Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

(2015) Lukas Folkman et al.   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Martin Kircher et al.   NATURE GENETICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

CRAVAT: cancer-related analysis of variants toolkit

(2013) Christopher Douville et al.   BIOINFORMATICS

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Predicting the functional consequences of non-synonymous DNA sequence variants — evaluation of bioinformatics tools and development of a consensus strategy

(2013) Kimon Frousios et al.   GENOMICS

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins

(2013) Jing Hu et al.   PLoS One

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

(2013) Huiying Zhao et al.   GENOME BIOLOGY

Bioinformatics for personal genome interpretation

(2012) E. Capriotti et al.   BRIEFINGS IN BIOINFORMATICS

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

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

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

Correlation of Somatic Mutation and Expression Identifies Genes Important in Human Glioblastoma Progression and Survival

(2011) D. L. Masica et al.   CANCER RESEARCH

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

(2011) Emidio Capriotti et al.   GENOMICS

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

(2011) Stephanie Hicks et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Signatures of positive selection apparent in a small sample of human exomes

(2010) J. A. Tennessen et al.   GENOME RESEARCH

Loss-of-function variants in the genomes of healthy humans

(2010) D. G. MacArthur et al.   HUMAN MOLECULAR GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Fewer permutations, more accurate P-values

(2009) Theo A. Knijnenburg et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Proportionally more deleterious genetic variation in European than in African populations

(2008) Kirk E. Lohmueller et al.   NATURE

Genetic Variation in an Individual Human Exome

(2008) Pauline C. Ng et al.   PLoS Genetics