Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

P Kerpedjiev, S Hammer, IL Hofacker - Bioinformatics, 2015 - academic.oup.com
Motivation: The secondary structure of RNA is integral to the variety of functions it carries out
in the cell and its depiction allows researchers to develop hypotheses about which …

Vivern–a virtual environment for multiscale visualization and modeling of DNA nanostructures

D Kuťák, MN Selzer, J Byška… - … on Visualization and …, 2021 - ieeexplore.ieee.org
DNA nanostructures offer promising applications, particularly in the biomedical domain, as
they can be used for targeted drug delivery, construction of nanorobots, or as a basis for …

Protein-RNA interactions in the single-stranded RNA bacteriophages

J Rūmnieks, K Tārs - Virus Protein and Nucleoprotein Complexes, 2018 - Springer
Bacteriophages of the Leviviridae family are small viruses with short single-stranded RNA
(ssRNA) genomes. Protein-RNA interactions play a key role throughout the phage life cycle …

R-chie: a web server and R package for visualizing cis and trans RNA–RNA, RNA–DNA and DNA–DNA interactions

V Tsybulskyi, M Mounir, IM Meyer - Nucleic acids research, 2020 - academic.oup.com
Interactions between biological entities are key to understanding their potential functional
roles. Three fields of research have recently made particular progress: the investigation of …

RNA visualization: relevance and the current state-of-the-art focusing on pseudoknots

B Shabash, KC Wiese - IEEE/ACM Transactions on …, 2016 - ieeexplore.ieee.org
RNA visualization is crucial in order to understand the relationship that exists between RNA
structure and its function, as well as the development of better RNA structure prediction …

TRAVeLer: a tool for template-based RNA secondary structure visualization

R Elias, D Hoksza - BMC bioinformatics, 2017 - Springer
Background Visualization of RNA secondary structures is a complex task, and, especially in
the case of large RNA structures where the expected layout is largely habitual, the existing …

RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure

JS Lu, E Bindewald, WK Kasprzak, BA Shapiro - Bioinformatics, 2018 - academic.oup.com
Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their
interactions is important to facilitate and communicate insights related to nucleic acid …

Interactive visualization of RNA and DNA structures

N Lindow, D Baum, M Leborgne… - IEEE transactions on …, 2018 - ieeexplore.ieee.org
The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly
important role due to their fundamental importance for all forms of life and the growing …

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures

D Wiegreffe, D Alexander, PF Stadler… - Bioinformatics, 2019 - academic.oup.com
Motivation RNA secondary structure is a useful representation for studying the function of
RNA, which captures most of the free energy of RNA folding. Using empirically determined …

Associating transcription factors and conserved RNA structures with gene regulation in the human brain

N Hecker, SE Seemann, A Silahtaroglu, WL Ruzzo… - Scientific reports, 2017 - nature.com
Anatomical subdivisions of the human brain can be associated with different neuronal
functions. This functional diversification is reflected by differences in gene expression. By …