spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data

F Bocci, P Zhou, Q Nie - Molecular systems biology, 2022 - embopress.org
Extracting dynamical information from single‐cell transcriptomics is a novel task with the
promise to advance our understanding of cell state transition and interactions between …

SpliceSeq 2.0: A tool for analysis and visualization of splicing variation in RNASeq data

MC Ryan, J Cleland, R Kim, WC Wong… - Europe PMC free … - researchgate.net
Alternative mRNA splicing enables a single gene to produce multiple protein products that
are specific to tissue type or developmental stage. Aberrant splicing patterns lead to …

PennDiff: detecting differential alternative splicing and transcription by RNA sequencing

Y Hu, J Lin, J Hu, G Hu, K Wang, H Zhang… - …, 2018 - academic.oup.com
Motivation Alternative splicing and alternative transcription are a major mechanism for
generating transcriptome diversity. Differential alternative splicing and transcription (DAST) …

acorde unravels functionally interpretable networks of isoform co-usage from single cell data

A Arzalluz-Luque, P Salguero, S Tarazona… - Nature …, 2022 - nature.com
Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to
modulate isoform expression within genes and contribute to cell-type identity. However, the …

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

D Singh, CF Orellana, Y Hu, CD Jones, Y Liu… - …, 2011 - academic.oup.com
Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts
and plays an important role in tissue-specific differentiation, and can be misregulated in …

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples

C Wilks, P Gaddipati, A Nellore, B Langmead - Bioinformatics, 2018 - academic.oup.com
Motivation As more and larger genomics studies appear, there is a growing need for
comprehensive and queryable cross-study summaries. These enable researchers to …

McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

I Alqassem, Y Sonthalia, E Klitzke-Feser, H Shim… - …, 2021 - academic.oup.com
Motivation Alternative splicing removes intronic sequences from pre-mRNAs in alternative
ways to produce different forms (isoforms) of mature mRNA. The composition of expressed …

Leveraging transcript quantification for fast computation of alternative splicing profiles

GP Alamancos, A Pagès, JL Trincado, N Bellora… - Rna, 2015 - rnajournal.cshlp.org
Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

D Wyman, G Balderrama-Gutierrez, F Reese, S Jiang… - Biorxiv, 2019 - biorxiv.org
Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and
is a key contributor to both normal developmental processes and disease states. While cost …

Analysis of RNA Transcripts by High‐Throughput RNA Sequencing

P Ribeca, V Lacroix, M Sammeth… - Alternative pre‐mRNA …, 2012 - Wiley Online Library
For many years, array‐based methods have been used successfully to interrogate the
transcriptome of the cell. These methods rely on quantification of the hybridization intensity …