ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

Potential Targets for Prevention of Colorectal Cancer: a Focus on PI3K/Akt/mTOR and Wnt Pathways

(2013) Ashok Kumar Pandurangan   Asian Pacific Journal of Cancer Prevention

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Cristina Mitrea et al.   Frontiers in Physiology

Structure and mechanism for recognition of peptide hormones by Class B G-protein-coupled receptors

(2012) Kuntal Pal et al.   ACTA PHARMACOLOGICA SINICA

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

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

(2012) Yu Liu et al.   BMC Systems Biology

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

parmigene—a parallel R package for mutual information estimation and gene network reconstruction

(2011) Gabriele Sales et al.   BIOINFORMATICS

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

(2011) Hui Yu et al.   BMC BIOINFORMATICS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Type 2 Diabetes Is Associated with Altered NF-κB DNA Binding Activity, JNK Phosphorylation, and AMPK Phosphorylation in Skeletal Muscle after LPS

(2011) Anne Sofie Andreasen et al.   PLoS One

SPIKE: a database of highly curated human signaling pathways

(2010) Arnon Paz et al.   NUCLEIC ACIDS RESEARCH

Opening Up the Group II Chaperonins

(2010) Zihe Rao   STRUCTURE

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

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

Role of microRNA in anticancer drug resistance

(2009) Tongsen Zheng et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2009) Da Wei Huang et al.   Nature Protocols

Identifying Gene Interaction Enrichment for Gene Expression Data

(2009) Jigang Zhang et al.   PLoS One

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

(2008) Kartik M Mani et al.   Molecular Systems Biology

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival

(2008) Maria Teresa Landi et al.   PLoS One