pypi: ViennaRNA | Projects | Ecosyste.ms: Papers

10.7150/thno.44176

LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1
Cited by: 53
Author(s): Stella Logotheti, Stephan Marquardt, Satish Gupta, Christin Richter, Berdien A. H. Edelhäuser, David Engelmann, Julia Brenmoehl, Christoph Söhnchen, Nico Murr, Michael P. Alpers, Krishna Pal Singh, Olaf Wolkenhauer, Dirk Heckl, Alf Spitschak, Brigitte M. Pützer
Software Mentions: 1
Published: almost 5 years ago

10.1128/mBio.02296-16

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance
Cited by: 22
Author(s): Céline Loot, Aleksandra Nivina, Jean Cury, José Antonio Escudero, Magaly Ducos-Galand, David Bikard, Eduardo P. C. Rocha, Didier Mazel
Software Mentions: 1
Published: over 7 years ago

10.3892/ijmm.2014.2005

Peptide nucleic acids targeting β-globin mRNAs selectively inhibit hemoglobin production in murine erythroleukemia cells
Cited by: 3
Author(s): Giulia Montagner, Chiara Gemmo, Enrica Fabbri, Alex Manicardi, Igea Accardo, Nicoletta Bianchi, Alessia Finotti, Giulia Breveglieri, Francesca Salvatori, Monica Borgatti, Alberto Bresciani, Sergio Altamura, Roberto Corradini, Roberto Gambari
Software Mentions: 1
Published: about 10 years ago

10.7554/eLife.53535

Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome
Cited by: 12
Author(s): Andrew B. Morgenthaler, Wallis R. Kinney, Christopher C. Ebmeier, Corinne M. Walsh, Donald R. Snyder, Vaughn S. Cooper, William M. Old, Shelley D. Copley
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms19010321

Identification of a Rare Germline Heterozygous Deletion Involving the Polycistronic miR-17–92 Cluster in Two First-Degree Relatives from a BRCA 1/2 Negative Chilean Family with Familial Breast Cancer: Possible Functional Implications
Cited by: 3
Author(s): Tomás de Mayo, Annemarie Ziegler, Sebastián Morales, Lilian Jara
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms22168498

Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater
Cited by: 9
Author(s): Margaritis Avgeris, Panagiotis G. Adamopoulos, Aikaterini Galani, Marieta Xagorari, Dimitrios Gourgiotis, Ioannis P. Trougakos, N. Voulgaris, Meletios Α. Dimopoulos, Nikolaos S. Thomaidis, Andreas Scorilas
Software Mentions: 1
Published: over 3 years ago

10.1098/rsif.2019.0332

Model genotype–phenotype mappings and the algorithmic structure of evolution
Cited by: 28
Author(s): Daniel Nichol, Mark Robertson-Tessi, Alexander R.A. Anderson, Peter Jeavons
Software Mentions: 1
Published: about 5 years ago

10.1098/rsif.2018.0107

Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems
Cited by: 11
Author(s): Joseph Berleant, Christopher G. Berlind, Stefan Badelt, Frits Dannenberg, Joseph Schaeffer, Erik Winfree
Software Mentions: 1
Published: almost 6 years ago

10.1107/S0907444912001084

Challenges and surprises that arise with nucleic acids during model building and refinement
Cited by: 4
Author(s): William G. Scott
Software Mentions: 1
Published: over 12 years ago

10.1186/s12967-021-02731-7

tRFTars: predicting the targets of tRNA-derived fragments
Cited by: 19
Author(s): Qiu Xiao, Peng Gao, Xiaoxian Huang, Xiaowan Chen, Quan Chen, Xinger Lv, Yu Fu, Yongxi Song, Zhenning Wang
Software Mentions: 1
Published: over 3 years ago

10.32607/20758251-2019-11-3-66-74

Long Noncoding RNA LL35/Falcor Regulates Expression of Transcription Factor Foxa2 in Hepatocytes in Normal and Fibrotic Mouse Liver
Cited by: 3
Author(s): Olga V. Sergeeva, Svetlana Korinfskaya, Ilya I. Kurochkin, Timofei S. Zatsepin
Software Mentions: 1
Published: about 5 years ago

10.1155/2021/5569844

In Vitro Comparison of the Internal Ribosomal Entry Site Activity from Rodent Hepacivirus and Pegivirus and Construction of Pseudoparticles
Cited by: 2
Author(s): Stuart Sims, Kevin Michaelsen, Sara Burkhard, Cornel Fraefel
Software Mentions: 1
Published: over 3 years ago

10.1186/1748-7188-6-3

RNA Accessibility in cubic time
Cited by: 43
Author(s): Stephan H. Bernhart, Ulrike Mückstein, Ivo L. Hofacker
Software Mentions: 1
Published: over 13 years ago

10.1186/s13015-020-00176-z

On an enhancement of RNA probing data using information theory
Cited by: 4
Author(s): Thomas J. X. Li, Christian M. Reidys
Software Mentions: 1
Published: over 4 years ago

10.1007/s00705-017-3383-4

Complete nucleotide sequence and annotation of the temperate corynephage ϕ16 genome
Cited by: 10
Author(s): Juliya S. Lobanova, Evgueni R. Gak, И. Г. Андреева, Konstantin V. Rybak, A. A. Krylov, Sergey V. Mashko
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-018-2007-7

Bi-objective integer programming for RNA secondary structure prediction with pseudoknots
Cited by: 10
Author(s): Audrey Legendre, Éric Angel, Fariza Tahi
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-9-474

RNAalifold: improved consensus structure prediction for RNA alignments
Cited by: 503
Author(s): Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas Gruber, Peter F. Stadler
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2105-7-400

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
Cited by: 117
Author(s): Robin D. Dowell, Sean R. Eddy
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-7-S5-S20

MicroTar: predicting microRNA targets from RNA duplexes
Cited by: 113
Author(s): Rahul Thadani, Martti T. Tammi
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12859-016-1353-6

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length
Cited by: 12
Author(s): Yu Bao, Morihiro Hayashida, Tatsuya Akutsu
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-018-2497-3

Degeneracy and genetic assimilation in RNA evolution
Cited by: 5
Author(s): Reza Rezazadegan, Christian M. Reidys
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-019-3279-2

Fast and accurate microRNA search using CNN
Cited by: 7
Author(s): Xubo Tang, Yanni Sun
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12859-014-0423-x

Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine
Cited by: 27
Author(s): Jun Meng, Liang Dong, Chao Sun, Yushi Luan
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12896-018-0463-9

Heterologous expression of cyclodextrin glycosyltransferase from Paenibacillus macerans in Escherichia coli and its application in 2-O-α-D-glucopyranosyl-L-ascorbic acid production
Cited by: 8
Author(s): Yujia Jiang, Jie Zhou, Ruofan Wu, Fengxue Xin, Wenming Zhang, Yan Fang, Jiangfeng Ma, Weiliang Dong, Min Jiang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-016-2755-6

Genome-wide analyses of long noncoding RNA expression profiles correlated with radioresistance in nasopharyngeal carcinoma via next-generation deep sequencing
Cited by: 43
Author(s): Li Guo, Yong Liu, Chao Liu, Zhi Su, Shuling Ren, Yunyun Wang, Tengbo Deng, Donghai Huang, Yongquan Tian, Yuanzheng Qiu
Software Mentions: 1
Published: about 8 years ago

10.1186/s12862-015-0555-2

Distribution of mutational fitness effects and of epistasis in the 5’ untranslated region of a plant RNA virus
Cited by: 14
Author(s): Guillermo P. Bernet, Santiago F. Elena
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12862-015-0458-2

Origin and higher-level diversification of acariform mites – evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment
Cited by: 49
Author(s): Almir R. Pepato, Pavel B. Klimov
Software Mentions: 1
Published: about 9 years ago

10.1186/s12862-017-1037-5

Divergence of functional effects among bacterial sRNA paralogs
Cited by: 8
Author(s): I‐Chen Kimberly Chen, Gregory J. Velicer, Yuen‐Tsu Nicco Yu
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-15-115

Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes
Cited by: 14
Author(s): Klas Hatje, Martin Kollmar
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-12-S5-S8

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1
Cited by: 21
Author(s): Xinxin Wang, Liran Juan, Jun-Jie Liu, Kejun Wang, Jeremy R. Sanford, Yunlong Liu
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-017-4309-y

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
Cited by: 1
Author(s): Yuki Kato, Jan Gorodkin, Jakob Hull Havgaard
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-11-529

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi
Cited by: 14
Author(s): Nuno D. Mendes, Ana T. Freitas, Ana Tereza Ribeiro de Vasconcelos, Marie‐France Sagot
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-015-2221-x

Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana
Cited by: 20
Author(s): Ge Qu, Katarzyna Kruszka, Patrycja Plewka, Shu‐Yi Yang, Tzyy‐Jen Chiou, Artur Jarmołowski, Zofia Szweykowska-Kulińska, Manuel Echeverrı́a, Wojciech M. Karłowski
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-020-07044-5

Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei
Cited by: 9
Author(s): Yumei Xiao, Fei Yi, Juanjuan Ling, Guijuan Yang, Na Lü, Zirui Jia, Junchen Wang, Kun Zhao, Junhui Wang, Wenjun Ma
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-15-525

Thermal plasticity of the miRNA transcriptome during Senegalese sole development
Cited by: 48
Author(s): Catarina Campos, Arvind Sundaram, Luísa Valente, Luı́s E.C. Conceição, Sofía Engrola, Jorge M.O. Fernandes
Software Mentions: 1
Published: over 10 years ago

10.1093/bioinformatics/btv523

SHAPE directed RNA folding
Cited by: 75
Author(s): Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Software Mentions: 1
Published: about 9 years ago

10.1186/s13062-015-0090-5

RNA motif discovery: a computational overview
Cited by: 17
Author(s): Avinash Achar, Pål Sætrom
Software Mentions: 1
Published: about 9 years ago

10.1155/2021/9926128

Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-α Protein
Cited by: 4
Author(s): Homayoun Asadzadeh, Ali Moosavi, Georgios Alexandrakis, Mohammad R. K. Mofrad
Software Mentions: 1
Published: over 3 years ago

10.1155/2019/6193673

An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs
Cited by: 1
Author(s): Ying Wang, Jidong Ru, Tao Jin, Mingbo Sun, Lizhu Jia, Sun Gui-jiang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-020-01342-4

MicroRNAs signatures, bioinformatics analysis of miRNAs, miRNA mimics and antagonists, and miRNA therapeutics in osteosarcoma
Cited by: 38
Author(s): Babak Otoukesh, Mehdi Abbasi, Habib-o-lah Gorgani, Hossein Farahini, Mehdi Moghtadaei, Bahram Boddouhi, Peyman Kaghazian, Shayan Hosseinzadeh, Atefe Alaee
Software Mentions: 1
Published: over 4 years ago

10.3390/life7040048

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems
Cited by: 26
Author(s): András Szilágyi, István Zachar, István Scheuring, András István Kun, Balázs Könnyü, Tamás Czárán
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12934-018-0882-2

Translation efficiency of heterologous proteins is significantly affected by the genetic context of RBS sequences in engineered cyanobacterium Synechocystis sp. PCC 6803
Cited by: 48
Author(s): Kati Thiel, Edita Mulaku, Hariharan Dandapani, Csaba István Nagy, Eva‐Mari Aro, Pauli T. Kallio
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms7110493

Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Ciliophora, Spirotrichea)
Cited by: 13
Author(s): Zifeng Zhan, Ju Li, Kuidong Xu
Software Mentions: 1
Published: about 5 years ago

10.15252/msb.20167449

High‐throughput CRISPRi phenotyping identifies new essential genes in <i>Streptococcus pneumoniae</i>
Cited by: 211
Author(s): Xue Liu, Clément Gallay, Morten Kjos, Arnau Domenech, Jelle Slager, Sebastiaan P. van Kessel, Kèvin Knoops, Robin A. Sorg, Jing-Ren Zhang, Jan‐Willem Veening
Software Mentions: 1
Published: over 7 years ago

10.1093/ve/vev012

CodonShuffle: a tool for generating and analyzing synonymously mutated sequences
Cited by: 18
Author(s): Daniel Macedo de Melo Jorge, Ryan E. Mills, Adam S. Lauring
Software Mentions: 1
Published: almost 10 years ago

10.3390/v12091017

Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia
Cited by: 10
Author(s): Christida Estu Wastika, Hayato Harima, Michihito Sasaki, Bernard M. Hang’ombe, Yuki Eshita, Yongjin Qiu, William W. Hall, Michael T. Wolfinger, Hirofumi Sawa
Software Mentions: 1
Published: about 4 years ago

10.3390/v12101068

Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae)
Cited by: 3
Author(s): Ruihao Shu, Qian Meng, Lin Ma, Hongbin Liang, Jun Chen, Xu Yue, Lingpeng Cheng, Wenyi Jin, Qilian Qin, Huan Zhang
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj.10505

DisCoVering potential candidates of RNAi-based therapy for COVID-19 using computational methods
Cited by: 9
Author(s): Narjes Rohani, Fatemeh Ahmadi Moughari, Changiz Eslahchi
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.5509

Association of CYBA gene (-930 A/G and 242 C/T) polymorphisms with oxidative stress in breast cancer: a case-control study
Cited by: 3
Author(s): Mohini Aiyengar Tupurani, Chiranjeevi Padala, Kaushik Puranam, Rajesh Kumar Galimudi, Keerthi Kupsal, Nivas Shyamala, Srilatha Reddy Gantala, Ramanjaneyulu Kummari, Sanjeeva Kumari Chinta, Surekha Rani Hanumanth
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pbio.3000219

Dhh1 promotes autophagy-related protein translation during nitrogen starvation
Cited by: 27
Author(s): Xu Liu, Zhiyuan Yao, Meiyan Jin, Sim Namkoong, Zhangyuan Yin, Jun Hee Lee, Daniel J. Klionsky
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3000423

Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms
Cited by: 14
Author(s): Idan Frumkin, Ido Yofe, Raz Bar‐Ziv, Yonat Gurvich, Yen-Yun Lu, Yoav Voichek, Ruth Towers, Dvir Schirman, Heike Krebber, Yitzhak Pilpel
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1006176

Solving the RNA design problem with reinforcement learning
Cited by: 21
Author(s): Peter Eastman, Jade Shi, Bharath Ramsundar, Vijay S. Pande
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1004473

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis
Cited by: 51
Author(s): Pablo Cordero, Rhiju Das
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.1003172

Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
Cited by: 32
Author(s): Guillermo Rodrigo, Thomas E. Landrain, Eszter Majer, José‐Antonio Daròs, Alfonso Jaramillo
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1006185

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
Cited by: 55
Author(s): Albert Plà, Xiao Zhong, Simon Rayner
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1003613

The Conserved Intronic Cleavage and Polyadenylation Site of CstF-77 Gene Imparts Control of 3′ End Processing Activity through Feedback Autoregulation and by U1 snRNP
Cited by: 43
Author(s): Wenting Luo, Zhe Ji, Zhengxia Pan, Bo You, Mainul Hoque, Wencheng Li, Samuel Gunderson, Bin Tian
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1007350

Transcription and translation of the sigG gene is tuned for proper execution of the switch from early to late gene expression in the developing Bacillus subtilis spore
Cited by: 11
Author(s): Elizabeth B. Mearls, Jacquelin Jackter, Jennifer M. Colquhoun, Veronica Farmer, Allison J. Matthews, Laura Murphy, Colleen Fenton, Amy H. Camp
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0005019

Characterization of a Zika Virus Isolate from Colombia
Cited by: 25
Author(s): Anismrita Lahon, Ravi Prakash Arya, Alexander R. Kneubehl, Megan B. Vogt, Natalie J. M. Dailey Garnes, Rebeca Rico-Hesse
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0006535

The small RNA complement of adult Schistosoma haematobium
Cited by: 17
Author(s): Andreas J. Stroehlein, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Aaron R. Jex, Bonnie L. Webster, David Rollinson, Paul J. Brindley, Robin B. Gasser
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0219210

The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology
Cited by: 10
Author(s): Jonathan L. Chen, William C. Moss, A. Benjamin Spencer, Peiyuan Zhang, Jessica L. Childs‐Disney, Matthew D. Disney
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0070136

Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire
Cited by: 31
Author(s): Michaël Bekaert, Natalie R Lowe, Stephen Bishop, James E. Bron, John B. Taggart, Ross D. Houston
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0113380

On the Normalization of the Minimum Free Energy of RNAs by Sequence Length
Cited by: 57
Author(s): Edoardo Trotta
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0137859

RNA Thermodynamic Structural Entropy
Cited by: 20
Author(s): Juan Antonio García-Martín, Peter Clote
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0092107

Genetic Characterization of a Novel Iflavirus Associated with Vomiting Disease in the Chinese Oak Silkmoth Antheraea pernyi
Cited by: 22
Author(s): Peng Geng, Wenli Li, Le Lin, Joachim R. de Miranda, Scott J. Emrich, An Liu, Olle Terenius
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0213758

RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression
Cited by: 13
Author(s): Collin A. O’Leary, Ryan J. Andrews, Van S. Tompkins, Jonathan L. Chen, Jessica L. Childs‐Disney, Matthew D. Disney, William C. Moss
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0020484

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families
Cited by: 7
Author(s): Anuj Srivastava, Liming Cai, Jan Mrázek, Russell L. Malmberg
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0247215

