Leveraging models of cell regulation and GWAS data in integrative network-based association studies

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Why Is There a Lack of Consensus on Molecular Subgroups of Glioblastoma? Understanding the Nature of Biological and Statistical Variability in Glioblastoma Expression Data

(2011) Nicholas F. Marko et al.   PLoS One

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

(2010) Hua Zhong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pathway discovery in metabolic networks by subgraph extraction

(2010) Karoline Faust et al.   BIOINFORMATICS

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

(2010) Peilin Jia et al.   BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Insulin Signaling in Osteoblasts Integrates Bone Remodeling and Energy Metabolism

(2010) Mathieu Ferron et al.   CELL

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Using biological knowledge to discover higher order interactions in genetic association studies

(2010) Gary K. Chen et al.   GENETIC EPIDEMIOLOGY

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

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

Identification and validation of genes affecting aortic lesions in mice

(2010) Xia Yang et al.   JOURNAL OF CLINICAL INVESTIGATION

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets

(2010) Manikandan Narayanan et al.   PLoS Computational Biology

An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions

(2010) Gaurav Pandey et al.   PLoS Computational Biology

Characterizing Dynamic Changes in the Human Blood Transcriptional Network

(2010) Jun Zhu et al.   PLoS Computational Biology

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

A study of miRNAs targets prediction and experimental validation

(2010) Yong Huang et al.   Protein & Cell

The N-Myc-DLL3 Cascade Is Suppressed by the Ubiquitin Ligase Huwe1 to Inhibit Proliferation and Promote Neurogenesis in the Developing Brain

(2009) Xudong Zhao et al.   DEVELOPMENTAL CELL

The effect of food intake on gene expression in human peripheral blood

(2009) Amy S. Leonardson et al.   HUMAN MOLECULAR GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Mutations of multiple genes cause deregulation of NF-κB in diffuse large B-cell lymphoma

(2009) Mara Compagno et al.   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks

(2009) Xia Yang et al.   NATURE GENETICS

Mechanisms of drug combinations: interaction and network perspectives

(2009) Jia Jia et al.   NATURE REVIEWS DRUG DISCOVERY

Genetic Risk Prediction — Are We There Yet?

(2009) Peter Kraft et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomewide Association Studies and Human Disease

(2009) John Hardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Common Genetic Variation and Human Traits

(2009) David B. Goldstein   NEW ENGLAND JOURNAL OF MEDICINE

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

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

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Autoimmune Disease Classification by Inverse Association with SNP Alleles

(2009) Marina Sirota et al.   PLoS Genetics

Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

(2009) Gregory Hannum et al.   PLoS Genetics

Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease

(2009) Radu Dobrin et al.   GENOME BIOLOGY

Network-based model weighting to detect multiple loci influencing complex diseases

(2008) Wei Pan   HUMAN GENETICS

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

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

(2008) Eleftheria Zeggini et al.   NATURE GENETICS

Stromal Gene Signatures in Large-B-Cell Lymphomas

(2008) G. Lenz et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clinical Risk Factors, DNA Variants, and the Development of Type 2 Diabetes

(2008) Valeriya Lyssenko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Interaction networks: From protein functions to drug discovery. A review

(2008) E. Chautard et al.   PATHOLOGIE BIOLOGIE

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE