An unbiased evaluation of gene prioritization tools

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Bioinform.

• Publication date

  2012-12-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/bts581PMID 23047555
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• CONFLICT OF INTEREST: None declared.

  2013cited by this paper
• Computational tools for prioritizing candidate genes: boosting disease gene discovery

  2012cited by this paper
• Recent approaches to the prioritization of candidate disease genes

  2012cited by this paper
• Computational approaches to disease‐gene prediction: rationale, classification and successes

  2012cited by this paper
• A guide to web tools to prioritize candidate genes

  2011cited by this paper
• Genome‐wide association study of theta band event‐related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence

  2011cited by this paper
• Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis.

  2011cited by this paper
• Conceptual thinking for in silico prioritization of candidate disease genes.

  2011cited by this paper
• Web tools for the prioritization of candidate disease genes.

  2011cited by this paper
• Association of RANBP1 haplotype with smooth pursuit eye movement abnormality

  2011cited by this paper
• Haploinsufficiency of the LIM domain containing preferred translocation partner in lipoma (LPP) gene in patients with tetralogy of Fallot and VACTERL association

  2010cited by this paper
• Haploinsufficiency of TAB2 causes congenital heart defects in humans.

  2010cited by this paper
• Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies a susceptibility locus at PLCE1

  2010cited by this paper
• Common variants at TRAF3IP2 are associated with susceptibility to psoriatic arthritis and psoriasis

  2010cited by this paper
• Mutations in the G6PC3 gene cause Dursun syndrome

  2010influential reference
• WDR62 is associated with the spindle pole and is mutated in human microcephaly

  2010cited by this paper
• Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes

  2010cited by this paper
• Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease.

  2010cited by this paper
• TBX2 gene duplication associated with complex heart defect and skeletal malformations

  2010cited by this paper
• TRAF6 promotes atypical ubiquitination of mutant DJ-1 and alpha-synuclein and is localized to Lewy bodies in sporadic Parkinson's disease brains.

  2010cited by this paper
• Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.

  2010cited by this paper
• Evidence for CRHR1 in multiple sclerosis using supervised machine learning and meta-analysis in 12,566 individuals.

  2010cited by this paper
• Association between colony-stimulating factor 1 receptor gene polymorphisms and asthma risk

  2010cited by this paper
• Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2

  2010cited by this paper
• Copy Number Variation Analysis in Single-Suture Craniosynostosis: Multiple Rare Variants Including RUNX2 Duplication in Two Cousins With Metopic Craniosynostosis

  2010cited by this paper
• GeneCards Version 3: the human gene integrator

  2010cited by this paper
• IFNG +874 T>A single nucleotide polymorphism is associated with leprosy among Brazilians

  2010cited by this paper
• A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B

  2010cited by this paper
• Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis

  2010cited by this paper
• Characterization of the chromosome 1q41q42.12 region, and the candidate gene DISP1, in patients with CDH

  2010cited by this paper
• Deletions of Xp provide evidence for the role of holocytochrome C‐type synthase (HCCS) in congenital diaphragmatic hernia

  2010cited by this paper
• Molecular characterization of a de novo 6q24.2q25.3 duplication interrupting UTRN in a patient with arthrogryposis

  2010cited by this paper
• Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a scandinavian case–control sample

  2010cited by this paper
• Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy.

  2010cited by this paper
• Mutation in PQBP1 is associated with periventricular heterotopia

  2010cited by this paper
• Loss‐of‐function mutations of CHST14 in a new type of Ehlers‐Danlos syndrome

  2010cited by this paper
• A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma

  2010cited by this paper
• Evidence for a recurrent microdeletion at chromosome 16p11.2 associated with congenital anomalies of the kidney and urinary tract (CAKUT) and Hirschsprung disease

  2010cited by this paper
• Variation at the GABAA receptor gene, Rho 1 (GABRR1) associated with susceptibility to bipolar schizoaffective disorder

  2010cited by this paper
• A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci

  2010cited by this paper
• Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm

  2010cited by this paper
• Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behçet's disease susceptibility loci

  2010cited by this paper
• Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis

  2010cited by this paper
• Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations

  2010cited by this paper
• Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin‐bound vitamin B12

  2010cited by this paper
• Follow‐up association studies of chromosome region 9q and nonsyndromic cleft lip/palate

  2010cited by this paper
• Candidate gene prioritization by network analysis of differential expression using machine learning approaches

  2010cited by this paper
• Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy

  2010cited by this paper
• Fatal Cardiac Arrhythmia and Long-QT Syndrome in a New Form of Congenital Generalized Lipodystrophy with Muscle Rippling (CGL4) Due to PTRF-CAVIN Mutations

  2010cited by this paper
• Metopic craniosynostosis due to mutations in GLI3: A novel association

  2010cited by this paper
• Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer

  2010cited by this paper
• Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency

  2010cited by this paper
• Mutations in WDR62, encoding a centrosome-associated protein, cause microcephaly with simplified gyri and abnormal cortical architecture

  2010cited by this paper
• BioMart Central Portal—unified access to biological data

  2009cited by this paper
• Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

  2009cited by this paper
• Genome-wide association study in esophageal squamous cell carcinoma.

  2009cited by this paper
• Linking genes to diseases: it's all in the data

  2009influential reference
• PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning

  2009cited by this paper
• Integrating Computational Biology and Forward Genetics in Drosophila

  2009cited by this paper
• Genomewide association studies and human disease.

  2009cited by this paper
• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

  2009influential reference
• Next-generation sequencing transforms today's biology

  2008cited by this paper
• Walking the interactome for prioritization of candidate disease genes.

  2008cited by this paper
• HHEX gene polymorphisms are associated with type 2 diabetes in the Dutch Breda cohort

  2008cited by this paper
• GeneDistiller—Distilling Candidate Genes from Linkage Intervals

  2008cited by this paper
• CANDID: a flexible method for prioritizing candidate genes for complex human traits

  2008cited by this paper
• Improved human disease candidate gene prioritization using mouse phenotype

  2007cited by this paper
• A strategy to search for common obesity and type 2 diabetes genes.

  2007influential reference
• Prioritization of Positional Candidate Genes Using Multiple Web-Based Software Tools

  2007cited by this paper
• Systematic identification of human mitochondrial disease genes through integrative genomics

  2006cited by this paper
• Gene prioritization through genomic data fusion

  2006cited by this paper
• A text-mining analysis of the human phenome

  2006cited by this paper
• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes

  2006cited by this paper
• SUSPECTS: enabling fast and effective prioritization of positional candidates

  2006cited by this paper
• GoPubMed: exploring PubMed with the Gene Ontology

  2005cited by this paper
• The Genetic Association Database

  2004cited by this paper
• Genetic association database

  2004cited by this paper
• Mendelian Inheritance in Man: A Catalog of Human Genes and Genetic Disorders

  1997influential reference
• Human Mutation Research Article Mutations in Sox17 Are Associated with Congenital Anomalies of the Kidney and the Urinary Tract

  year unknowncited by this paper

• Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results

  2024cites this paper
• Biological Network Mining.

  2023cites this paper
• Individualised human phenotype ontology gene panels improve clinical whole exome and genome sequencing analytical efficacy in a cohort of developmental and epileptic encephalopathies

  2023cites this paper
• DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants

  2023cites this paper
• Detecting biased validation of predictive models in the positive-unlabeled setting: disease gene prioritization case study

  2023cites this paper
• Creating an Ignorance-Base: Exploring Known Unknowns in the Scientific Literature

  2023cites this paper
• DeepGenePrior: A deep learning model to prioritize genes affected by copy number variants

  2022cites this paper
• HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

  2022cites this paper
• Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs

  2020cites this paper
• Rank-Similarity Measures for Comparing Gene Prioritizations: A Case Study in Autism

  2020cites this paper
• Heterogeneous networks integration for disease-gene prioritization with node kernels

  2020cites this paper
• Gene Prioritization through Consensus Strategy, Enrichment Methodologies Analysis, and Networking for Osteosarcoma Pathogenesis

  2020cites this paper
• Kernel Based Approaches to Identify Hidden Connections in Gene Networks Using NetAnalyzer

  2020cites this paper
• CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data

  2020cites this paper
• Augmenting subnetwork inference with information extracted from the scientific literature

  2019cites this paper
• Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data

  2019cites this paper
• Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing

  2019influential citation
• Gene Prioritization Tools

  2019cites this paper
• Identifying disease-associated genes based on artificial intelligence

  2019cites this paper
• A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases

  2019cites this paper
• Integrated genomic analysis revealed associated genes for Alzheimer's disease in APOE4 non-carriers.

  2019cites this paper
• GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes.

  2019cites this paper
• BEERE: a web server for biomedical entity expansion, ranking and explorations

  2019cites this paper
• Benchmarker: an unbiased, association-data-driven strategy to evaluate gene prioritization algorithms

  2018cites this paper
• Scuba: scalable kernel-based gene prioritization

  2018influential citation
• ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci

  2018cites this paper
• Interactive network visualization in Jupyter notebooks: visJS2jupyter

  2018cites this paper
• HumanNet v2: human gene networks for disease research

  2018cites this paper
• In Silico Methods to Predict Disease-Resistance Candidate Genes in Plants

  2018cites this paper
• Gene prioritization, communality analysis, networking and metabolic integrated pathway to better understand breast cancer pathogenesis

  2018cites this paper
• GenePANDA—a novel network-based gene prioritizing tool for complex diseases

  2017cites this paper
• Identification of susceptibility variants in prion disease by integrative causal analysis

  2017cites this paper
• Novel Algorithm Development for ‘NextGeneration’ Sequencing Data Analysis

  2017influential citation
• Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis

  2017influential citation
• ProGeM: A framework for the prioritisation of candidate causal genes at molecular quantitative trait loci

  2017cites this paper
• Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

  2017cites this paper
• Complementary Domain Prioritization: A Method to Improve Biologically Relevant Detection in Multi-Omic Data Sets

  2017cites this paper
• Exploiting Negative Sample Selection for Prioritizing Candidate Disease Genes

  2017cites this paper
• Gene2DisCo: Gene to disease using disease commonalities

  2017cites this paper
• A large-scale benchmark of gene prioritization methods

  2017cites this paper
• Functional association networks for disease gene prediction

  2017influential citation
• VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization

  2017cites this paper
• Positive and negative forms of replicability in gene network analysis

  2016cites this paper
• Gene-Disease Prioritization Through Cost-Sensitive Graph-Based Methodologies

  2016cites this paper
• A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization

  2016cites this paper
• Open Peer Review

  2016cites this paper
• A PubMed-wide study of endometriosis.

  2016cites this paper
• Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer

  2016cites this paper
• KNGP: A network-based gene prioritization algorithm that incorporates multiple sources of knowledge.

  2015cites this paper
• OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization

  2015cites this paper
• GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles

  2015cites this paper
• Dintor: functional annotation of genomic and proteomic data

  2015influential citation
• PhenomeExpress: A refined network analysis of expression datasets by inclusion of known disease phenotypes

  2015cites this paper
• Gene prioritization through geometric-inspired kernel data fusion

  2015cites this paper
• Evolutionary Signatures amongst Disease Genes Permit Novel Methods for Gene Prioritization and Construction of Informative Gene-Based Networks

  2015cites this paper
• Systematic noise degrades gene co-expression signals but can be corrected

  2015cites this paper
• Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets

  2015cites this paper
• Beegle: from literature mining to disease-gene discovery

  2015cites this paper
• Genome-wide association studies suggest sex-specific loci associated with abdominal and visceral fat

  2015cites this paper
• Disease Gene Prioritization Using Network and Feature

  2015cites this paper
• MUSIC PERCEPTI ON AND PERFORMANCE

  2015cites this paper
• Computational Approaches for Prioritizing Candidate Disease Genes Based on PPI Networks

  2015cites this paper
• NetRanker: A network-based gene ranking tool using protein-protein interaction and gene expression data

  2015cites this paper
• Genomics approaches to study music perception and performance

  2015cites this paper
• Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Analysis Pipeline

  2015cites this paper
• Kernel Data Fusion

  2015cites this paper
• Whole-Exome Sequencing of Patients with Severe Disorders of Insulin Action

  2014cites this paper
• Improving the interpretability of integer linear programming methods for biological subnetwork inference

  2014cites this paper
• Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

  2014cites this paper
• Computational approaches for human disease gene prediction and ranking.

  2014cites this paper
• Systems Analysis of Human Multigene Disorders

  2014cites this paper
• MaxLink: network-based prioritization of genes tightly linked to a disease seed set

  2014cites this paper
• MicroRNA Prioritization based on Target Profile Similarities

  2014influential citation
• A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

  2014cites this paper
• Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

  2014cites this paper
• Inductive matrix completion for predicting gene–disease associations

  2014cites this paper
• Determining microbial products and identifying molecular targets in the human microbiome.

  2014cites this paper
• Inferring Host Gene Subnetworks Involved in Viral Replication

  2014cites this paper
• Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives

  2014cites this paper
• How Do Bioinformatics Approaches Apply to the Analysis and Understanding of Disease Pathology

  2014cites this paper
• Prioritization of candidate genes for periodontitis using multiple computational tools.

  2014cites this paper
• High-throughput translational medicine: challenges and solutions.

  2014cites this paper
• The influence of disease categories on gene candidate predictions from model organism phenotypes

  2014cites this paper
• Anàlisi in silico de malalties: des de les mutacions fins les xarxes biològiques

  2013cites this paper
• Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

  2013cites this paper
• Filtering for Compound Heterozygous Sequence Variants in Non-Consanguineous Pedigrees

  2013cites this paper
• Progress in detecting genetic alterations and their association with human disease.

  2013cites this paper
• Identifying proteins controlling key disease signaling pathways

  2013cites this paper
• Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update

  2013cites this paper
• Lynx: a database and knowledge extraction engine for integrative medicine

  2013cites this paper
• PhenoDigm: analyzing curated annotations to associate animal models with human diseases

  2013cites this paper
• Building a genome analysis pipeline to predict disease risk and prevent disease.

  2013cites this paper