AlnC: An extensive database of long non-coding RNAs in angiosperms
Cited by: 12
Author(s): Ajeet Singh, A.T. Vivek, Shailesh Kumar
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0113796

Optimization of Fluorescent Tools for Cell Biology Studies in Gram-Positive Bacteria
Cited by: 3
Author(s): Maria João Catalão, Joana Figueiredo, Mafalda Xavier Henriques, João Paulo Gomes, Sérgio R. Filipe
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0164726

Accurate Classification of RNA Structures Using Topological Fingerprints
Cited by: 7
Author(s): Jiajie Huang, Kejie Li, Michael Gribskov
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0231704

Allele mining of TaGRF-2D gene 5’-UTR in Triticum aestivum and Aegilops tauschii genotypes
Cited by: 6
Author(s): Pavel Yu. Kroupin, Anastasiya G. Chernook, Mikhail S. Bazhenov, Г. И. Карлов, Н. П. Гончаров, Н. Н. Чикида, Mikhail G. Divashuk
Software Mentions: 1
Published: over 4 years ago

10.1007/s00018-019-03344-6

The RNA–RNA base pairing potential of human Dicer and Ago2 proteins
Cited by: 12
Author(s): Maria Pokornowska, Marek C. Milewski, Kinga Ciechanowska, Agnieszka Szczepańska, Marta Wojnicka, Ziemowit Radogostowicz, Marek Figlerowicz, Anna Kurzyńska-Kokorniak
Software Mentions: 1
Published: about 5 years ago

10.1038/s42003-020-01589-7

A risk marker of tribasic hemagglutinin cleavage site in influenza A (H9N2) virus
Cited by: 6
Author(s): Jiahao Zhang, Kaixiong Ma, Bo Li, Yiqun Chen, Ziwen Qiu, Jinchao Xing, Jiayu Huang, Chen Hu, Yifan Huang, Huanan Li, Ding Xiang Liu, Ming Liao, Wenbao Qi
Software Mentions: 1
Published: almost 4 years ago

10.1093/database/bay004

miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal
Cited by: 16
Author(s): Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, K. Emily Knott, Garry Wong
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41426-018-0027-z

Identification of tell-tale patterns in the 3′ non-coding region of hantaviruses that distinguish HCPS-causing hantaviruses from HFRS-causing hantaviruses
Cited by: 6
Author(s): Sathish Sankar, Jayanta Borkakoti, Mageshbabu Ramamurthy, Balaji Nandagopal, Perumal Vivekanandan, Gopalan Sridharan
Software Mentions: 1
Published: over 6 years ago

10.12688/f1000research.38156.1

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)
Cited by: 21
Author(s): Xiao Ma, Jeanine L. Olsen, Thorsten B.H. Reusch, Gabriele Procaccini, Dave Kudrna, Melissa E. Williams, Jane Grimwood, Shanmugam Rajasekar, Jerry Jenkins, Jeremy Schmutz, Xiao Ma
Software Mentions: 1
Published: over 3 years ago

10.3389/fbioe.2021.630367

Optimizing Granulocyte Colony-Stimulating Factor Transcript for Enhanced Expression in Escherichia coli
Cited by: 1
Author(s): Sonal Datta
Software Mentions: 1
Published: over 3 years ago

10.3389/fcell.2021.686894

DeepOMe: A Web Server for the Prediction of 2′-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture
Cited by: 5
Author(s): Hongyu Li, Li Chen, Zaoli Huang, Xiaotong Luo, Huiqin Li, Jian Ren, Yubin Xie
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2019.00637

PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees
Cited by: 23
Author(s): Lei Deng, Wenyi Yang, Hui Liu
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.686977

Ribosome Biogenesis in Archaea
Cited by: 20
Author(s): Paola Londei, Sébastien Ferreira-Cerca
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.00200

A Glycine Riboswitch in Streptococcus pyogenes Controls Expression of a Sodium:Alanine Symporter Family Protein Gene
Cited by: 14
Author(s): Afsaneh Khani, Nicole Popp, Bernd Kreikemeyer, Nadja Patenge
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.01730

A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R
Cited by: 7
Author(s): Fei Xie, Wenlong Zhao, Wang Xiao, Jing Zhang, Bin Hao, Zou Zhengzheng, Bin-Guang Ma, Youguo Li
Software Mentions: 1
Published: about 7 years ago

