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1998 Biocomputing '99  
There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA  ...  It is based on three hypotheses about the secondary structure space of a switching RNA molecule, which can be evaluated by RNA folding and structure comparison.  ...  1 Motivation 1.1 Conformational Switching in RNA RNA ful lls a broad range of functions in living cells.  ... 
doi:10.1142/9789814447300_0013 fatcat:tapaqy2fybdp5hwu4pf5bswwqq

Deep Learning for RNA Synthetic Biology [article]

Nicolaas Angenent-Mari, Alexander Garruss, Luis Ruben Soenksen, George Church, James Collins
2019 bioRxiv   pre-print
This deep learning approach constitutes a major step forward in engineering and understanding of RNA synthetic biology.  ...  To facilitate DNN training, we synthesized and characterized in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors.  ...  Donghia and Peter Q. 15 Nguyen for their support in experimental activities of this work.  ... 
doi:10.1101/872077 fatcat:33xuzxkcwfbb5dyyjwiie2zgc4

RNA-related tools on the Bielefeld Bioinformatics Server

A. Sczyrba
2003 Nucleic Acids Research  
They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison (including local structure alignment) and prediction of structures potentially  ...  We present four tools for the analysis of RNA secondary structure.  ...  ACKNOWLEDGEMENTS We acknowledge the continuing support of our networking group, Peter Koch and Rainer Orth, and the work of Kai Runte and Michael Ho ¨hl who have served several years as BiBiServ administrators  ... 
doi:10.1093/nar/gkg576 pmid:12824414 pmcid:PMC168982 fatcat:j4h6hv4d5jbnjnm36yrfjickhu

A deep learning approach to programmable RNA switches

Nicolaas M. Angenent-Mari, Alexander S. Garruss, Luis R. Soenksen, George Church, James J. Collins
2020 Nature Communications  
This work shows that deep learning approaches can be used for functionality predictions and insight generation in RNA synthetic biology.  ...  To facilitate DNN training, we synthesize and characterize in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors.  ...  Code availability All custom code used in this work, including that used to train and test deep-learning models, perform saliency visualizations, and perform ViennaRNA/Nupack/Kinfold calculations, can  ... 
doi:10.1038/s41467-020-18677-1 pmid:33028812 fatcat:t2ivenxwxzeqtmgs6gerzra6xm

RNA movies: visualizing RNA secondary structure spaces

D Evers, R Giegerich
1999 Bioinformatics  
Results: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts.  ...  Motivation: RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information.  ...  The work presented in this paper was partially supported by the German Ministry for Education and Sciences (BMBF), the Ministry of Science of North Rhine Westphalia (MWF-NRW) and the German Research Council  ... 
doi:10.1093/bioinformatics/15.1.32 pmid:10068690 fatcat:77aygl6gi5b7fdeks6z6t2qmfe

Indels in SARS-CoV-2 occur at template-switching hotspots

Brianna Sierra Chrisman, Kelley Paskov, Nate. Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Woo Sun, Sepideh Maleki, Dennis P. Wall
2021 BioData Mining  
We briefly analyze the indels in the context of RNA secondary structure, noting that indels preferentially occur in "arms" and loop structures of the predicted folded RNA, suggesting that secondary structure  ...  the process of RdRp template-switching in RNA viruses.  ...  The full acknowledgements for the GISAID sequence providers can be found in Table S2 .  ... 
doi:10.1186/s13040-021-00251-0 pmid:33743803 fatcat:oal6zfxygjbqnck3umkcauoczu

RNA folding on the 3D triangular lattice

Joel Gillespie, Martin Mayne, Minghui Jiang
2009 BMC Bioinformatics  
The visualization software for the lattice conformations of RNA structures is a valuable tool for the study of RNA folding and is a great pedagogic device.  ...  We implemented a suite of computer programs for the simulation and visualization of RNA folding on the 3D triangular lattice.  ...  We also thank the students of Utah State University in the class Bioinformatics II Spring 2009, Shanhong Cheng, D. Scott Fechser, Ramoni O. Lasisi, Pedro J.  ... 
doi:10.1186/1471-2105-10-369 pmid:19891777 pmcid:PMC2780420 fatcat:ctuyylqdofebrecsc4vfuuxe7u

A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs

Akito Taneda, Kengo Sato
2021 International Journal of Molecular Sciences  
We benchmarked the RNA switch design approaches (MODENA+RactIP and MODENA+RNAcofold) for the target structures based on natural RNA-RNA interactions.  ...  By predicting the secondary structures with RactIP during the design process, we can design RNAs that form a joint secondary structure with an external pseudoknot.  ...  In RNA-RNA switch design, structure-constrained secondary structure prediction is useful for predicting an interaction seed between two structured RNA strands.  ... 
doi:10.3390/ijms22052720 pmid:33800268 fatcat:gysmuwgbvrdwlflnewmwge77mi

