Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
S Bryce-Smith, D Burri, MR Gazzara, CJ Herrmann… - RNA, 2023 - rnajournal.cshlp.org
The tremendous rate with which data is generated and analysis methods emerge makes it
increasingly difficult to keep track of their domain of applicability, assumptions, limitations …
increasingly difficult to keep track of their domain of applicability, assumptions, limitations …
A survey on methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq, and single-cell RNA-seq
Alternative polyadenylation (APA) plays important roles in modulating mRNA stability,
translation, and subcellular localization, and contributes extensively to shaping eukaryotic …
translation, and subcellular localization, and contributes extensively to shaping eukaryotic …
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with
different 3′ ends, which is dynamic across different cell types or conditions. Many …
different 3′ ends, which is dynamic across different cell types or conditions. Many …
scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data
Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to
transcriptome diversity and gene expression regulation by affecting mRNA stability …
transcriptome diversity and gene expression regulation by affecting mRNA stability …
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution
Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript
diversification in eukaryotes, which is increasingly recognized as an important layer for …
diversification in eukaryotes, which is increasingly recognized as an important layer for …
PlantAPAdb: a comprehensive database for alternative polyadenylation sites in plants
Alternative cleavage and polyadenylation (APA) is increasingly recognized as an important
regulatory mechanism in eukaryotic gene expression and is dynamically modulated in a …
regulatory mechanism in eukaryotic gene expression and is dynamically modulated in a …
[HTML][HTML] PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data
Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism; yet, its
regulation and impact on human diseases remain understudied. Existing bulk RNA …
regulation and impact on human diseases remain understudied. Existing bulk RNA …
Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence
R Lusk, E Stene, F Banaei-Kashani, B Tabakoff… - Nature …, 2021 - nature.com
Annotation of polyadenylation sites from short-read RNA sequencing alone is a challenging
computational task. Other algorithms rooted in DNA sequence predict potential …
computational task. Other algorithms rooted in DNA sequence predict potential …
Alternative splicing affects synapses in the hippocampus of offspring after maternal fructose exposure during gestation and lactation
Y Zou, Q Guo, Y Chang, Y Zhong, L Cheng… - Chemico-Biological …, 2023 - Elsevier
Increased fructose over-intake is a global issue. Maternal fructose exposure during gestation
and lactation can impair brain development in offspring. However, the effect on synapses is …
and lactation can impair brain development in offspring. However, the effect on synapses is …
The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer
Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of
cis-regulatory elements such as microRNA (miRNA) target sites in the 3′-untranslated …
cis-regulatory elements such as microRNA (miRNA) target sites in the 3′-untranslated …