pypi: ViennaRNA | Projects | Ecosyste.ms: Papers

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
Software Mentions: 10
Published: almost 5 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: about 10 years ago

10.1186/s13059-019-1641-3

dStruct: identifying differentially reactive regions from RNA structurome profiling data
Cited by: 20
Author(s): Krishna Choudhary, Yi-Chun Lai, Elizabeth Tran, Sharon Aviran
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12859-021-04009-7

SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
Cited by: 7
Author(s): Marius Wenzel, Berndt Müller, Jonathan Pettitt
Software Mentions: 8
Published: almost 4 years ago

10.3389/fgene.2012.00287

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges
Cited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: almost 13 years ago

10.3390/genes9080392

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Cited by: 16
Author(s): Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, Ivo L. Hofacker
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0175330

Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis
Cited by: 8
Author(s): Xuehua Wan, Kent J. Koster, Lishi Qian, Edward Desmond, Richard Brostrom, Shaobin Hou, James T. Douglas
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0078316

Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes
Cited by: 15
Author(s): Lydia Smith, Arpit Tandon, Ruchir Shah, Deepak Mav, Alyson B. Scoltock, John A. Cidlowski
Software Mentions: 5
Published: about 11 years ago

10.3389/fcimb.2020.600325

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
Cited by: 12
Author(s): Charlotte Michaux, Elisabeth E Hansen, Laura Jenniches, Milan Gerovac, Lars Barquist, Jörg Vogel
Software Mentions: 5
Published: about 4 years ago

10.3389/fmolb.2021.612881

Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach
Cited by: 7
Author(s): Jiali Yu, Dennis Bennett, Christopher Dardick, Tetyana Zhebentyayeva, Albert G. Abbott, Zongrang Liu, Margaret Staton
Software Mentions: 5
Published: over 3 years ago

10.15252/msb.20209844

Integrative characterization of the near‐minimal bacterium Mesoplasma florum
Cited by: 8
Author(s): Dominick Matteau, Jean-Christophe Lachance, Frédéric Grenier, Samuel Gauthier, James M. Daubenspeck, Kevin Dybvig, Daniel Garneau, Thomas F. Knight, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-019-6432-4

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis
Cited by: 2
Author(s): Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W. Davis, Mitchell V. Finnegan, Matthew Geniza, David A. Hendrix, Christiane V. Löhr, Vanessa M. Petro, Thomas J. Sharpton, Jackson Wells, Clinton W. Epps, Pankaj Jaiswal, Brett M. Tyler, Stephen A. Ramsey
Software Mentions: 5
Published: almost 5 years ago

10.1002/wrna.1649

Evolutionary conservation of <scp>RNA</scp> sequence and structure
Cited by: 22
Author(s): Elena Rivas
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-021-04164-x

Comprehensive machine-learning-based analysis of microRNA–target interactions reveals variable transferability of interaction rules across species
Cited by: 5
Author(s): Gilad Ben Or, Isana Veksler-Lublinsky
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.19760

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation
Cited by: 551
Author(s): Max A. Horlbeck, Luke A. Gilbert, Jacqueline E. Villalta, Brittany Susan Adamson, Ryan A. Pak, Yu‐Wen Chen, Alexander P. Fields, Chong Yon Park, Jacob E. Corn, Martin Kampmann, Jonathan S. Weissman
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.50530

Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
Cited by: 5
Author(s): Carlos Gorbea, Tim Mosbruger, David A. Nix, Demián Cazalla
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.574485

Advances in RNA 3D Structure Modeling Using Experimental Data
Cited by: 49
Author(s): Bing Li, Yang Cao, Éric Westhof, Zhichao Miao
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-018-25578-3

Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods
Cited by: 32
Author(s): Grzegorz Rorbach, Olgierd Unold, Bogumił M. Konopka
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008387

RNA structure prediction using positive and negative evolutionary information
Cited by: 39
Author(s): Elena Rivas
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-019-1869-y

Characterizing the interplay between gene nucleotide composition bias and splicing
Cited by: 16
Author(s): Sébastien Lemaire, Nicolas Fontrodona, Fabien Aubé, Jean‐Baptiste Claude, Hélène Polvèche, Laurent Modolo, Cyril F. Bourgeois, Franck Mortreux, Didier Auboeuf
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.116.032805

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
Cited by: 45
Author(s): Daniel González-Ibeas, Pedro Manuel Martínez-García, Randi Famula, Annette Delfino-Mix, Kristian Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, Jill L. Wegrzyn
Software Mentions: 4
Published: about 8 years ago

10.20411/pai.v6i2.460

Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level
Cited by: 40
Author(s): Shay Leary, Silvana Gaudieri, Matthew Parker, Abha Chopra, Ian James, Suman B. Pakala, Eric Alves, Mina John, Benjamin B. Lindsey, Alexander J Keeley, Sarah Rowland‐Jones, Maurice S. Swanson, David A. Ostrov, Jodi L. Bubenik, Suman Das, John Sidney, Alessandro Sette, Thushan I. de Silva, Elizabeth Phillips, S. Mallal, Covid Genomics Uk
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-14017-4

Machine learning model for sequence-driven DNA G-quadruplex formation
Cited by: 97
Author(s): Aleksandr B. Sahakyan, Vicki S. Chambers, Giovanni Marsico, Tobias Santner, Marco Di Antonio, Shankar Balasubramanian
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-26841-3

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)
Cited by: 19
Author(s): Jun Zhang, Peng Yu, Qinyan Zhou, Xilei Li, Shuquan Ding, Shiping Su, Xiaohua Zhang, Xiaoli Yang, Weicheng Zhou, Qing Wan, Jian‐Fang Gui
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-27474-2

A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions
Cited by: 7
Author(s): Abigail N. Leistra, Grant Gelderman, Steven W. Sowa, Alex Moon-Walker, Howard M. Salis, Lydia M. Contreras
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-35925-z

Endogenous toxins and the coupling of gregariousness to conspicuousness in Argidae and Pergidae sawflies
Cited by: 5
Author(s): Jean‐Luc Boevé, Tommi Nyman, Akihiko Shinohara, Stefan Schmidt
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-016-3287-9

AnnoLnc: a web server for systematically annotating novel human lncRNAs
Cited by: 43
Author(s): Mei Hou, Xing Tang, Feng Tian, Fang-Yuan Shi, Fenglin Liu, Ge Gao
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0163688

Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic
Cited by: 1
Author(s): Amirhossein Manzourolajdad, Mileidy Gonzalez, John L. Spouge
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-44457-z

Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction
Cited by: 53
Author(s): Hengyi Xu, Jun Yao, Douglas C. Wu, Alan M. Lambowitz
Software Mentions: 3
Published: over 5 years ago

10.1128/MRA.00424-21

StemLoop-Finder: a Tool for the Detection of DNA Hairpins with Conserved Motifs
Cited by: 3
Author(s): Alyssa A. Pratt, Ellis L. Torrance, George W. Kasun, Kenneth M. Stedman, Ignacio de la Higuera
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-017-3684-8

Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth
Cited by: 8
Author(s): Lydgia A. Jackson, Michael Day, Jennie Allen, Edgar J. Scott, David W. Dyer
Software Mentions: 3
Published: over 7 years ago

10.1186/s12943-020-01293-4

Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine
Cited by: 154
Author(s): Simeng Wen, Yulei Wei, Chong Zen, Wei Xiong, Yuanjie Niu, Yu Zhao
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-018-1463-8

Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human
Cited by: 38
Author(s): Karol Szlachta, Ryan G. Thys, Naomi D Atkin, Levi C. T. Pierce, Stefan Bekiranov, Yuh‐Hwa Wang
Software Mentions: 3
Published: over 6 years ago

10.1007/s12064-020-00330-6

Are spliced ncRNA host genes distinct classes of lncRNAs?
Cited by: 1
Author(s): Riturparno Sen, Jörg Fallmann, Maria Emília M. T. Walter, Peter F. Stadler
Software Mentions: 3
Published: about 4 years ago

10.1101/2020.08.22.262931

Theoretical basis for stabilizing messenger RNA through secondary structure design
Cited by: 16
Author(s): Hannah K. Wayment-Steele, Do Soon Kim, Christian A. Choe, John J Nicol, Roger Wellington-Oguri, Andrew Watkins, R Andres Parra Sperberg, Po-Ssu Huang, Eterna Participants, Rhiju Das
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0190992

HAfTs are novel lncRNA transcripts from aflatoxin exposure
Cited by: 9
Author(s): B. Alex Merrick, Justin Chang, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Xinguo Wang, Oksana Gordon, Garron M. Wright
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13059-020-02142-9

RNA G-quadruplex structures exist and function in vivo in plants
Cited by: 63
Author(s): Xiaofei Yang, Jitender Cheema, Yueying Zhang, Huiyong Deng, Susan Duncan, Mubarak Ishaq Umar, Jieyu Zhao, Qi Liu, Xiaofeng Cao, Chun Kit Kwok, Yiliang Ding
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.00482

Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs
Cited by: 15
Author(s): Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.71611

A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
Cited by: 3
Author(s): Michèle Felletti, Cédric Romilly, E. Gerhart H. Wagner, Kristina Jonas
Software Mentions: 3
Published: over 3 years ago

10.1186/1748-7188-6-26

ViennaRNA Package 2.0
Cited by: 3,394
Author(s): Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2105-11-133

MapMi: automated mapping of microRNA loci
Cited by: 60
Author(s): José Afonso Guerra-Assunção, Anton J. Enright
Software Mentions: 3
Published: almost 15 years ago

10.3390/ijms22158012

Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
Cited by: 3
Author(s): Rongxin Zhang, Yajun Li, Xingxing Zhang, Ke Xiao, Yue Hou, Hongde Liu, Xiao Sun
Software Mentions: 3
Published: over 3 years ago

10.3390/v10040192

Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in Africa
Cited by: 22
Author(s): Lidia Lasecka-Dykes, Caroline F. Wright, Antonello Di Nardo, Greg Logan, Valérie Mioulet, Terry Jackson, Tobias J. Tuthill, Nick J. Knowles, Donald P. King
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22179349

Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
Cited by: 16
Author(s): Nicole Rachinger, Stefan Fischer, Ines Böhme, Lisa Linck-Paulus, Silke Kuphal, Melanie Kappelmann‐Fenzl, Anja‐Katrin Bosserhoff
Software Mentions: 3
Published: over 3 years ago

10.3390/genes12020239

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
Cited by: 7
Author(s): Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-10-S1-S39

Sequence-structure relations of pseudoknot RNA
Cited by: 5
Author(s): Fenix W. D. Huang, Linda Y. M. Li, Christian M. Reidys
Software Mentions: 2
Published: almost 16 years ago

10.12688/f1000research.25148.2

First draft genome assembly of the desert locust, Schistocerca gregaria
Cited by: 13
Author(s): Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Ho‐Jun Song, Spencer T. Behmer, Gregory A. Sword, Troy Matheson, Swidbert R. Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de Peer, Jozef Vanden Broeck
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-021-03993-0

ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites
Cited by: 1
Author(s): Pengyu Liu, Jiangning Song, Chun Yuan Lin, Tatsuya Akutsu
Software Mentions: 2
Published: almost 4 years ago

10.3389/fbioe.2014.00001

Predicting Translation Initiation Rates for Designing Synthetic Biology
Cited by: 89
Author(s): Benjamin Reeve, Thomas Hargest, Charlie Gilbert, Tom Ellis
Software Mentions: 2
Published: almost 11 years ago

10.3389/fbioe.2014.00041

Computational Tools and Algorithms for Designing Customized Synthetic Genes
Cited by: 65
Author(s): Nathan Gould, Oliver Hendy, Dimitris Papamichail
Software Mentions: 2
Published: about 10 years ago

10.3389/fcimb.2021.673966

In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum
Cited by: 4
Author(s): Yanwei Qi, Yuhong Zhang, Guixing Zheng, Bingxia Chen, Mengxin Zhang, Jian Li, Tao Peng, Jun Huang, Xinhua Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.633125

Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus
Cited by: 3
Author(s): Dayle Johnston, Bernadette Earley, Matthew S. McCabe, Jae-Woo Kim, Jeremy F. Taylor, Ken Lemon, Michael McMenamy, Catherine Duffy, S. L. Cosby, Sinéad M. Waters
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.573395

Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta
Cited by: 11
Author(s): Nikola Palevich, Paul Maclean, Young‐Jun Choi, Makedonka Mitreva
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-019-3151-4

Prediction of sgRNA on-target activity in bacteria by deep learning
Cited by: 19
Author(s): Lei Wang, Juhua Zhang
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.00557

Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica
Cited by: 5
Author(s): Franck Panabières, Corinne Rancurel, Martine Da Rocha, Marie-Line Kühn
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-13-S7-S13

Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs
Cited by: 29
Author(s): Jia-Shiun Khoo, San Jiun Chai, Rahmah Mohamed, Sheila Nathan, Mohd Firdaus-Raih
Software Mentions: 2
Published: about 12 years ago

10.7717/peerj.3692

The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)
Cited by: 14
Author(s): Fabrizio Ghiselli, Liliana Milani, Mariangela Iannello, Emanuele Procopio, Peter L. Chang, Sergey V. Nuzhdin, Marco Passamonti
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-1490-8

An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress
Cited by: 23
Author(s): Zahra Agharbaoui, Mickaël Leclercq, Mohamed Amine Remita, Mohamed Badawi, Étienne Lord, Mario Houde, Jean Danyluk, Abdoulaye Baniré Diallo, Fathey Sarhan
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-018-2452-3

PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization
Cited by: 0
Author(s): Florian Bürger, Michele Angioni, Gianluca Russo, Martina Schad, Jim Kallarackal
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2021.664933

RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.)
Cited by: 3
Author(s): Guibin Cui, Mei Zhao, Hongbin Tan, Zhulin Wang, Meng Meng, Fengli Sun, Chao Zhang, Yajun Xi
Software Mentions: 2
Published: over 3 years ago

10.3390/genes9070356

An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons
Cited by: 12
Author(s): Timofei Ivanov, Dmitri D. Pervouchine
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pbio.1000475

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
Cited by: 359
Author(s): Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin, Muhammad Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W. Burt, Oswald Crasta, R.P.M.A. Crooijmans, Kristal Cooper, Roger A. Coulombe, Supriyo De, Mary E. Delany, Jerry B. Dodgson, Jennifer J. Dong, Clive Evans, Karin M. Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A. M. Groenen, Tim Harkins, Javier Herrero, Steve Hoffmann, Hendrik‐Jan Megens, Andrew Jiang, Pieter J. de Jong, Pete Kaiser, Heebal Kim, Kyu‐Won Kim, Sung-Won Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao P. Mane, Guillaume Marçais, Manja Marz, A. P. McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R. Paton, William S. Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L. Salzberg, Michael C. Schatz, Chantel F. Scheuring, Carl J. Schmidt, Steven G. Schroeder, Stephen M. J. Searle, E. J. Smith, Jacqueline Smith, Tad S. Sonstegard, Peter F. Stadler, Hakim Tafer, Zhijian Tu, Curtis P. Van Tassell, Albert J. Vilella, Kelly P. Williams, James A. Yorke, Liqing Zhang, Hongbin Zhang, Xiaojun Zhang, Yang Zhang, Kent M. Reed
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1005383

Computational identification of the selenocysteine tRNA (tRNASec) in genomes
Cited by: 43
Author(s): Didac Santesmasses, Marco Mariotti, Roderic Guigó
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1008415

Deep learning predicts short non-coding RNA functions from only raw sequence data
Cited by: 16
Author(s): Teresa Maria Rosaria Noviello, Francesco Ceccarelli, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1007059

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame
Cited by: 16
Author(s): Rohan V. Koodli, Benjamin Keep, Katherine R. Coppess, Fernando Gutiérrez Pórtela, Eterna Participants, Rhiju Das
Software Mentions: 2
Published: over 5 years ago

10.1093/gigascience/giaa161

Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles
Cited by: 3
Author(s): Sergio Andreu‐Sánchez, Wanjun Chen, Josefin Stiller, Guojie Zhang
Software Mentions: 2
Published: almost 4 years ago

10.1093/gigascience/giab023

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population
Cited by: 12
Author(s): Jeff Gaither, Grant Lammi, James L. Li, David Gordon, Harkness Kuck, Benjamin J. Kelly, James Fitch, Peter White
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-6-160

Multiple sequence alignments of partially coding nucleic acid sequences
Cited by: 23
Author(s): Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
Software Mentions: 2
Published: over 19 years ago

10.1093/bioinformatics/btx263

RNAblueprint: flexible multiple target nucleic acid sequence design
Cited by: 17
Author(s): Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-019-3303-6

Base-pair ambiguity and the kinetics of RNA folding
Cited by: 2
Author(s): Guangyao Zhou, Jackson Loper, Stuart Geman
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-019-2711-y

SSS-test: a novel test for detecting positive selection on RNA secondary structure
Cited by: 12
Author(s): Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjić, Peter F. Stadler, Katja Nowick
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13015-016-0070-z

RNA folding with hard and soft constraints
Cited by: 76
Author(s): Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-019-2689-5

An algebraic language for RNA pseudoknots comparison
Cited by: 15
Author(s): Michela Quadrini, Luca Tesei, Emanuela Merelli
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000126

A long and abundant non-coding RNA in Lactobacillus salivarius
Cited by: 6
Author(s): Fabien Cousin, Denise B. Lynch, Victoria Chuat, Maxence J. B. Bourin, Pat G. Casey, Marion Dalmasso, Hugh M. B. Harris, A. McCann, Paul W. O’Toole
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0087723

Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome
Cited by: 40
Author(s): Jia Wang, Dijun Chen, Lei Yang, Jiangfang Chang, Bin Hao, Xing Feng, Sen Li, Qiang Xu, Xiuxin Deng, Lingling Chen
Software Mentions: 2
Published: almost 11 years ago

10.3390/molecules26082287

The Art of Designing DNA Nanostructures with CAD Software
Cited by: 16
Author(s): Martin Gläser, Sourav Deb, Florian Seier, Amay Agrawal, Tim Liedl, Shawn M. Douglas, Manish Gupta, David M. Smith
Software Mentions: 2
Published: over 3 years ago

10.18699/VJ20.643

Study of the effect of the introduction of mitochondrial import determinants into the gRNA structure on the activity of the gRNA/SpCas9 complex in vitro
Cited by: 1
Author(s): Elvira G Zakirova, Yuri Vyatkin, N Verechshagina, Vladimir Vladimirovich Muzyka, И. О. Мазунин, Кonstantin E. Orishchenko
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.02298-16

Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin
Cited by: 97
Author(s): Naganori Nao, Junya Yamagishi, Hiroko Miyamoto, Manabu Igarashi, Rashid Manzoor, Aiko Ohnuma, Yuichi Tsuda, Wakako Furuyama, Asako Shigeno, Masahiro Kajihara, Noriko Kishida, Reiko Yoshida, Ayato Takada
Software Mentions: 2
Published: almost 8 years ago

10.1128/mBio.01410-20

Unveiling Crucivirus Diversity by Mining Metagenomic Data
Cited by: 18
Author(s): Ignacio de la Higuera, George W. Kasun, Ellis L. Torrance, Alyssa A. Pratt, Amberlee Maluenda, Jonathan Colombet, Maxime Bisseux, Viviane Ravet, Anisha Dayaram, Daisy Stainton, Simona Kraberger, Peyman Zawar-Reza, Sharyn J. Goldstien, James V. Briskie, Robyn White, Helen R. Taylor, Christopher Gomez, David G. Ainley, Jon S. Harding, Rafaela S. Fontenele, Joshua Schreck, S. G. Ribeiro, Stephen A. Oswald, Jennifer M. Arnold, François Enault, Arvind Varsani, Kenneth M. Stedman
Software Mentions: 2
Published: about 4 years ago

10.1038/s41419-020-2735-2

Low GAS5 expression may predict poor survival and cisplatin resistance in cervical cancer
Cited by: 26
Author(s): Xingyu Fang, Guangyu Zhong, Yuhan Wang, Zhongqiu Lin, Rong Lin, Tingting Yao
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-016-2692-4

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage
Cited by: 26
Author(s): Edoardo Trotta
Software Mentions: 2
Published: over 8 years ago

10.3390/cells7080106

The Unfolded Protein Response Pathway in the Yeast Kluyveromyces lactis. A Comparative View among Yeast Species
Cited by: 22
Author(s): Mariana Hernández-Elvira, Francisco Torres-Quiroz, Abril Escamilla-Ayala, Eunice Domínguez-Martín, Ricardo Escalante, Laura Kawasaki, Laura Ongay‐Larios, Roberto Coria
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20225610

Secondary Structural Model of Human MALAT1 Reveals Multiple Structure–Function Relationships
Cited by: 38
Author(s): Phillip J. McCown, Matthew C. Wang, Luc Jaeger, Jessica A. Brown
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22020941

De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives
Cited by: 2
Author(s): Maciej Florczyk, Paweł Brzuzan, Maciej Woźny
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22136874

De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation
Cited by: 7
Author(s): Francesco Morena, Chiara Argentati, Ilaria Tortorella, Carla Emiliani, Sabata Martino
Software Mentions: 2
Published: over 3 years ago

10.1098/rsob.160239

Leveraging genome-wide datasets to quantify the functional role of the anti-Shine–Dalgarno sequence in regulating translation efficiency
Cited by: 23
Author(s): Adam J. Hockenberry, Adam R. Pah, Michael C. Jewett, Luı́s A. Nunes Amaral
Software Mentions: 2
Published: almost 8 years ago

10.3390/v11030298

Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses
Cited by: 43
Author(s): Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger
Software Mentions: 2
Published: over 5 years ago

10.1016/j.ydbio.2014.06.007

Staufen targets coracle mRNA to Drosophila neuromuscular junctions and regulates GluRIIA synaptic accumulation and bouton number
Cited by: 21
Author(s): Alejandra Gardiol, Daniel St Johnston
Software Mentions: 2
Published: over 10 years ago

10.1186/s12302-018-0168-7

Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism
Cited by: 0
Author(s): Sarah Zanon Agapito-Tenfen, Vinicius Vilperte, Terje Traavik, Rubens Onofre Nodari
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-55570-4

Altered microRNA and target gene expression related to Tetralogy of Fallot
Cited by: 11
Author(s): Marcel Grunert, Sandra Appelt, Ilona Dunkel, Felix Berger, Silke Sperling
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-56986-8

Dynamics and stability in prebiotic information integration: an RNA World model from first principles
Cited by: 5
Author(s): András Szilágyi, Balázs Könnyü, Tamás Czárán
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-62588-6

Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome
Cited by: 11
Author(s): Gideon Omariba, Fuyi Xu, Maochun Wang, Kai Li, Yuxun Zhou, Junhua Xiao
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-65084-z

Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs
Cited by: 12
Author(s): Marco Passamonti, Marco Calderone, Manuel Delpero, Federico Plazzi
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-84365-9

An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3′-untranslated region
Cited by: 4
Author(s): Hayato Harima, Yasuko Orba, Shiho Torii, Yongjin Qiu, Masahiro Kajihara, Yoshiki Eto, Naoya Matsuta, Bernard M. Hang’ombe, Yuki Eshita, Kentaro Uemura, Keita Matsuno, Michihito Sasaki, Kentaro Yoshii, Ryo Nakao, William W. Hall, Ayato Takada, Takashi Abe, Michael T. Wolfinger, Martin Simuunza
Software Mentions: 1
Published: almost 4 years ago

10.1126/scisignal.aat6409

Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions
Cited by: 182
Author(s): M. C. Torrent, Guilhem Chalancon, Natalia Sánchez de Groot, Arthur Wüster, M. Madan Babu
Software Mentions: 1
Published: over 6 years ago

Projects: pypi: ViennaRNA

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