In Silico Design of Small RNA Switches

Assaf Avihoo, Idan Gabdank, Michal Shapira, Danny Barash
2007 IEEE Transactions on Nanobioscience  
In the assembled RNA sequence, energy minimization folding predictions should then show no difference between the folded structure of the entire sequence relative to the folded structure of each of its  ...  Index Terms-Design of RNA switches, energy minimization methods, RNA folding predictions.  ...  All of these approaches utilize RNA secondary structure predictions in their core.  ... 
doi:10.1109/tnb.2007.891894 pmid:17393844 fatcat:oa7ur7nc2fcmheelpyzm2nxyka

Functionally-interdependent shape-switching nanoparticles with controllable properties

Justin R. Halman, Emily Satterwhite, Brandon Roark, Morgan Chandler, Mathias Viard, Anna Ivanina, Eckart Bindewald, Wojciech K. Kasprzak, Martin Panigaj, My N. Bui, Jacob S. Lu, Johann Miller (+4 others)
2017 Nucleic Acids Research  
Computational algorithms were developed to accurately predict melting temperatures of nanoparticles of various compositions and trace the process of their re-association in silico.  ...  pathways including transcription, energy transfer, functional aptamers and RNA interference.  ...  of Nebraska Medical Center and Lauren Lee (UNCC) for her assistance with cell culture experiments.  ... 
doi:10.1093/nar/gkx008 pmid:28108656 pmcid:PMC5389727 fatcat:lrnrszxqnzhwrc7kmwnotxfypu

In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader

Julia C. Kenyon, Liam J. Prestwood, Stuart F. J. Le Grice, Andrew M. L. Lever
2013 Nucleic Acids Research  
The results support a recently proposed structural switch model of RNA genomic dimerization and packaging, and demonstrate the discriminatory power of in-gel SHAPE.  ...  Definitive secondary structural mapping of RNAs in vitro can be complicated by the presence of more than one structural conformer or multimerization of some of the molecules.  ...  Although the vast majority of nucleotides would be predicted to have a similar SHAPE profile in each of these structural switch models, even in regions that change structure between a monomer and a dimer  ... 
doi:10.1093/nar/gkt690 pmid:23935074 pmcid:PMC3794615 fatcat:z7qqwbpksjdn5pf5mzi3jvxlni

Generation of synthetic RNA-based thermosensors

Torsten Waldminghaus, Jens Kortmann, Stefan Gesing, Franz Narberhaus
2008 Biological chemistry  
Structured RNAs with fundamental sensory and regulatory potential have been discovered in all kingdoms of life.  ...  Bacterial RNA thermometers are located in the 59untranslated region of certain heat shock and virulence genes.  ...  Acknowledgments We thank Christoph Flamm (University of Vienna, Austria) for providing us with the switch program and for help with computing.  ... 
doi:10.1515/bc.2008.150 pmid:18713019 fatcat:2af3nwwsrbb4xmu3gpvut5dipm

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

Kristoffer Vitting-Seerup, Bo Porse, Albin Sandelin, Johannes Waage
2014 BMC Bioinformatics  
RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events.  ...  Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.  ...  Work in the BTP lab was supported through a center grant from the Novo Nordisk Foundation (The Novo Nordisk Foundation Section for Stem Cell Biology in Human Disease).  ... 
doi:10.1186/1471-2105-15-81 pmid:24655717 pmcid:PMC3998036 fatcat:4x6boeup2nfl3e5xpyxng34mra

Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation

D. Barash
2004 Bioinformatics  
Current methods for detecting bi-stable RNAs that can lead to structural switching when triggered by an outside event rely on kinetics, energetics and properties of the combinatorial structure space of  ...  Motivation: Conformational switching in RNAs is thought to be of fundamental importance in several biological processes, including translational regulation, regulation of self-cleavage in viruses, protein  ...  The work was conducted at the Genome Diversity Center and supported by the Institute of Evolution, University of Haifa, Israel.  ... 
doi:10.1093/bioinformatics/bth157 pmid:14988109 fatcat:es5rfjunebg2fmynlyqwtgngcu

A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo [article]

Khalid K Alam, Kwaku D Tawiah, Matthew F Lichte, David Porciani, Donald H Burke
2017 bioRxiv   pre-print
Split-Broccoli fluorescence is digital in vivo and retains functional modularity when fused to RNAs that regulate circuit function through RNA-RNA hybridization, as demonstrated with an RNA Toehold switch  ...  Characterizing RNA assembly in living cells often involves monitoring fluorescent reporter proteins, which are at best indirect measures of underlying RNA-RNA hybridization events and are subject to additional  ...  Acknowledgements We acknowledge support for this work from the University of Missouri Department of Biochemistry, the National Institute of Allergy and Infectious Diseases of the National Institutes of  ... 
doi:10.1101/109306 fatcat:ffwvon6cprbdjei6nvetyey5va
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