Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes

Data Fusion by Matrix Factorization

(2015) Marinka Zitnik et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods

(2014) Giorgio Valentini et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Integration of molecular network data reconstructs Gene Ontology

(2014) Vladimir Gligorijević et al.   BIOINFORMATICS

Bias tradeoffs in the creation and analysis of protein–protein interaction networks

(2014) Jesse Gillis et al.   Journal of Proteomics

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks

(2014) Murat Taşan et al.   NATURE METHODS

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

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Discovering disease-disease associations by fusing systems-level molecular data

(2013) Marinka Žitnik et al.   Scientific Reports

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data

(2012) Yongjin Li et al.   BMC GENOMICS

Th17 Cells in Multiple Sclerosis Express Higher Levels of JAK2, Which Increases Their Surface Expression of IFN- R2

(2012) L. Conti et al.   JOURNAL OF IMMUNOLOGY

Genenames.org: the HGNC resources in 2013

(2012) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores

(2012) Joana P. Gonçalves et al.   PLoS One

Abundant Pleiotropy in Human Complex Diseases and Traits

(2011) Shanya Sivakumaran et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci

(2011) Nikolaos A. Patsopoulos et al.   ANNALS OF NEUROLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus

(2011) Matlock Jeffries et al.   Epigenetics

Genetic analysis of biological pathway data through genomic randomization

(2011) Brian L. Yaspan et al.   HUMAN GENETICS

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

(2011) Stephen Sawcer et al.   NATURE

Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility

(2011) David M Evans et al.   NATURE GENETICS

CoPub update: CoPub 5.0 a text mining system to answer biological questions

(2011) W. W. M. Fleuren et al.   NUCLEIC ACIDS RESEARCH

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

Exploring and Exploiting Disease Interactions from Multi-Relational Gene and Phenotype Networks

(2011) Darcy A. Davis et al.   PLoS One

ppiTrim: constructing non-redundant and up-to-date interactomes

(2011) Aleksandar Stojmirović et al.   Database-The Journal of Biological Databases and Curation

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

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

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

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval

(2010) S. J. Swamidass et al.   BIOINFORMATICS

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

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

(2010) Peilin Jia et al.   BIOINFORMATICS

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

On beyond GWAS

(2010)   NATURE GENETICS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

(2010) M. Gremse 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

Link prediction in complex networks: A survey

(2010) Linyuan Lü et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Simple means to improve the interpretability of regression coefficients

(2010) Holger Schielzeth   Methods in Ecology and Evolution

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

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

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

Genetic Risk Prediction — Are We There Yet?

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

Genomewide Association Studies — Illuminating Biologic Pathways

(2009) Joel N. Hirschhorn   NEW ENGLAND JOURNAL OF MEDICINE

Common Genetic Variation and Human Traits

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

A Dynamic Network Approach for the Study of Human Phenotypes

(2009) César A. Hidalgo et al.   PLoS Computational Biology

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

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

The complex genetics of multiple sclerosis: pitfalls and prospects

(2008) Stephen Sawcer   BRAIN

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrated approach to inferring gene-disease associations in humans

(2008) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS