Search · four archives
Search · four archives
13 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…
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…
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…
Alexandre Segers, Jeroen Gilis, Mattias Van Heetvelde, Davide Risso + 2 more
RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and limitations. Indeed, tools for differential transcript usage or rare disease diagnosis through splicing and expression outliers, either lack performance, discard information, or do not…
Alexandre Segers, Jeroen Gilis, Mattias Van Heetvelde, Davide Risso + 2 more
RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and restrictions. Indeed, tools for differential transcript usage, or diagnosing patients with rare diseases through splicing and expression outliers, either lack in performance, discard…
Shuhua Fu, Parker Wilson, Bo Zhang
Cells can transcribe different isoforms of a gene by using distinct Transcriptional Start Regions (TSRs), which are recognized by RNA-Polymerase II and regulated by cell-type-specific expressed transcription factors, eventually forming tissue and cell-type-specific expression during development. However, how the…
Chun Shen Lim, Gabrielle S.W. Chieng
Protein synthesis is regulated by multiple cis-regulatory elements, including small ORFs, yet current differential translation methods assume uniform changes at the gene level. We present DOTSeq, a Differential ORF Translation statistical framework that resolves ORF-level regulation in bulk ribosome profiling…
Kevin Vo, Ryan Mohamadi, Yashica Sharma, Amelia Mohamadi + 2 more
RNA sequencing (RNA-Seq) has become a widely adopted genome-wide technique for investigating gene expression patterns. However, conventional RNA-Seq analyses typically rely on gene expression (GE) values that aggregate all the transcripts produced by a gene under a single identifier, overlooking the complexity of…
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…
Ruiqi Li, Junchen Yang, Pei-Chun Su, Ariel Jaffe + 2 more
Detecting changes in gene coordination patterns between biological conditions and identifying the cell populations in which these changes occur are key challenges in single-cell analysis. Existing approaches often compare gene co-expression between predefined cell clusters or rely on aligning cells across conditions.…
Vighnesh Ghatpande, Uma Paul, MacKenzie A Howard, Can Cenik
In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca^2+^ regulation in muscle, and signaling during embryonic…
Anna Grandchamp, Peter Czuppon, Erich Bornberg-Bauer
Most of the transcribed genome in eukaryotes does not code for proteins but produces non-genic transcripts. Among these non-genic transcripts, some are newly transcribed when compared to an evolutionary close outgroup, and are referred to as de novo transcript. Despite their creative role for genomic innovations as…