DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments

CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis

(2015) Aristidis G. Vrahatis et al.   BIOINFORMATICS

Updates on drug–target network; facilitating polypharmacology and data integration by growth of DrugBank database

(2015) Farnaz Barneh et al.   BRIEFINGS IN BIOINFORMATICS

PATHOME: an algorithm for accurately detecting differentially expressed subpathways

(2014) S Nam et al.   ONCOGENE

Identification of miRNA-Mediated Core Gene Module for Glioma Patient Prediction by Integrating High-Throughput miRNA, mRNA Expression and Pathway Structure

(2014) Chunlong Zhang et al.   PLoS One

Topologically inferring risk-active pathways toward precise cancer classification by directed random walk

(2013) Wei Liu et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Mojo Hand, a TALEN design tool for genome editing applications

(2013) Kevin L Neff et al.   BMC BIOINFORMATICS

Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways

(2013) Chunquan Li et al.   NUCLEIC ACIDS RESEARCH

Differential Expression Analysis for Pathways

(2013) Winston A. Haynes et al.   PLoS Computational Biology

Network-based drug discovery by integrating systems biology and computational technologies

(2012) E. L. Leung et al.   BRIEFINGS IN BIOINFORMATICS

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

TEAK: Topology Enrichment Analysis frameworK for detecting activated biological subpathways

(2012) Thair Judeh et al.   NUCLEIC ACIDS RESEARCH

The Implications of Relationships between Human Diseases and Metabolic Subpathways

(2011) Xia Li et al.   PLoS One

A sub-pathway-based approach for identifying drug response principal network

(2010) Xiujie Chen et al.   BIOINFORMATICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

SubpathwayMiner: a software package for flexible identification of pathways

(2009) C. Li et al.   NUCLEIC ACIDS RESEARCH