[HTML][HTML] Learning the regulatory code of gene expression
Data-driven machine learning is the method of choice for predicting molecular phenotypes
from nucleotide sequence, modeling gene expression events including protein-DNA …
from nucleotide sequence, modeling gene expression events including protein-DNA …
Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer …
It is possible to estimate the prior probability of pathogenicity for germline disease gene
variants based on bioinformatic prediction of variant effect/s. However, routinely used …
variants based on bioinformatic prediction of variant effect/s. However, routinely used …
Flood susceptibility mapping using an improved analytic network process with statistical models
Flooding is a natural disaster that causes considerable damage to different sectors and
severely affects economic and social activities. The city of Saqqez in Iran is susceptible to …
severely affects economic and social activities. The city of Saqqez in Iran is susceptible to …
Genome-wide detection of human variants that disrupt intronic branchpoints
P Zhang, Q Philippot, W Ren, WT Lei… - Proceedings of the …, 2022 - National Acad Sciences
Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic
branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 …
branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 …
[HTML][HTML] A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project
AJM Blakes, HA Wai, I Davies, HE Moledina, A Ruiz… - Genome Medicine, 2022 - Springer
Background Genomic variants which disrupt splicing are a major cause of rare genetic
diseases. However, variants which lie outside of the canonical splice sites are difficult to …
diseases. However, variants which lie outside of the canonical splice sites are difficult to …
Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
K Hamanaka, D Yamauchi, E Koshimizu… - Genome …, 2023 - genome.cshlp.org
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is
associated with gene regulation. Although previous studies reported several tandem repeats …
associated with gene regulation. Although previous studies reported several tandem repeats …
SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing
Modeling splicing is essential for tackling the challenge of variant interpretation as each
nucleotide variation can be pathogenic by affecting pre‐mRNA splicing via …
nucleotide variation can be pathogenic by affecting pre‐mRNA splicing via …
Exonic splicing code and coordination of divalent metals in proteins
D Bakhtiar, K Vondraskova, RJ Pengelly… - Nucleic Acids …, 2024 - academic.oup.com
Exonic sequences contain both protein-coding and RNA splicing information but the
interplay of the protein and splicing code is complex and poorly understood. Here, we have …
interplay of the protein and splicing code is complex and poorly understood. Here, we have …
[HTML][HTML] Variations of intronic branchpoint motif: identification and functional implications in splicing and disease
J Xie, L Wang, RJ Lin - Communications Biology, 2023 - nature.com
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA
splicing. In mammals, its sequence composition, distance to the downstream exon, and …
splicing. In mammals, its sequence composition, distance to the downstream exon, and …
[HTML][HTML] Identification of an elusive spliceogenic MYBPC3 variant in an otherwise genotype-negative hypertrophic cardiomyopathy pedigree
M Torrado, E Maneiro, A Lamounier Junior… - Scientific Reports, 2022 - nature.com
The finding of a genotype-negative hypertrophic cardiomyopathy (HCM) pedigree with
several affected members indicating a familial origin of the disease has driven this study to …
several affected members indicating a familial origin of the disease has driven this study to …