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 …

Statistical methods for assessing the effects of de novo variants on birth defects

Y Xie, R Wu, H Li, W Dong, G Zhou, H Zhao - Human Genomics, 2024 - Springer
With the development of next-generation sequencing technology, de novo variants (DNVs)
with deleterious effects can be identified and investigated for their effects on birth defects …

Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges

YA Barbitoff, MO Ushakov, TE Lazareva… - Briefings in …, 2024 - academic.oup.com
Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics.
Whole exome and whole genome sequencing are now routinely used for diagnostic …

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles

M Tiberti, T Terkelsen, K Degn, L Beltrame… - Briefings in …, 2022 - academic.oup.com
Mutations, which result in amino acid substitutions, influence the stability of proteins and
their binding to biomolecules. A molecular understanding of the effects of protein mutations …

Mutational landscape of the proglucagon-derived peptides

P Lindquist, JS Madsen, H Bräuner-Osborne… - Frontiers in …, 2021 - frontiersin.org
Strong efforts have been placed on understanding the physiological roles and therapeutic
potential of the proglucagon peptide hormones including glucagon, GLP-1 and GLP-2 …

Unveiling clinically significant PPARγ mutations for thiazolidinedione treatment responsiveness through atomistic simulations

S Shahrear, ABMMK Islam - International Journal of Biological …, 2023 - Elsevier
In Type 2 diabetes, increased insulin sensitivity is induced by thiazolidinedione activation of
the peroxisome proliferator-activated receptor gamma (PPARγ). Recent data indicate a …

Estimating clinical risk in gene regions from population sequencing cohort data

JD Fife, CA Cassa - The American Journal of Human Genetics, 2023 - cell.com
While pathogenic variants can significantly increase disease risk, it is still challenging to
estimate the clinical impact of rare missense variants more generally. Even in genes such as …

An insight into the iPSCs-derived two-dimensional culture and three-dimensional organoid models for neurodegenerative disorders

A Bhargava, AM Sandoval Castellanos… - Interface …, 2022 - royalsocietypublishing.org
The use of induced pluripotent stem cells (iPSCs) is a promising approach when used as
models to study neurodegenerative disorders (NDDs) in vitro. iPSCs have been used in in …

Using computational approaches to enhance the interpretation of missense variants in the PAX6 gene

NS Andhika, S Biswas, C Hardcastle… - European Journal of …, 2024 - nature.com
The PAX6 gene encodes a highly-conserved transcription factor involved in eye
development. Heterozygous loss-of-function variants in PAX6 can cause a range of …

Initial Investigations of Intrinsically Disordered Regions in Inherited Retinal Diseases

KE Lee, R Procopio, JS Pulido, KB Gunton - International Journal of …, 2023 - mdpi.com
Intrinsically disordered regions (IDRs) are protein regions that are unable to fold into stable
tertiary structures, enabling their involvement in key signaling and regulatory functions via …