Network biology methods integrating biological data for translational science

Subnetwork State Functions Define Dysregulated Subnetworks in Cancer

(2011) Salim A. Chowdhury et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Protein Networks as Logic Functions in Development and Cancer

(2011) Janusz Dutkowski et al.   PLoS Computational Biology

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

(2011) Rosemary Braun et al.   PLoS Genetics

DA DA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

(2011) Sinan Erten et al.   BioData Mining

Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

(2010) Marylyn D. Ritchie   ANNALS OF HUMAN GENETICS

Inferring cancer subnetwork markers using density-constrained biclustering

(2010) Phuong Dao et al.   BIOINFORMATICS

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Bioinformatics challenges for genome-wide association studies

(2010) J. H. Moore et al.   BIOINFORMATICS

dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks

(2010) Peilin Jia et al.   BIOINFORMATICS

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

Identification of epistatic effects using a protein-protein interaction database

(2010) Y. V. Sun et al.   HUMAN MOLECULAR GENETICS

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Towards genome-scale signalling-network reconstructions

(2010) Daniel R. Hyduke et al.   NATURE REVIEWS GENETICS

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

INTERSNP: genome-wide interaction analysis guided by a priori information

(2009) C. Herold et al.   BIOINFORMATICS

The SNP ratio test: pathway analysis of genome-wide association datasets

(2009) Colm O'Dushlaine et al.   BIOINFORMATICS

Predicting metabolic biomarkers of human inborn errors of metabolism

(2009) Tomer Shlomi et al.   Molecular Systems Biology

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification of gene interactions associated with disease from gene expression data using synergy networks

(2008) John Watkinson et al.   BMC Systems Biology

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

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY