Tools for protein-protein interaction network analysis in cancer research

Separating the Drivers from the Driven: Integrative Network and Pathway Approaches Aid Identification of Disease Biomarkers from High-Throughput Data

(2013) Jason E. McDermott et al.   DISEASE MARKERS

Expression of Endoplasmic Reticulum Stress Proteins Is a Candidate Marker of Brain Metastasis in both ErbB-2+ and ErbB-2− Primary Breast Tumors

(2011) Rebeca Sanz-Pamplona et al.   AMERICAN JOURNAL OF PATHOLOGY

A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

(2011) Yu-Chao Wang et al.   BMC Medical Genomics

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties

(2011) Pablo Minguez et al.   PLoS One

Biana: a software framework for compiling biological interactions and analyzing networks

(2010) Javier Garcia-Garcia et al.   BMC BIOINFORMATICS

NeMo: Network Module identification in Cytoscape

(2010) Corban G Rivera et al.   BMC BIOINFORMATICS

EGAN: exploratory gene association networks

(2009) Jesse Paquette et al.   BIOINFORMATICS

POINeT: protein interactome with sub-network analysis and hub prioritization

(2009) Sheng-An Lee et al.   BMC BIOINFORMATICS

Disease candidate gene identification and prioritization using protein interaction networks

(2009) Jing Chen et al.   BMC BIOINFORMATICS

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Molecular networks and system-level properties

(2009) Lilia Alberghina et al.   JOURNAL OF BIOTECHNOLOGY

Identifying responsive functional modules from protein-protein interaction network

(2009) Zikai Wu et al.   MOLECULES AND CELLS

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Molecular Basis of Colorectal Cancer

(2009) Sanford D. Markowitz et al.   NEW ENGLAND JOURNAL OF MEDICINE

SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks

(2009) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

Bridging the gap between systems biology and medicine

(2009) Gilles Clermont et al.   Genome Medicine

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

Translational disease interpretation with molecular networks

(2009) Anaïs Baudot et al.   GENOME BIOLOGY

Arena3D: visualization of biological networks in 3D

(2008) Georgios A Pavlopoulos et al.   BMC Systems Biology

Increasing the reliability of protein interactomes

(2008) Hon Nian Chua et al.   DRUG DISCOVERY TODAY

Decreased Expression of the RAS-GTPase Activating Protein RASAL1 Is Associated With Colorectal Tumor Progression

(2008) Miki Ohta et al.   GASTROENTEROLOGY

Network integration and graph analysis in mammalian molecular systems biology

(2008) A. Ma'ayan   IET Systems Biology

Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology

(2008) Chung-Yen Lin et al.   NUCLEIC ACIDS RESEARCH

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance

(2008) J. Reimand et al.   NUCLEIC ACIDS RESEARCH

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

(2008) S. Brohee et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining