delineate increased oxidative stress accompanied by reduced inflammation and hypertriglyceremia

(2015) Johannes Fahrmann et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

NDEx, the Network Data Exchange

(2015) Dexter Pratt et al.   Cell Systems

Pathway-based Analysis Tools for Complex Diseases: A Review

(2014) Lv Jin et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

(2013) Timothy Jewison et al.   NUCLEIC ACIDS RESEARCH

graphite - a Bioconductor package to convert pathway topology to gene network

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

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

(2012) Zuguang Gu et al.   BMC Systems Biology

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A Topology-Based Score for Pathway Enrichment

(2012) Maysson Al-Haj Ibrahim et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Network Enrichment Analysis in Complex Experiments

(2010) Ali Shojaie et al.   Statistical Applications in Genetics and Molecular Biology

Analysis of Gene Sets Based on the Underlying Regulatory Network

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

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