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

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

The diabetes gene Hhex maintains  -cell differentiation and islet function

(2014) J. Zhang et al.   GENES & DEVELOPMENT

Integrating GWASs and Human Protein Interaction Networks Identifies a Gene Subnetwork Underlying Alcohol Dependence

(2013) Shizhong Han et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Distilling Pathophysiology from Complex Disease Genetics

(2013) Aravinda Chakravarti et al.   CELL

Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish

(2013) G. Musso et al.   DEVELOPMENT

HNF1b is involved in prostate cancer risk via modulating androgenic hormone effects and coordination with other genes

(2013) Y.L. Hu et al.   GENETICS AND MOLECULAR RESEARCH

Genome-wide association study identifies three novel loci for type 2 diabetes

(2013) Kazuo Hara et al.   HUMAN MOLECULAR GENETICS

FGF Receptors: Cancer Biology and Therapeutics

(2013) Masaru Katoh et al.   MEDICINAL RESEARCH REVIEWS

Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

(2013)   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Prognostication of OCT4 isoform expression in prostate cancer

(2013) Marina França de Resende et al.   TUMOR BIOLOGY

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Diabetes Risk Gene and Wnt Effector Tcf7l2/TCF4 Controls Hepatic Response to Perinatal and Adult Metabolic Demand

(2012) Sylvia F. Boj et al.   CELL

Leptin revisited: its mechanism of action and potential for treating diabetes

(2012) Roberto Coppari et al.   NATURE REVIEWS DRUG DISCOVERY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

(2012) Murat Taşan et al.   G3-Genes Genomes Genetics

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism

(2011) D. Savic et al.   GENOME RESEARCH

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

(2011) I. Lee et al.   GENOME RESEARCH

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

(2011) Sohyun Hwang et al.   Nature Protocols

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

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

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

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

Androgen receptor as a therapeutic target

(2010) Wenqing Gao   ADVANCED DRUG DELIVERY REVIEWS

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

(2010) Rita M. Cantor 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

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

(2010) Sara Mostafavi et al.   BIOINFORMATICS

It's the machine that matters: Predicting gene function and phenotype from protein networks

(2010) Peggy I. Wang et al.   Journal of Proteomics

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

(2010) Benjamin F Voight et al.   NATURE GENETICS

Entrez Gene: gene-centered information at NCBI

(2010) D. Maglott 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

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Genomewide Association Studies — Illuminating Biologic Pathways

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

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

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

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

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

Molecular determinants of brown adipocyte formation and function

(2008) S. R. Farmer   GENES & DEVELOPMENT

Common and rare variants in multifactorial susceptibility to common diseases

(2008) Walter Bodmer et al.   NATURE GENETICS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function

(2008) Weidong Tian et al.   GENOME BIOLOGY

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

(2008) Martin Krallinger et al.   GENOME BIOLOGY

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY