Chapter 15: Disease Gene Prioritization

SNPdbe: constructing an nsSNP functional impacts database

(2012) C. Schaefer et al.   BIOINFORMATICS

ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings

(2012) Ernesto Iacucci et al.   BIOINFORMATICS

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

Co-expression of GPR30 and ERβ and their association with disease progression in uterine carcinosarcoma

(2010) Gloria S. Huang et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms

(2010) Andreas Schlicker et al.   BIOINFORMATICS

Structural variation analysis with strobe reads

(2010) A. Ritz et al.   BIOINFORMATICS

CNVineta: a data mining tool for large case–control copy number variation datasets

(2010) Michael Wittig et al.   BIOINFORMATICS

DMDM: domain mapping of disease mutations

(2010) T. A. Peterson et al.   BIOINFORMATICS

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Algorithms and semantic infrastructure for mutation impact extraction and grounding

(2010) Jonas B Laurila et al.   BMC GENOMICS

A comparative study of cancer proteins in the human protein-protein interaction network

(2010) Jingchun Sun et al.   BMC GENOMICS

Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension

(2010) Jesmin et al.   BMC Medical Genomics

A guide to web tools to prioritize candidate genes

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

Mutation@A Glance: An Integrative Web Application for Analysing Mutations from Human Genetic Diseases

(2010) A. Hijikata et al.   DNA RESEARCH

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing

(2010) Jeffrey A. Rosenfeld et al.   NUCLEIC ACIDS RESEARCH

LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

(2010) Shruti Rastogi et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

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

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

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Entrez Gene: gene-centered information at NCBI

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

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Non-Synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association

(2010) Rong Chen et al.   PLoS One

Pathbase and the MPATH Ontology

(2010) P. N. Schofield et al.   VETERINARY PATHOLOGY

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Genome-Wide Copy Number Variation in Epilepsy: Novel Susceptibility Loci in Idiopathic Generalized and Focal Epilepsies

(2010) Heather C. Mefford et al.   PLoS Genetics

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

Gene Clusters, Molecular Evolution and Disease: A Speculation

(2009) Leah Elizondo et al.   CURRENT GENOMICS

Two Distinct Pathways for Metabolism of Theophylline and Caffeine Are Coexpressed in Pseudomonas putida CBB5

(2009) C. L. Yu et al.   JOURNAL OF BACTERIOLOGY

Network-based Identification of Novel Cancer Genes

(2009) Gabriel Östlund et al.   MOLECULAR & CELLULAR PROTEOMICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

FunSimMat update: new features for exploring functional similarity

(2009) Andreas Schlicker et al.   NUCLEIC ACIDS RESEARCH

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

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

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Radiation carcinogenesis: lessons from Chernobyl

(2009) D Williams   ONCOGENE

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

(2009) Cynthia L. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

(2009) Nicole L. Washington et al.   PLOS BIOLOGY

Linkage, Association, and Gene-Expression Analyses Identify CNTNAP2 as an Autism-Susceptibility Gene

(2008) Maricela Alarcón et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

(2008) C. Chelala et al.   BIOINFORMATICS

PGMapper: a web-based tool linking phenotype to genes

(2008) Q. Xiong et al.   BIOINFORMATICS

SNAP predicts effect of mutations on protein function

(2008) Yana Bromberg et al.   BIOINFORMATICS

Defining functional distances over Gene Ontology

(2008) Angela del Pozo et al.   BMC BIOINFORMATICS

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

(2008) Wei Yu et al.   BMC BIOINFORMATICS

Sporadic mutations in melanocortin receptor 3 in morbid obese individuals

(2008) Monica Mencarelli 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

Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase

(2008) Yum L. Yip et al.   HUMAN MUTATION

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

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

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

Reactome knowledgebase of human biological pathways and processes

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

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology

GeneDistiller—Distilling Candidate Genes from Linkage Intervals

(2008) Dominik Seelow et al.   PLoS One

An integrated approach to inferring gene-disease associations in humans

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

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

(2008) Marco Punta et al.   PLoS Computational Biology

Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis

(2008) Ugo Ala et al.   PLoS Computational Biology

Role of Duplicate Genes in Robustness against Deleterious Human Mutations

(2008) Tzu-Lin Hsiao et al.   PLoS Genetics

Text mining for biology - the way forward: opinions from leading scientists

(2008) Russ B Altman et al.   GENOME BIOLOGY

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS