Search · four archives
Search · four archives
11 papers · ranked by Valyu relevance
Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo + 4 more
Most approaches to transcript quantification rely on fixed reference annotations. However, the transcriptome is dynamic, and depending on the context, such static annotations contain inactive isoforms for some genes while they are incomplete for others. To address this, we have developed Bambu, a method that performs…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
B. Poggiali, L. Putzeys, J. D. Andersen, A. Vidaki
The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on…
José L Ruiz, Laura C Terrón-Camero, Julia Castillo-González, Iván Fernández-Rengel + 3 more
In the current context of transcriptomics democratization, there is an unprecedented surge in the number of studies and datasets. However, advances are hampered by aspects such as the reproducibility crisis, and lack of standardization, in particular with scarce reanalyses of secondary data. reanalyzerGSE, is a…
Ludwig Mann, Kristin Balasch, Nicola Schmidt, Tony Heitkam
Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read…
Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang + 6 more
Forensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing.…
Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao
A tandem repeat is a sequence of nucleotides that occurs as multiple contiguous and near-identical copies positioned next to each other. These repeats play critical roles in genetic diversity, gene regulation, and are strongly linked to various neurological and developmental disorders. While several methods exist for…
Alessandro Napoli, Niccolò Liorni, Tommaso Biagini, Agnese Giovannetti + 7 more
Short tandem repeat expansions in exon 1 of the HTT gene drive Huntington’s disease (HD) pathogenesis, with disease onset and progression heavily influenced by somatic mosaicism and sequence interruptions. While sequencing technologies enable repeat sizing, many computational tools lack the resolution to capture subtle…
Yoshiki Tanaka, Rei Kajitani, Takehiko Itoh
Repeat sequences in the genome can be classified into interspersed and tandem repeats, both of which are important for understanding genome evolution and important traits such as disease. They are also noteworthy as regions of high frequency of genome rearrangement in somatic cells and high inter-individual diversity.…
Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga + 1 more
Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have…
Yang Qi, Yiqi Chen, Yingfu Wu, Yanyan Li + 4 more
Transposable elements (TEs) are DNA sequences capable of translocating within a genome. They constitute a substantial portion of eukaryotic genomes and play significant roles in genome evolution and gene regulation. The correct classification of these repetitive elements is essential to investigate their potential…