Scalable functional assays for the interpretation of human genetic variation

D Tabet, V Parikh, P Mali, FP Roth… - Annual Review of …, 2022 - annualreviews.org
Scalable sequence–function studies have enabled the systematic analysis and cataloging of
hundreds of thousands of coding and noncoding genetic variants in the human genome …

Accurate proteome-wide missense variant effect prediction with AlphaMissense

J Cheng, G Novati, J Pan, C Bycroft, A Žemgulytė… - Science, 2023 - science.org
The vast majority of missense variants observed in the human genome are of unknown
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …

Proteingym: Large-scale benchmarks for protein fitness prediction and design

P Notin, A Kollasch, D Ritter… - Advances in …, 2024 - proceedings.neurips.cc
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …

Folate-dependent hypermobility syndrome: A proposed mechanism and diagnosis

J Courseault, C Kingry, V Morrison, C Edstrom… - Heliyon, 2023 - cell.com
Hypermobility involves excessive flexibility and systemic manifestations of connective tissue
fragility. We propose a folate-dependent hypermobility syndrome model based on clinical …

Updated benchmarking of variant effect predictors using deep mutational scanning

BJ Livesey, JA Marsh - Molecular systems biology, 2023 - embopress.org
The assessment of variant effect predictor (VEP) performance is fraught with biases
introduced by benchmarking against clinical observations. In this study, building on our …

[HTML][HTML] Improved pathogenicity prediction for rare human missense variants

Y Wu, H Liu, R Li, S Sun, J Weile, FP Roth - The American Journal of …, 2021 - cell.com
The success of personalized genomic medicine depends on our ability to assess the
pathogenicity of rare human variants, including the important class of missense variation …

A comprehensive map of human glucokinase variant activity

S Gersing, M Cagiada, M Gebbia, AP Gjesing, AG Coté… - Genome Biology, 2023 - Springer
Background Glucokinase (GCK) regulates insulin secretion to maintain appropriate blood
glucose levels. Sequence variants can alter GCK activity to cause hyperinsulinemic …

Cross-protein transfer learning substantially improves disease variant prediction

M Jagota, C Ye, C Albors, R Rastogi, A Koehl… - Genome Biology, 2023 - Springer
Background Genetic variation in the human genome is a major determinant of individual
disease risk, but the vast majority of missense variants have unknown etiological effects …

[HTML][HTML] Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens

Y Zhao, D Tabet, DR Contreras, L Lao, AN Kousholt… - Molecular Cell, 2023 - cell.com
To maintain genome integrity, cells must accurately duplicate their genome and repair DNA
lesions when they occur. To uncover genes that suppress DNA damage in human cells, we …

[HTML][HTML] Proteingym: Large-scale benchmarks for protein design and fitness prediction

P Notin, AW Kollasch, D Ritter, L van Niekerk, S Paul… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins that can address our most …