Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

V Pejaver, J Urresti, J Lugo-Martinez, KA Pagel… - Nature …, 2020 - nature.com
… and widely used machine learning approach, MutPred 10 , by … MutPred2 is a machine
learning-based method, and … of that study, we predict that the disruption of allosteric sites is an …

Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing

K Gupta, C Yang, K McCue, O Bastani, P Sharp… - BioRxiv, 2023 - biorxiv.org
exonic SREs into a simple splicing simulator was found to substantially improve the predictions
of a simple splicing … RBPs in splicing and to interpret variants that alter RBP binding. …

DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions

Q Liu, H Fang, X Wang, M Wang, S Li, LJM Coin… - …, 2022 - academic.oup.com
… a novel generalized deep learning framework, referred to as DeepGenGrep (Deep learning-based
model for genomic signals and regions prediction), for predicting multiple GSRs in the …

[PDF][PDF] Daniel Danis, Julius OB Jacobsen, 2 Leigh C. Carmody, Michael A. Gargano, Julie A. McMurry, 3

A Hegde, MA Haendel, G Valentini… - The American Journal …, 2021 - researchgate.net
… that contextualize predicted effects of variants on splicing to make it easier to interpret …
10% of all exonic variants, including missense and nonsense variants, may alter splicing.However, …

[HTML][HTML] Gene Regulation via RNA Isoform Variations

B Zhang, C Xu - 2024 - intechopen.com
exonic and intronic regions could also enhance (splicing … thus its mutations should impair
splicing globally. Compared to … well as deep-learning-based methods for predicting isoform …

Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing

K Gupta, C Yang, K McCue, O Bastani, PA Sharp… - Genome Biology, 2024 - Springer
… Incorporating known exonic SREs into a simple splicing … This two-step process ensures that
we predict splicing from a … RBPs in splicing and to interpret variants that alter RBP binding. …

An interpretable model of pre-mRNA splicing for animal and plant genes

K McCue, CB Burge - Science Advances, 2024 - science.org
… to predict splicing disruption caused by genetic variants and … the likelihood of a variant
disrupting splicing (27, 28). … silencing splicing in local regions, we defined an exonic splicing

Splicing mutations in the CFTR gene as therapeutic targets

K Deletang, M Taulan-Cadars - Gene Therapy, 2022 - nature.com
… regulatory sequences (intronic and exonic splicing silencers … can predict the consequence
only of variants affecting the 5’ … to identify splicing variants (MutPred Splice [41], Splice AI [42]…

Challenges related to the use of next-generation sequencing for the optimization of drug therapy

Y Zhou, VM Lauschke - Precision Medicine, 2022 - Springer
… interpretation of variant categories beyond missense variants. Variants affecting splicing
contribute … SpliceAI significantly outperformed other splicing variant prediction methods in both …

Genome-wide sequence analysis of human splice acceptor regions for motif discovery

G Karaduman Bahçe - 2020 - open.metu.edu.tr
MutPred Splice concentrates only on the variants at coding regions, ie, … deep learning-based
tools to identify splice variants. It annotates the genetic variants with their predictive splicing