10.3389/fpls.2018.00589

Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes
Cited by: 8
Author(s): Kira C. M. Neller, Alexander Klenov, Juan Carlos Torres Guzmán, Katalin A. Hudak
Software Mentions: 1
Published: over 6 years ago

10.3390/genes12010014

RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application
Cited by: 5
Author(s): Ronny Lorenz, Peter F. Stadler
Software Mentions: 1
Published: almost 4 years ago

10.3390/genes12081128

Allelic Variants in Established Hypopituitarism Genes Expand Our Knowledge of the Phenotypic Spectrum
Cited by: 0
Author(s): Marilena Nakaguma, Nathalia Garcia Bianchi Pereira Ferreira, A. Benedetti, Mariana Cotarelli Madi, Juliana Moreira Silva, Jun Z. Li, Qianyi Ma, Ayse Bilge Ozel, Qing Fang, Amanda de Moraes Narcizo, Laís Cavalca Cardoso, Luciana Ribeiro Montenegro, Mariana Ferreira de Assis Funari, Mirian Yumie Nishi, Ivo Jorge Prado Arnhold, Alexander Augusto de Lima Jorge, Berenice B. Mendonca, Sally A. Camper, Luciani R. Carvalho
Software Mentions: 1
Published: over 3 years ago

10.1186/s13059-016-0900-9

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design
Cited by: 150
Author(s): Justin D. Smith, Sundari Suresh, Ulrich Schlecht, Manhong Wu, Omar Wagih, Gary Peltz, Ronald W. Davis, Lars M. Steinmetz, Leopold Parts, Robert P. St.Onge
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-018-1399-z

PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures
Cited by: 18
Author(s): Mirko Ledda, Sharon Aviran
Software Mentions: 1
Published: over 6 years ago

10.1093/gbe/evv011

Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate ncRNAs
Cited by: 15
Author(s): Andrew D. Kern, Daniel A. Barbash, Joshua Chang Mell, Daniel Hupalo, Amanda Jensen
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13073-014-0076-4

A large scale expression study associates uc.283-plus lncRNA with pluripotent stem cells and human glioma
Cited by: 33
Author(s): Marco Galasso, Paola Dama, Maurizio Previati, Sukhinder K. Sandhu, Jeff Palatini, Vincenzo Coppola, Sarah Warner, Maria Elena Sana, Riccardo Zanella, Ramzey Abujarour, Caroline Desponts, Michael A. Teitell, Ramiro Garzon, George A. Calin, Carlo M. Croce, Stefano Volinia
Software Mentions: 1
Published: about 10 years ago

10.1093/gigascience/giab054

RNAProt: an efficient and feature-rich RNA binding protein binding site predictor
Cited by: 8
Author(s): Michaël Uhl, Dinh Van Tran, Florian Heyl, Rolf Backofen
Software Mentions: 1
Published: over 3 years ago

10.1186/s40709-018-0081-7

StarSeeker: an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule
Cited by: 2
Author(s): Paschalis Natsidis, Ilias Kappas, Wojciech M. Karłowski
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1008344

Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function
Cited by: 32
Author(s): Robert C. Shields, Alejandro R. Walker, Natalie Maricic, Brinta Chakraborty, Simon A. M. Underhill, Robert A. Burne
Software Mentions: 1
Published: over 4 years ago

10.1080/15476286.2020.1795409

Synergistic regulation of <i>Rgs4</i> mRNA by HuR and miR-26/RISC in neurons
Cited by: 9
Author(s): Janina Ehses, Sandra M. Fernández‐Moya, Luise Schröger, Michael A. Kiebler
Software Mentions: 1
Published: over 4 years ago

10.1038/srep19309

The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs
Cited by: 13
Author(s): Wolf-Matthias Leeder, Christin Voigt, Michael Brecht, H. Ulrich Göringer
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep29810

Multiple G-quartet structures in pre-edited mRNAs suggest evolutionary driving force for RNA editing in trypanosomes
Cited by: 28
Author(s): Wolf-Matthias Leeder, Niklas F. C. Hummel, H. Ulrich Göringer
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34381

Distribution and characteristics of rodent picornaviruses in China
Cited by: 18
Author(s): Jie Du, Liang Lu, Feng Liu, Haoxiang Su, Jie Dong, Lu Sun, Yafang Zhu, Xianwen Ren, Fan Yang, Fei Guo, Qiyong Liu, Zhìqiáng Wú, Qi Jin
Software Mentions: 1
Published: about 8 years ago

Projects: pypi: ViennaRNA

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