Search · four archives
Search · four archives
17 papers · ranked by Valyu relevance
Jishu Xu, Michaela Hörner, Elena Buena Atienza, Kalaivani Manibarathi + 6 more
Long-read RNA sequencing has transformed transcriptome analysis by enabling comprehensive mapping of full-length transcripts, providing an unprecedented resolution of transcript diversity, alternative splicing, and transcript-specific regulation. In this study, we employed nanopore long-read RNA sequencing to profile…
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…
Chit Tong Lio, Tolga Düz, Markus Hoffmann, Lina-Liv Willruth + 3 more
RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential transcript usage (DTU) analysis. The choice of the right analysis tool is…
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…
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…
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 doesn’t change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level of…
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…
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…
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…
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…
Marjan Hosseini, Devin McConnell, Derek Aguiar
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a…
B.L. Draper, Mark Dunning, David C. James
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed examination of their statistical methods, case applications, and benefits. A…
Melania Barile, Shirom Chabra, Tomoya Isobe, Berthold Gottgens
A defining characteristic of all metazoan organisms is the existence of different cell states or cell types, driven by changes in gene expression kinetics, principally transcription, splicing and degradation rates. The RNA velocity framework utilizes both spliced and unspliced reads in single cell mRNA preparations to…
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…
Franziska Hoerbst, G. S. Sidhu, Melissa Tomkins, Richard J. Morris
in Gene Expression using Bayes Factors Authors: ['Franziska Hoerbst' 'G. S. Sidhu' 'Melissa Tomkins' 'Richard J. Morris'] Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for…
Hilbert Lam Yuen In, Robbe Pincket
Current popular methods in literature of RNA sequencing normalisation do not account for gene length when compared across samples, whilst adjusting for count biases in the data. This creates a gap in the normalisation as bigger genes in RNA sequencing accumulate more reads due to shotgun sequencing methods. As a…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…