Computational tools for prioritizing candidate genes: boosting disease gene discovery

Transcriptional profiling of bovine milk using RNA sequencing

(2012) Saumya Wickramasinghe et al.   BMC GENOMICS

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

(2012) Rosario M. Piro et al.   FEBS Journal

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

(2012) Jesse Gillis et al.   PLoS Computational Biology

MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets

(2011) Daniel Baron et al.   BIOINFORMATICS

BioCreative III interactive task: an overview

(2011) Cecilia N Arighi et al.   BMC BIOINFORMATICS

Comparison of genomic and proteomic data in recurrent airway obstruction affected horses using ingenuity pathway analysis®

(2011) Julien Racine et al.   BMC Veterinary Research

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes

(2011) Tune H. Pers et al.   GENETIC EPIDEMIOLOGY

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

(2011) Y. Erlich et al.   GENOME RESEARCH

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

(2011) I. Lee et al.   GENOME RESEARCH

Identification of Parkinson’s disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson’s disease patients

(2011) Rowena J. Keyser et al.   JOURNAL OF NEURAL TRANSMISSION

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

(2011) Sohyun Hwang et al.   Nature Protocols

Something old, something new

(2011) Tanita Casci   NATURE REVIEWS GENETICS

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

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

PINTA: a web server for network-based gene prioritization from expression data

(2011) D. Nitsch et al.   NUCLEIC ACIDS RESEARCH

Génie: literature-based gene prioritization at multi genomic scale

(2011) Jean-Fred Fontaine et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Jesse Gillis et al.   PLoS One

In Silico Gene Prioritization by Integrating Multiple Data Sources

(2011) Yixuan Chen et al.   PLoS One

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

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

(2011) R. J. Prill et al.   Science Signaling

Haploinsufficiency of TAB2 Causes Congenital Heart Defects in Humans

(2010) Bernard Thienpont et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Infantile Cerebral and Cerebellar Atrophy Is Associated with a Mutation in the MED17 Subunit of the Transcription Preinitiation Mediator Complex

(2010) Rami Kaufmann 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

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Large-scale benchmark of Endeavour using MetaCore maps

(2010) Sven Schuierer et al.   BIOINFORMATICS

A guide to web tools to prioritize candidate genes

(2010) L.-C. Tranchevent et al.   BRIEFINGS IN BIOINFORMATICS

Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics

(2010) Y. Qiao et al.   HUMAN GENETICS

Network medicine: a network-based approach to human disease

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

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

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

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

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

(2010) Roland Barriot et al.   Genome Medicine

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

(2010) Anna Rajab et al.   PLoS Genetics

The Biological Coherence of Human Phenome Databases

(2009) Martin Oti et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2009) Helen V. Firth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction

(2009) Curtis Huttenhower et al.   BIOINFORMATICS

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

(2009) Erdahl T Teber et al.   BMC BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Annotating the human genome with Disease Ontology

(2009) John D Osborne et al.   BMC GENOMICS

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

(2009) M. G. Kann   BRIEFINGS IN BIOINFORMATICS

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning

(2009) Y. Yoshida et al.   NUCLEIC ACIDS RESEARCH

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Linking genes to diseases: it's all in the data

(2009) Nicki Tiffin et al.   Genome Medicine

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

(2009) David C. Hess et al.   PLoS Genetics

Integrating Computational Biology and Forward Genetics in Drosophila

(2009) Stein Aerts et al.   PLoS Genetics

Translational disease interpretation with molecular networks

(2009) Anaïs Baudot et al.   GENOME BIOLOGY

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

(2009) Bolan Linghu et al.   GENOME BIOLOGY

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease

(2008) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

(2008) Wei Yu et al.   BMC BIOINFORMATICS

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

(2008) R. Winnenburg et al.   BRIEFINGS IN BIOINFORMATICS

HHEX gene polymorphisms are associated with type 2 diabetes in the Dutch Breda cohort

(2008) Jana V van Vliet-Ostaptchouk et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

CANDID: a flexible method for prioritizing candidate genes for complex human traits

(2008) Janna E. Hutz et al.   GENETIC EPIDEMIOLOGY

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

(2008) D. B. Sparrow et al.   HUMAN MOLECULAR GENETICS

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

(2008) Lincoln D. Stein   NATURE REVIEWS GENETICS

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

(2008) L.-C. Tranchevent et al.   NUCLEIC ACIDS RESEARCH

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

(2008) D. Cheng et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes

(2008) Karine Tremblay et al.   PLoS One

GeneDistiller—Distilling Candidate Genes from Linkage Intervals

(2008) Dominik Seelow et al.   PLoS One

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

(2008) Martin Krallinger et al.   GENOME BIOLOGY