The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation …

PD Stenson, M Mort, EV Ball, K Evans, M Hayden… - Human genetics, 2017 - Springer
Abstract The Human Gene Mutation Database (HGMD®) constitutes a comprehensive
collection of published germline mutations in nuclear genes that underlie, or are closely …

Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Y Yang, J Gao, J Wang, R Heffernan… - Briefings in …, 2018 - academic.oup.com
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …

SPIDER2: a package to predict secondary structure, accessible surface area, and main-chain torsional angles by deep neural networks

Y Yang, R Heffernan, K Paliwal, J Lyons… - Prediction of protein …, 2017 - Springer
Predicting one-dimensional structure properties has played an important role to improve
prediction of protein three-dimensional structures and functions. The most commonly …

Assessing the pathogenicity of insertion and deletion variants with the variant effect scoring tool (VEST‐Indel)

C Douville, DL Masica, PD Stenson… - Human …, 2016 - Wiley Online Library
Insertion/deletion variants (indels) alter protein sequence and length, yet are highly
prevalent in healthy populations, presenting a challenge to bioinformatics classifiers …

Effects of short indels on protein structure and function in human genomes

M Lin, S Whitmire, J Chen, A Farrel, X Shi, J Guo - Scientific reports, 2017 - nature.com
Insertions and deletions (indels) represent the second most common type of genetic
variations in human genomes. Indels can be deleterious and contribute to disease …

EASE-MM: sequence-based prediction of mutation-induced stability changes with feature-based multiple models

L Folkman, B Stantic, A Sattar, Y Zhou - Journal of molecular biology, 2016 - Elsevier
Protein engineering and characterisation of non-synonymous single nucleotide variants
(SNVs) require accurate prediction of protein stability changes (ΔΔ G u) induced by single …

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants

KA Pagel, V Pejaver, GN Lin, HJ Nam, M Mort… - …, 2017 - academic.oup.com
Motivation Loss-of-function genetic variants are frequently associated with severe clinical
phenotypes, yet many are present in the genomes of healthy individuals. The available …

Computational methods for the pharmacogenetic interpretation of next generation sequencing data

Y Zhou, K Fujikura, S Mkrtchian… - Frontiers in …, 2018 - frontiersin.org
Up to half of all patients do not respond to pharmacological treatment as intended. A
substantial fraction of these inter-individual differences is due to heritable factors and a …

Computational and experimental methods for classifying variants of unknown clinical significance

M Spielmann, M Kircher - Molecular Case Studies, 2022 - molecularcasestudies.cshlp.org
The increase in sequencing capacity, reduction in costs, and national and international
coordinated efforts have led to the widespread introduction of next-generation sequencing …