Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

Whole-genome sequence–based analysis of high-density lipoprotein cholesterol

(2013) Alanna C Morrison et al.   NATURE GENETICS

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease

(2013) Peter Carbonetto et al.   PLoS Genetics

PON-P: Integrated predictor for pathogenicity of missense variants

(2012) Ayodeji Olatubosun et al.   HUMAN MUTATION

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

(2012) Miao-Xin Li et al.   NUCLEIC ACIDS RESEARCH

Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization

(2012) Emre Guney et al.   PLoS One

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

(2010) Sarah E. Flanagan et al.   Genetic Testing and Molecular Biomarkers

Massively parallel sequencing and rare disease

(2010) S. B. Ng et al.   HUMAN MOLECULAR GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

(2010) Gregory M Cooper et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods

(2009) Janita Thusberg et al.   HUMAN MUTATION

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

(2009) Prateek Kumar et al.   Nature Protocols