Intron-centric estimation of alternative splicing from RNA-seq data
DD Pervouchine, DG Knowles, R Guigo - Bioinformatics, 2013 - academic.oup.com
Motivation: Novel technologies brought in unprecedented amounts of high-throughput
sequencing data along with great challenges in their analysis and interpretation. The …
sequencing data along with great challenges in their analysis and interpretation. The …
SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing
I Pulyakhina, I Gazzoli, PAC 't Hoen… - Nucleic acids …, 2015 - academic.oup.com
Alternative splicing is a powerful mechanism present in eukaryotic cells to obtain a wide
range of transcripts and protein isoforms from a relatively small number of genes. The …
range of transcripts and protein isoforms from a relatively small number of genes. The …
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays
E Mancini, A Rabinovich, J Iserte, M Yanovsky… - …, 2021 - academic.oup.com
Motivation Genome-wide analysis of alternative splicing has been a very active field of
research since the early days of next generation sequencing technologies. Since then, ever …
research since the early days of next generation sequencing technologies. Since then, ever …
[HTML][HTML] KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data
GAT Sacomoto, J Kielbassa, R Chikhi, R Uricaru… - BMC …, 2012 - Springer
Background In this paper, we address the problem of identifying and quantifying
polymorphisms in RNA-seq data when no reference genome is available, without …
polymorphisms in RNA-seq data when no reference genome is available, without …
[HTML][HTML] PASTA: splice junction identification from RNA-Sequencing data
S Tang, A Riva - BMC bioinformatics, 2013 - Springer
Background Next generation transcriptome sequencing (RNA-Seq) is emerging as a
powerful experimental tool for the study of alternative splicing and its regulation, but requires …
powerful experimental tool for the study of alternative splicing and its regulation, but requires …
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data
Motivation: Understanding the occurrence and regulation of alternative splicing (AS) is a key
task towards explaining the regulatory processes that shape the complex transcriptomes of …
task towards explaining the regulatory processes that shape the complex transcriptomes of …
One pipeline to predict them all? On the prediction of alternative splicing from RNA-Seq data
D Olofsson, M Preußner, A Kowar, F Heyd… - Biochemical and …, 2023 - Elsevier
RNA-Seq has become the standard approach to quantify and compare gene expression and
alternative splicing in different conditions. In many cases the limiting factor is not the …
alternative splicing in different conditions. In many cases the limiting factor is not the …
Two-pass alignment improves novel splice junction quantification
BA Veeneman, S Shukla, SM Dhanasekaran… - …, 2016 - academic.oup.com
Motivation: Discovery of novel splicing from RNA sequence data remains a critical and
exciting focus of transcriptomics, but reduced alignment power impedes expression …
exciting focus of transcriptomics, but reduced alignment power impedes expression …
Methods to study splicing from high-throughput RNA sequencing data
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq)
has provided a very powerful mean to study splicing under multiple conditions at …
has provided a very powerful mean to study splicing under multiple conditions at …
Alternative splicing signatures in RNA‐seq data: percent spliced in (PSI)
Thousands of alternative exons are spliced out of messenger RNA to increase protein
diversity. High‐throughput sequencing of short cDNA fragments (RNA‐seq) generates a …
diversity. High‐throughput sequencing of short cDNA fragments (RNA‐seq) generates a …