Integration of biological networks and pathways with genetic association studies

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Knowledge-Driven Analysis Identifies a Gene–Gene Interaction Affecting High-Density Lipoprotein Cholesterol Levels in Multi-Ethnic Populations

(2012) Li Ma et al.   PLoS Genetics

SNP-based pathway enrichment analysis for genome-wide association studies

(2011) Lingjie Weng et al.   BMC BIOINFORMATICS

Characterizing genetic interactions in human disease association studies using statistical epistasis networks

(2011) Ting Hu et al.   BMC BIOINFORMATICS

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies

(2011) Daniel J. Schaid et al.   GENETIC EPIDEMIOLOGY

Statistical analysis of rare sequence variants: an overview of collapsing methods

(2011) Carmen Dering et al.   GENETIC EPIDEMIOLOGY

Identification of genetic association of multiple rare variants using collapsing methods

(2011) Yan V. Sun et al.   GENETIC EPIDEMIOLOGY

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Ion channels and schizophrenia: a gene set-based analytic approach to GWAS data for biological hypothesis testing

(2011) Kathleen Askland et al.   HUMAN GENETICS

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

(2011) Georg B. Ehret et al.   NATURE

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

(2011) Nirmala Akula et al.   PLoS One

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

Insights into Colon Cancer Etiology via a Regularized Approach to Gene Set Analysis of GWAS Data

(2010) Lin S. Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) Peilin Jia et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine

(2010) N A Davis et al.   GENES AND IMMUNITY

Identification of epistatic effects using a protein-protein interaction database

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

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study

(2010) K. Zhang et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits

(2010) Ayellet V. Segrè et al.   PLoS Genetics

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

(2010) Hua Zhong et al.   PLoS Genetics

Epistasis and Its Implications for Personal Genetics

(2009) Jason H. Moore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SCAN: SNP and copy number annotation

(2009) Eric R. Gamazon et al.   BIOINFORMATICS

Comparative study of gene set enrichment methods

(2009) Luca Abatangelo et al.   BMC BIOINFORMATICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Complex Diseases, Complex Genes

(2009) Peter Kraft et al.   EPIDEMIOLOGY

Role for protein–protein interaction databases in human genetics

(2009) Kristine A Pattin et al.   Expert Review of Proteomics

The IntAct molecular interaction database in 2010

(2009) B. Aranda et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

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

GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies

(2008) Marit Holden et al.   BIOINFORMATICS

Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases

(2008) Kristine A. Pattin et al.   HUMAN GENETICS

Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission

(2008) Kathleen Askland et al.   HUMAN GENETICS

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

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

(2008) Jun Zhu et al.   NATURE GENETICS

Human Protein Reference Database--2009 update

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

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY