Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

(2013) Romain A. Studer et al.   BIOCHEMICAL JOURNAL

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility

(2013) C. Mirabello et al.   BIOINFORMATICS

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

(2013) S. Castellana et al.   BRIEFINGS IN BIOINFORMATICS

Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease

(2013) David N. Cooper et al.   HUMAN GENETICS

A probabilistic model for secondary structure prediction from protein chemical shifts

(2013) Martin Mechelke et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Deleterious Nonsynonymous Single-Nucleotide Polymorphism for Human Diseases

(2013) Jiaxin Wu et al.   TheScientificWorldJOURNAL

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies

(2013) Miao-Xin Li et al.   PLoS Genetics

Heuristic Methods for Finding Pathogenic Variants in Gene Coding Sequences

(2013) Monique Ohanian et al.   Journal of the American Heart Association

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

(2012) Sophie Coutant et al.   BMC BIOINFORMATICS

Prioritization of pathogenic mutations in the protein kinase superfamily

(2012) Jose MG Izarzugaza et al.   BMC GENOMICS

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

(2012) Ezequiel Juritz et al.   BMC GENOMICS

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

(2012) Mauno Vihinen   BMC GENOMICS

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Inferring causality and functional significance of human coding DNA variants

(2012) S. R. Sunyaev   HUMAN MOLECULAR GENETICS

Calibration of Multiple In Silico Tools for Predicting Pathogenicity of Mismatch Repair Gene Missense Substitutions

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

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

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

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

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

Sequencing for diagnosis

(2012) Mary Muers   NATURE REVIEWS GENETICS

Exploring functional variant discovery in non-coding regions with SInBaD

(2012) Kjong-Van Lehmann et al.   NUCLEIC ACIDS RESEARCH

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

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

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

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

(2012) Mingjun Wang et al.   PLoS One

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

(2012) Abel Gonzalez-Perez et al.   Genome Medicine

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

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

Exome sequencing: Dual role as a discovery and diagnostic tool

(2011) Chee-Seng Ku et al.   ANNALS OF NEUROLOGY

Human Genome Sequencing in Health and Disease

(2011) Claudia Gonzaga-Jauregui et al.   Annual Review of Medicine

KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels

(2011) L. F. Stead et al.   BIOINFORMATICS

Improving the prediction of disease-related variants using protein three-dimensional structure

(2011) Emidio Capriotti et al.   BMC BIOINFORMATICS

Predicting disease-associated substitution of a single amino acid by analyzing residue interactions

(2011) Yizhou Li et al.   BMC BIOINFORMATICS

Annotating individual human genomes

(2011) Ali Torkamani 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

LOVD v.2.0: the next generation in gene variant databases

(2011) Ivo F. A. C. Fokkema et al.   HUMAN MUTATION

Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants

(2011) David K Crockett et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

(2011) Víctor Quesada et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing and disease

(2011) Eddo Kim et al.   RNA Biology

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

Using bioinformatics to predict the functional impact of SNVs

(2010) M. S. Cline et al.   BIOINFORMATICS

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

(2010) Hanka Venselaar et al.   BMC BIOINFORMATICS

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

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

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

Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties

(2010) Tao Huang et al.   PLoS One

Lessons from the lysozyme of phage T4

(2010) Walter A. Baase et al.   PROTEIN SCIENCE

Functional modules, mutational load and human genetic disease

(2010) Norann A. Zaghloul et al.   TRENDS IN GENETICS

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

(2010) Nicholas J. Marini et al.   PLoS Genetics

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li 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

Compensated Pathogenic Deviations: Analysis of Structural Effects

(2009) Anja Barešić et al.   JOURNAL OF MOLECULAR BIOLOGY

Bi-Directional SIFT Predicts a Subset of Activating Mutations

(2009) William Lee et al.   PLoS One

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

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

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

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

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

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers

(2008) Maxim Barenboim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein interactions in human genetic diseases

(2008) Benjamin Schuster-Böckler et al.   GENOME BIOLOGY