Computational tools for prioritizing candidate genes: boosting disease gene discovery

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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Cytoscape: A software Environment for integrated models of biomolecular interaction networks

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

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A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection

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Network medicine: a network-based approach to human disease

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KEGG for integration and interpretation of large-scale molecular data sets

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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

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The human disease network

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ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

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Towards a proteome-scale map of the human protein–protein interaction network

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A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules

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Recurring mutations found by sequencing an acute myeloid leukemia genome

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DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

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Human Gene Mutation Database (HGMD®): 2003 update

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Interactome Networks and Human Disease

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Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion

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Walking the Interactome for Prioritization of Candidate Disease Genes

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STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

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BioMart – biological queries made easy

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The human phenotype ontology: a tool for annotating and analyzing human hereditary disease

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STITCH: interaction networks of chemicals and proteins

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A human phenome-interactome network of protein complexes implicated in genetic disorders

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The Genetic Association Database

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Gene prioritization through genomic data fusion

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The Human Gene Mutation Database: 2008 update

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A literature network of human genes for high-throughput analysis of gene expression

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Ensembl 2012

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Molecular networks as sensors and drivers of common human diseases

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Guilt by association

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Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

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Inparanoid: a comprehensive database of eukaryotic orthologs

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Diffusion Kernels on Graphs and Other Discrete Input Spaces

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Critical assessment of methods of protein structure prediction (CASP) — round x

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

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A statistical framework for genomic data fusion

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

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The human gene mutation database

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Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

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Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA RegulogsPreprint

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GoPubMed: exploring PubMed with the Gene Ontology

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Overview of BioCreAtIvE: critical assessment of information extraction for biology

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A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae )

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Reconstruction of a Functional Human Gene Network, with an Application for Prioritizing Positional Candidate Genes

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MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion

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The modular nature of genetic diseases

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The power of protein interaction networks for associating genes with diseases

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Edgetic perturbation models of human inherited disorders

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Association of genes to genetically inherited diseases using data mining

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The UCSC Genome Browser database: extensions and updates 2011

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ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

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The GRID: The General Repository for Interaction Datasets

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Improved human disease candidate gene prioritization using mouse phenotype

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Annotating the human genome with Disease Ontology

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Pathway Mapping Tools for Analysis of High Content Data

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Genome-wide identification of genes likely to be involved in human genetic disease

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PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

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Speeding disease gene discovery by sequence based candidate prioritization

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Transcriptional profiling of bovine milk using RNA sequencing

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Fatal Cardiac Arrhythmia and Long-QT Syndrome in a New Form of Congenital Generalized Lipodystrophy with Muscle Rippling (CGL4) Due to PTRF-CAVIN Mutations

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A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss

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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

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

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ENDEAVOUR update: a web resource for gene prioritization in multiple species

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

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Critical assessment of methods of protein structure prediction (CASP)—round IX

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Protein interactions and disease: computational approaches to uncover the etiology of diseases

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Exploring the human genome with functional mapsPreprint

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Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesisPreprint

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A guide to web tools to prioritize candidate genes

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A survey of current software for network analysis in molecular biology

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G2D: a tool for mining genes associated with disease

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Genetic dissection of the biotic stress response using a genome-scale gene network for rice

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

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AILUN: reannotating gene expression data automatically

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Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

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Computational approaches to disease‐gene prediction: rationale, classification and successes

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Analysis of protein sequence and interaction data for candidate disease gene prediction

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Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

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Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes

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Kernel-based data fusion for gene prioritization

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Mutation of HAIRY-AND-ENHANCER-OF-SPLIT-7 in humans causes spondylocostal dysostosis

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Severely Incapacitating Mutations in Patients with Extreme Short Stature Identify RNA-Processing Endoribonuclease RMRP as an Essential Cell Growth Regulator

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BIOFILTER: A KNOWLEDGE-INTEGRATION SYSTEM FOR THE MULTI-LOCUS ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES

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Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex

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Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge Meeting Information: The DREAM4 Predictive Signaling Network Challenge took place in the summer of 2009. Results were presented at the DREAM4 conference, December 2009, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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GeneDistiller—Distilling Candidate Genes from Linkage Intervals

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CGI: a new approach for prioritizing genes by combining gene expression and protein–protein interaction data

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Haploinsufficiency of TAB2 Causes Congenital Heart Defects in Humans

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Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

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Advances in translational bioinformatics: computational approaches for the hunting of disease genes

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Human disease genes: patterns and predictions

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A new web-based data mining tool for the identification of candidate genes for human genetic disorders

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