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

Metab2MeSH: annotating compounds with medical subject headings

(2012) Maureen A. Sartor et al.   BIOINFORMATICS

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

(2011) L. Geistlinger et al.   BIOINFORMATICS

Multiple testing for gene sets from microarray experiments

(2011) Insuk Sohn et al.   BMC BIOINFORMATICS

c-Jun, at the crossroad of the signaling network

(2011) Qinghang Meng et al.   Protein & Cell

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

(2010) Daniel M Gatti et al.   BMC GENOMICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

genenames.org: the HGNC resources in 2011

(2010) R. L. Seal et al.   NUCLEIC ACIDS RESEARCH

The role of signaling pathways in the development and treatment of hepatocellular carcinoma

(2010) S Whittaker et al.   ONCOGENE

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

(2010) Jui-Hung Hung et al.   GENOME BIOLOGY

Statistical methods for gene set co-expression analysis

(2009) YounJeong Choi et al.   BIOINFORMATICS

Analyzing biological network parameters with CentiScaPe

(2009) Giovanni Scardoni et al.   BIOINFORMATICS

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

(2009) Reuben Thomas et al.   GENOME BIOLOGY

Microarray-based gene set analysis: a comparison of current methods

(2008) Sarah Song et al.   BMC BIOINFORMATICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer 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

Inferring MicroRNA Activities by Combining Gene Expression with MicroRNA Target Prediction

(2008) Chao Cheng et al.   PLoS One

A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions

(2008) C. J. Creighton et al.   RNA