[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 …

Decoding human genetic variation using a synthetic paradigm

AH Kachroo - Nature Reviews Genetics, 2024 - nature.com
Decoding human genetic variation using a synthetic paradigm | Nature Reviews Genetics Skip to
main content Thank you for visiting nature.com. You are using a browser version with limited …

Variant effect predictor correlation with functional assays is reflective of clinical classification performance

BJ Livesey, JA Marsh - bioRxiv, 2024 - biorxiv.org
Understanding the relationship between protein sequence and function is crucial for
accurate genetic variant classification. Variant effect predictors (VEPs) play a vital role in …

High-resolution functional mapping of RAD51C by saturation genome editing

R Olvera-León, F Zhang, V Offord, Y Zhao, HK Tan… - Cell, 2024 - cell.com
Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while
individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using …

Saturation mutagenesis-reinforced functional assays for disease-related genes

K Ma, S Huang, KK Ng, NJ Lake, S Joseph, J Xu, A Lek… - Cell, 2024 - cell.com
Interpretation of disease-causing genetic variants remains a challenge in human genetics.
Current costs and complexity of deep mutational scanning methods are obstacles for …

Assessing predictions on fitness effects of missense variants in HMBS in CAGI6

J Zhang, L Kinch, P Katsonis, O Lichtarge, M Jagota… - Human genetics, 2024 - Springer
This paper presents an evaluation of predictions submitted for the" HMBS" challenge, a
component of the sixth round of the Critical Assessment of Genome Interpretation held in …

FiTMuSiC: leveraging structural and (co) evolutionary data for protein fitness prediction

M Tsishyn, G Cia, P Hermans, J Kwasigroch… - Human genomics, 2024 - Springer
Systematically predicting the effects of mutations on protein fitness is essential for the
understanding of genetic diseases. Indeed, predictions complement experimental efforts in …

Large language models for biological prediction and design

AW Kollasch - 2023 - search.proquest.com
Predicting the functional impact of changes to biological sequences is a central challenge in
genetics and biology. Beyond genetics, sequence-to-function mapping has key applications …

[HTML][HTML] A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data

Y Zhao, G Zhong, J Hagen, H Pan, WK Chung, Y Shen - medRxiv, 2023 - ncbi.nlm.nih.gov
Accurately predicting the effect of missense variants is a central problem in interpretation of
genomic variation. Commonly used computational methods does not capture the …

A missense variant effect map for the human tumour suppressor protein CHK2

M Gebbia, DI Zimmerman, R Jiang, M Nguyen, J Weile… - bioRxiv, 2024 - biorxiv.org
The tumour suppressor CHEK2 encodes the serine/threonine protein kinase CHK2 which,
upon DNA damage, is important for pausing the cell cycle, initiating DNA repair and …