Recent advances in cancer fusion transcript detection

R Dorney, BP Dhungel, JEJ Rasko… - Briefings in …, 2023 - academic.oup.com
Extensive investigation of gene fusions in cancer has led to the discovery of novel
biomarkers and therapeutic targets. To date, most studies have neglected chromosomal …

Artifacts and biases of the reverse transcription reaction in RNA sequencing

J Verwilt, P Mestdagh, J Vandesompele - RNA, 2023 - rnajournal.cshlp.org
RNA sequencing has spurred a significant number of research areas in recent years. Most
protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA …

Challenges in identifying mRNA transcript starts and ends from long-read sequencing data

E Calvo-Roitberg, RF Daniels, AA Pai - Genome Research, 2024 - genome.cshlp.org
Long-read sequencing (LRS) technologies have the potential to revolutionize scientific
discoveries in RNA biology through the comprehensive identification and quantification of …

Strategic nucleic acid detection approaches for diagnosing African swine fever (ASF): navigating disease dynamics

Y Zhu, M Zhang, Z Jie, S Guo, Z Zhu, S Tao - Veterinary Research, 2024 - Springer
African swine fever (ASF) is a devastating disease caused by African swine fever virus
(ASFV) and leads to significant economic losses in the pig farming industry. Given the …

Ecosystem-specific microbiota and microbiome databases in the era of big data

V Lobanov, A Gobet, A Joyce - Environmental Microbiome, 2022 - Springer
The rapid development of sequencing methods over the past decades has accelerated both
the potential scope and depth of microbiota and microbiome studies. Recent developments …

Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach

Á Fülöp, G Torma, N Moldován, K Szenthe, F Bánáti… - Virology Journal, 2022 - Springer
Abstract Background Epstein–Barr virus (EBV) is an important human pathogenic
gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been …

Grapevine virology in the third-generation sequencing era: from virus detection to viral epitranscriptomics

VJ Javaran, P Moffett, P Lemoyne, D Xu… - Plants, 2021 - mdpi.com
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is
the most cultivated fruit plant. It has a significant impact on the economies of many countries …

Long-read assays shed new light on the transcriptome complexity of a viral pathogen

D Tombácz, I Prazsák, Z Csabai, N Moldován… - Scientific Reports, 2020 - nature.com
Abstract Characterization of global transcriptomes using conventional short-read
sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms …

KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing

I Prazsák, D Tombácz, Á Fülöp, G Torma, G Gulyás… - Msystems, 2024 - Am Soc Microbiol
Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus
belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with …

Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation

Y Hu, J Zhong, Y Xiao, Z Xing, K Sheu, S Fan… - Nature …, 2020 - nature.com
The differences in transcription start sites (TSS) and transcription end sites (TES) among
gene isoforms can affect the stability, localization, and translation efficiency of mRNA. Gene …