Representativeness of variation benchmark datasets

PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality

(2018) Yang Yang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Protein moonlighting: what is it, and why is it important?

(2017) Constance J. Jeffery   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How to Define Pathogenicity, Health, and Disease?

(2016) Mauno Vihinen   HUMAN MUTATION

The Complementarity Between Protein-Specific and General Pathogenicity Predictors for Amino Acid Substitutions

(2016) Casandra Riera et al.   HUMAN MUTATION

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

(2016) Abhishek Niroula et al.   HUMAN MUTATION

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Correct machine learning on protein sequences: a peer-reviewing perspective

(2015) Ian Walsh et al.   BRIEFINGS IN BIOINFORMATICS

Classification of Amino Acid Substitutions in Mismatch Repair Proteins Using PON-MMR2

(2015) Abhishek Niroula et al.   HUMAN MUTATION

VariSNP, A Benchmark Database for Variations From dbSNP

(2015) Gerard C.P. Schaafsma et al.   HUMAN MUTATION

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants

(2015) Abhishek Niroula et al.   PLoS One

Majority Vote and Other Problems when using Computational Tools

(2014) Mauno Vihinen   HUMAN MUTATION

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

(2014) Martin Kircher et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

(2012) Mauno Vihinen   BMC GENOMICS

PON-P: Integrated predictor for pathogenicity of missense variants

(2012) Ayodeji Olatubosun et al.   HUMAN MUTATION

Classification of mismatch repair gene missense variants with PON-MMR

(2012) Heidi Ali et al.   HUMAN MUTATION

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS)

(2011) Noralane M. Lindor et al.   HUMAN MUTATION

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar

(2010) Anaïs Mottaz et al.   BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

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

(2009) Remo Calabrese 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

Genetic evidence and integration of various data sources for classifying uncertain variants into a single model

(2008) David E. Goldgar et al.   HUMAN MUTATION