Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives

Network-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls

(2013) Sergio E. Baranzini et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Boosting signals in gene-based association studies via efficient SNP selection

(2013) C. Wu et al.   BRIEFINGS IN BIOINFORMATICS

Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies

(2013) Quan Wang et al.   PLoS One

Gene-Based Testing of Interactions in Association Studies of Quantitative Traits

(2013) Li Ma et al.   PLoS Genetics

Alzheimer Disease Susceptibility Loci: Evidence for a Protein Network under Natural Selection

(2012) Towfique Raj et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An unbiased evaluation of gene prioritization tools

(2012) Daniela Börnigen et al.   BIOINFORMATICS

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

(2012) Sam Ng et al.   BIOINFORMATICS

Common Genetic Variants and Gene-Expression Changes Associated with Bipolar Disorder Are Over-Represented in Brain Signaling Pathway Genes

(2012) Inti Pedroso et al.   BIOLOGICAL PSYCHIATRY

A genome-wide association study identifies a gene network of ADAMTS genes in the predisposition to pediatric stroke

(2012) A. Arning et al.   BLOOD

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer

(2012) Peilin Jia et al.   BMC Systems Biology

Integration of biological networks and pathways with genetic association studies

(2012) Yan V. Sun   HUMAN GENETICS

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia

(2012) Bin Xu et al.   NATURE GENETICS

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia

(2012) Sarah R Gilman et al.   NATURE NEUROSCIENCE

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

The TissueNet database of human tissue protein–protein interactions

(2012) Ruth Barshir et al.   NUCLEIC ACIDS RESEARCH

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

(2012) Luz García-Alonso et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Comparison of Pathway Analysis Approaches Using Lung Cancer GWAS Data Sets

(2012) Gordon Fehringer et al.   PLoS One

Protein-Protein Interaction Analysis Highlights Additional Loci of Interest for Multiple Sclerosis

(2012) Giammario Ragnedda et al.   PLoS One

Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

(2012) Pascal Braun   PROTEOMICS

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

(2012) Jun Zhu et al.   PLOS BIOLOGY

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia

(2012) Peilin Jia et al.   PLoS Computational Biology

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

Networks of Neuronal Genes Affected by Common and Rare Variants in Autism Spectrum Disorders

(2012) Eyal Ben-David et al.   PLoS Genetics

GATES: A Rapid and Powerful Gene-Based Association Test Using Extended Simes Procedure

(2011) Miao-Xin Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies

(2011) Lily Wang et al.   BIOINFORMATICS

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

(2011) Ting Hu et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease

(2011) Majken K. Jensen et al.   Circulation-Cardiovascular Genetics

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

(2011) Carmen Dering et al.   GENETIC EPIDEMIOLOGY

Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets

(2011) Q. Xiong et al.   GENOME RESEARCH

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

(2011) I. Lee et al.   GENOME RESEARCH

Gene set analysis of genome-wide association studies: Methodological issues and perspectives

(2011) Lily Wang et al.   GENOMICS

Integrating pathway analysis and genetics of gene expression for genome-wide association study of basal cell carcinoma

(2011) Mingfeng Zhang et al.   HUMAN GENETICS

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

(2011) Kathleen Askland et al.   HUMAN GENETICS

Pathway-based analysis of GWAS datasets: effective but caution required

(2011) Peilin Jia et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia

(2011) Peilin Jia et al.   JOURNAL OF MEDICAL GENETICS

Genome partitioning of genetic variation for complex traits using common SNPs

(2011) Jian Yang et al.   NATURE GENETICS

Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses

(2011) Sarah R. Gilman et al.   NEURON

A Systems Approach to the Biology of Mood Disorders through Network Analysis of Candidate Genes

(2011) S. D. Detera-Wadleigh et al.   PHARMACOPSYCHIATRY

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

(2011) Nirmala Akula et al.   PLoS One

A New Methodology to Associate SNPs with Human Diseases According to Their Pathway Related Context

(2011) Burcu Bakir-Gungor et al.   PLoS One

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

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

Functional Gene Group Analysis Reveals a Role of Synaptic Heterotrimeric G Proteins in Cognitive Ability

(2010) Dina Ruano et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

(2010) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Versatile Gene-Based Test for Genome-wide Association Studies

(2010) Jimmy Z. Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

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

(2010) Peilin Jia et al.   BIOINFORMATICS

Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis

(2010) Sergio E. Baranzini et al.   BRAIN

Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data

(2010) Charles R Farber   JOURNAL OF BONE AND MINERAL RESEARCH

Hints of hidden heritability in GWAS

(2010) Greg Gibson   NATURE GENETICS

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Common variants conferring risk of schizophrenia: A pathway analysis of GWAS data

(2010) Peilin Jia et al.   SCHIZOPHRENIA RESEARCH

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

(2009) Peter Holmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Diverse Genome-wide Association Studies Associate the IL12/IL23 Pathway with Crohn Disease

(2009) Kai Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case

(2009) Jingchun Sun et al.   BIOINFORMATICS

Comment on: Perry et al. (2009) Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach. Diabetes;58:1463-1467

(2009) C. C. Elbers et al.   DIABETES

Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach

(2009) J. R.B. Perry et al.   DIABETES

Gene and pathway-based second-wave analysis of genome-wide association studies

(2009) Gang Peng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

(2009) S. E. Baranzini et al.   HUMAN MOLECULAR GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Network Analysis of Differential Expression for the Identification of Disease-Causing Genes

(2009) Daniela Nitsch et al.   PLoS One

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

Capturing the Spectrum of Interaction Effects in Genetic Association Studies by Simulated Evaporative Cooling Network Analysis

(2009) Brett A. McKinney et al.   PLoS Genetics

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF 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

Genomewide association for schizophrenia in the CATIE study: results of stage 1

(2008) P F Sullivan et al.   MOLECULAR PSYCHIATRY

Integrated network analysis platform for protein-protein interactions

(2008) Jianmin Wu et al.   NATURE METHODS

A principal components regression approach to multilocus genetic association studies

(2007) Kai Wang et al.   GENETIC EPIDEMIOLOGY