RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Bioinformatic tools for the analysis and prediction of ncRNA interactions

A Rincón-Riveros, D Morales, JA Rodríguez… - International Journal of …, 2021 - mdpi.com
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via
their interactions with other biological molecules such as proteins and nucleic acids …

Biome‐microbiome interactions in peri‐implantitis: A pilot investigation

SM Ganesan, SM Dabdoub… - Journal of …, 2022 - Wiley Online Library
Background Dental implants replace missing teeth in at least 100 million people, yet over
one million implants fail every year due to peri‐implantitis, a bacterially induced …

The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle

I García-Pérez, A Molsosa-Solanas, M Perelló-Amorós… - Cells, 2022 - mdpi.com
Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate
gene expression at the transcriptional or translational levels. In the present work, previously …

Navigation through the twists and turns of RNA sequencing technologies: application to bacterial regulatory RNAs

E Desgranges, I Caldelari, S Marzi… - Biochimica et Biophysica …, 2020 - Elsevier
Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in
virtually all aspects of bacterial physiology and virulence. Together with transcriptional and …

RNAnue: efficient data analysis for RNA–RNA interactomics

RA Schäfer, B Voß - Nucleic Acids Research, 2021 - academic.oup.com
RNA–RNA inter-and intramolecular interactions are fundamental for numerous biological
processes. While there are reasonable approaches to map RNA secondary structures …

ChimericFragments: computation, analysis and visualization of global RNA networks

M Siemers, A Lippegaus… - NAR Genomics and …, 2024 - academic.oup.com
RNA–RNA interactions are a key feature of post-transcriptional gene regulation in all
domains of life. While ever more experimental protocols are being developed to study RNA …

[HTML][HTML] RNAcontacts: a pipeline for predicting contacts from RNA proximity ligation assays

L Guo, C Changchang - Acta Naturae (англоязычная версия), 2023 - cyberleninka.ru
High-throughput RNA proximity ligation assays are molecular methods that are used to
simultaneously analyze the spatial proximity of many RNAs in living cells. Their principle is …

Reprogramming gene expression by targeting RNA-based interactions: A novel pipeline utilizing RNA array technology

CA Henderson, HA Vincent… - ACS Synthetic Biology, 2021 - ACS Publications
Regulatory RNA-based interactions are critical for coordinating gene expression and are
increasingly being targeted in synthetic biology, antimicrobial, and therapeutic fields …

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites

T Müller, S Mautner, P Videm, F Eggenhofer… - …, 2024 - academic.oup.com
Background RNA–RNA interactions are key to a wide range of cellular functions. The
detection of potential interactions helps to understand the underlying processes. However …