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Results for differential transcript usage

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13 papers · ranked by Valyu relevance

01
PPubMed28 Jan 2022
A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis
Georgia Katsoula, Julia Steinberg, Margo Tuerlings, Rodrigo Coutinho de Almeida + 5 more
'Rodrigo Coutinho de Almeida' 'Lorraine Southam' 'Diane Swift' 'Ingrid Meulenbelt' 'J Mark Wilkinson' 'Eleftheria Zeggini'] Title: Abstract Osteoarthritis is a prevalent joint disease and a major cause of disability worldwide with no curative therapy. Development of disease-modifying therapies requires a better…
86relevance
02
PPubMed8 Aug 2022
<i> satuRn </i> : Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]
Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement
'Lieven Clement'] Alternative splicing produces multiple functional transcripts from a single gene. Dysregulation of splicing is known to be associated with disease and as a hallmark of cancer. Existing tools for differential transcript usage (DTU) analysis either lack in performance, cannot account for complex…
86relevance
03
PPubMed13 May 2025
Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers
Jingni He, Devika Ganesamoorthy, Jessie J.-Y. Chang, Jianshu Zhang + 7 more
'Sharon L. Trevor' 'Kristen S. Gibbons' 'Stephen J. McPherson' 'Jessica C. Kling' 'Luregn J. Schlapbach' 'Antje Blumenthal' 'Lachlan J. M. Coin' ''] Background RNA sequencing of whole blood has been increasingly employed to find transcriptomic signatures of disease states. These studies traditionally utilize short-read…
86relevance
04
PPubMed8 Dec 2025
Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR
Pedro L Baldoni, Lizhong Chen, Mengbo Li, Yunshun Chen + 1 more
Differential transcript usage (DTU) refers to changes in the relative abundance of transcript isoforms of the same gene between experimental conditions, even when the total expression of the gene does not change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level…
83relevance
05
PPubMed18 Jan 2022
Using machine learning to detect the differential usage of novel gene isoforms
Xiaopu Zhang, Musa A. Hassan, James G. D. Prendergast
Background Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene transcripts between groups can be difficult, in particular in less well annotated genomes where the…
82relevance
06
PPubMed10 Jan 2022
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes
David J. Wright, Nicola A. L. Hall, Naomi Irish, Angela L. Man + 8 more
'Will Glynn' 'Arne Mould' 'Alejandro De Los Angeles' 'Emily Angiolini' 'David Swarbreck' 'Karim Gharbi' 'Elizabeth M. Tunbridge' 'Wilfried Haerty'] Background Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of…
80relevance
07
PPubMed13 Jun 2023
Quantitative Analysis of Isoform Switching in Cancer
Georgii Dolgalev, Ekaterina Poverennaya, Christos K. Kontos, David Mu
'David Mu'] Over the past 8 years, multiple studies examined the phenomenon of isoform switching in human cancers and discovered that isoform switching is widespread, with hundreds to thousands of such events per cancer type. Although all of these studies used slightly different definitions of isoform switching, which…
79relevance
08
PPubMed16 Dec 2024
Transcriptome immune-regulatory differences between leprosy patients and type 1 reaction patients, before onset of symptoms Transcriptomics of vulnerability to type 1 reactions
Wilian Correa-Macedo, Monica Dallmann-Sauer, Marianna Orlova, Jeremy Manry + 7 more
'Jeremy Manry' 'Vinicius M. Fava' 'Nguyen Thu Huong' 'Nguyen Ngoc Ba' 'Nguyen Van Thuc' 'Vu Hong Thai' 'Erwin Schurr' 'Victor S. Santos'] Leprosy is a chronic disease of the skin and peripheral nerves caused by Mycobacterium leprae. A major public health and clinical problem are leprosy reactions, which are…
79relevance
09
PPubMed4 Jul 2022
Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells Vahlensieck et al. Transcriptional Adaption to Hypergravity
Christian Vahlensieck, Cora S. Thiel, Daniel Pöschl, Timothy Bradley + 4 more
'Sonja Krammer' 'Beatrice Lauber' 'Jennifer Polzer' 'Oliver Ullrich'] The transcriptome of human immune cells rapidly reacts to altered gravity in a highly dynamic way. We could show in previous experiments that transcriptional patterns show profound adaption after seconds to minutes of altered gravity. To gain further…
77relevance
10
PPubMed7 Jul 2022
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto + 35 more
'Juan Carlos Entizne' 'Wenbin Guo' 'Yamile Marquez' 'Linda Milne' 'Stefan Riegler' 'Akihiro Matsui' 'Maho Tanaka' 'Sarah Harvey' 'Yubang Gao' 'Theresa Wießner-Kroh' 'Alejandro Paniagua' 'Martin Crespi' 'Katherine Denby' 'Asa ben Hur' 'Enamul Huq' 'Michael Jantsch' 'Artur Jarmolowski' 'Tino Koester' 'Sascha Laubinger'…
77relevance
11
PPubMed19 Jun 2025
Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons
Jishu Xu, Michaela Hörner, Elena Buena Atienza, Kalaivani Manibarathi + 6 more
KIF2A (Kinesin Superfamily Protein 2A) plays a crucial role in neuronal migration and differentiation, primarily through its involvement in microtubule dynamics. Mutations in KIF2A are associated with cortical dysplasia and early-onset neurodegeneration . Alternative splicing of KIF2A mRNA produces multiple isoforms…
75relevance
12
PPubMed30 May 2025
Selecting differential splicing methods: Practical considerations for short-read RNA sequencing [version 2; peer review: 2 approved
Ben J. Draper, Mark J. Dunning, David C. James
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics short-read RNA-seq tools for investigating differential splicing; offering a detailed examination of their statistical methods, case applications, and…
72relevance
13
PPubMed6 Nov 2023
DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Arnaud Liehrmann, Etienne Delannoy, Alexandra Launay-Avon, Elodie Gilbault + 3 more
To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along…
67relevance

Results for differential transcript usage

A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis

<i> satuRn </i> : Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]

Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers

Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR

Using machine learning to detect the differential usage of novel gene isoforms

Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

Quantitative Analysis of Isoform Switching in Cancer

Transcriptome immune-regulatory differences between leprosy patients and type 1 reaction patients, before onset of symptoms Transcriptomics of vulnerability to type 1 reactions

Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells Vahlensieck et al. Transcriptional Adaption to Hypergravity

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons

Selecting differential splicing methods: Practical considerations for short-read RNA sequencing [version 2; peer review: 2 approved

DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection

A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis

<i> satuRn </i> : Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]

Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers

Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR

Using machine learning to detect the differential usage of novel gene isoforms

Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

Quantitative Analysis of Isoform Switching in Cancer

Transcriptome immune-regulatory differences between leprosy patients and type 1 reaction patients, before onset of symptoms Transcriptomics of vulnerability to type 1 reactions

Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells Vahlensieck et al. Transcriptional Adaption to Hypergravity

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons

Selecting differential splicing methods: Practical considerations for short-read RNA sequencing [version 2; peer review: 2 approved

DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection