PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned

Predicting Severity of Disease-Causing Variants

(2017) Abhishek Niroula et al.   HUMAN MUTATION

PON-Sol: prediction of effects of amino acid substitutions on protein solubility

(2016) Yang Yang et al.   BIOINFORMATICS

How to Define Pathogenicity, Health, and Disease?

(2016) Mauno Vihinen   HUMAN MUTATION

Human Variome Project Quality Assessment Criteria for Variation Databases

(2016) Mauno Vihinen et al.   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

Challenges: Crowdsourced solutions

(2016) Eric Bender   NATURE

Classification evaluation

(2016) Jake Lever et al.   NATURE METHODS

Crowdsourcing biomedical research: leveraging communities as innovation engines

(2016) Julio Saez-Rodriguez et al.   NATURE REVIEWS GENETICS

PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations

(2016) Abhishek Niroula et al.   NUCLEIC ACIDS RESEARCH

Computational assessment of feature combinations for pathogenic variant prediction

(2016) Eva König et al.   Molecular Genetics & Genomic Medicine

Harmful somatic amino acid substitutions affect key pathways in cancers

(2015) Abhishek Niroula et al.   BMC Medical Genomics

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

(2015) Ian Walsh et al.   BRIEFINGS IN BIOINFORMATICS

Types and effects of protein variations

(2015) Mauno Vihinen   HUMAN GENETICS

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

(2015) Abhishek Niroula et al.   HUMAN MUTATION

wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases

(2015) Miguel Vazquez et al.   HUMAN MUTATION

Characterization of All Possible Single-Nucleotide Change Caused Amino Acid Substitutions in the Kinase Domain of Bruton Tyrosine Kinase

(2015) Jouni Väliaho et al.   HUMAN MUTATION

The Importance of Proper Testing of Predictor Performance

(2015) Mauno Vihinen   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

No more hidden solutions in bioinformatics

(2015) Mauno Vihinen   NATURE

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Muddled genetic terms miss and mess the message

(2015) Mauno Vihinen   TRENDS IN GENETICS

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

(2015) Abhishek Niroula et al.   PLoS One

Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions

(2014) Heidi Ali et al.   HUMAN MUTATION

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

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian 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

Assessing genotype–phenotype correlation in Costello syndrome using a severity score

(2013) Elizabeth M. McCormick et al.   GENETICS IN MEDICINE

Variation Ontology for annotation of variation effects and mechanisms

(2013) M. Vihinen   GENOME RESEARCH

A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency

(2013) Yu Nee Lee et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database

(2013) Bryony A Thompson et al.   NATURE GENETICS

VarioML framework for comprehensive variation data representation and exchange

(2012) Myles Byrne et al.   BMC BIOINFORMATICS

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

Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis

(2012) David L. Masica et al.   HUMAN MUTATION

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics: A Report from the Colon Cancer Family Registry

(2012) Bryony A. Thompson et al.   HUMAN MUTATION

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

Flexibility in MuA Transposase Family Protein Structures: Functional Mapping with Scanning Mutagenesis and Sequence Alignment of Protein Homologues

(2012) Tiina S. Rasila et al.   PLoS One

Development and Validation of a Computational Method for Assessment of Missense Variants in Hypertrophic Cardiomyopathy

(2011) Daniel M. Jordan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Guidelines for establishing locus specific databases

(2011) Mauno Vihinen et al.   HUMAN MUTATION

Curating gene variant databases (LSDBs): Toward a universal standard

(2011) Jacopo Celli et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Different molecular behavior of CD40 mutants causing hyper-IgM syndrome

(2010) G. Lanzi et al.   BLOOD

A validated disease severity scoring system for adults with type 1 Gaucher disease

(2010) Neal J Weinreb et al.   GENETICS IN MEDICINE

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

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

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A three-state prediction of single point mutations on protein stability changes

(2008) Emidio Capriotti et al.   BMC BIOINFORMATICS

Genome wide analysis of pathogenic SH2 domain mutations

(2008) Ilkka Lappalainen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS