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For: Lorenz R, Hofacker IL, Stadler PF. RNA folding with hard and soft constraints. Algorithms Mol Biol 2016;11:8. [PMID: 27110276 PMCID: PMC4842303 DOI: 10.1186/s13015-016-0070-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Anver S, Sumit AF, Sun XM, Hatimy A, Thalassinos K, Marguerat S, Alic N, Bähler J. Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells. EMBO Rep 2024;25:4921-4949. [PMID: 39358553 PMCID: PMC11549352 DOI: 10.1038/s44319-024-00265-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024]  Open
2
Chen A, Dong Y, Jiang H, Wei M, Ren Y, Zhang J. Application of plasmid stabilization systems for heterologous protein expression in Escherichia coli. Mol Biol Rep 2024;51:939. [PMID: 39196367 DOI: 10.1007/s11033-024-09881-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024]
3
von Löhneysen S, Spicher T, Varenyk Y, Yao HT, Lorenz R, Hofacker I, Stadler PF. Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. J Comput Biol 2024;31:549-563. [PMID: 38935442 DOI: 10.1089/cmb.2024.0519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
4
Yang TH. DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. J Chem Inf Model 2024;64:3756-3766. [PMID: 38648189 PMCID: PMC11094721 DOI: 10.1021/acs.jcim.4c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
5
Hillung J, Olmo-Uceda MJ, Muñoz-Sánchez JC, Elena SF. Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses. Viruses 2024;16:644. [PMID: 38675984 PMCID: PMC11053736 DOI: 10.3390/v16040644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]  Open
6
Gray M, Will S, Jabbari H. SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration. Algorithms Mol Biol 2024;19:9. [PMID: 38433200 PMCID: PMC11289965 DOI: 10.1186/s13015-024-00256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024]  Open
7
von Löhneysen S, Mörl M, Stadler PF. Limits of experimental evidence in RNA secondary structure prediction. FRONTIERS IN BIOINFORMATICS 2024;4:1346779. [PMID: 38456157 PMCID: PMC10918467 DOI: 10.3389/fbinf.2024.1346779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 03/09/2024]  Open
8
Zhang Y, Lang M, Jiang J, Gao Z, Xu F, Litfin T, Chen K, Singh J, Huang X, Song G, Tian Y, Zhan J, Chen J, Zhou Y. Multiple sequence alignment-based RNA language model and its application to structural inference. Nucleic Acids Res 2024;52:e3. [PMID: 37941140 PMCID: PMC10783488 DOI: 10.1093/nar/gkad1031] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023]  Open
9
Thiel BC, Poblete S, Hofacker IL. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline. Methods Mol Biol 2024;2726:377-399. [PMID: 38780739 DOI: 10.1007/978-1-0716-3519-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
10
Varenyk Y, Lorenz R. Modified Nucleotides and RNA Structure Prediction. Methods Mol Biol 2024;2726:169-207. [PMID: 38780732 DOI: 10.1007/978-1-0716-3519-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
11
Chavez-Pena C. RNAi-Mediated Silencing in the Insect Cell-Baculovirus Expression System. Methods Mol Biol 2024;2829:91-107. [PMID: 38951329 DOI: 10.1007/978-1-0716-3961-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
12
Lorenz R. RNA Secondary Structure Thermodynamics. Methods Mol Biol 2024;2726:45-83. [PMID: 38780727 DOI: 10.1007/978-1-0716-3519-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
13
Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023;25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023]  Open
14
Varenyk Y, Spicher T, Hofacker IL, Lorenz R. Modified RNAs and predictions with the ViennaRNA Package. Bioinformatics 2023;39:btad696. [PMID: 37971965 PMCID: PMC10676514 DOI: 10.1093/bioinformatics/btad696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/24/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]  Open
15
Yang E, Zhang H, Zang Z, Zhou Z, Wang S, Liu Z, Liu Y. GCNfold: A novel lightweight model with valid extractors for RNA secondary structure prediction. Comput Biol Med 2023;164:107246. [PMID: 37487383 DOI: 10.1016/j.compbiomed.2023.107246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023]
16
Zhai R, Ruan K, Perez GF, Kubat M, Liu J, Hofacker I, Wuchty S. MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing. RESEARCH SQUARE 2023:rs.3.rs-2977025. [PMID: 37546804 PMCID: PMC10402249 DOI: 10.21203/rs.3.rs-2977025/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
17
Ruan K, Perez GF, Liu J, Kubat M, Hofacker I, Wuchty S, Zhai RG. MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536877. [PMID: 37425843 PMCID: PMC10327045 DOI: 10.1101/2023.04.14.536877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
18
Huszár K, Welker Z, Györgypál Z, Tóth E, Ligeti Z, Kulcsár P, Dancsó J, Tálas A, Krausz S, Varga É, Welker E. Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs. Nucleic Acids Res 2023;51:5847-5863. [PMID: 37140059 PMCID: PMC10287927 DOI: 10.1093/nar/gkad323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 04/04/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]  Open
19
Henderson AN, McDonnell RT, Elcock AH. Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543892. [PMID: 37333149 PMCID: PMC10274748 DOI: 10.1101/2023.06.06.543892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
20
Badelt S, Lorenz R, Hofacker IL. DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. Bioinformatics 2023;39:6992659. [PMID: 36655786 PMCID: PMC9889959 DOI: 10.1093/bioinformatics/btad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 01/17/2023] [Indexed: 01/20/2023]  Open
21
Saiyed AN, Vasavada AR, Johar SRK. Employing in silico investigations to determine the cross-kingdom approach for Curcuma longa miRNAs and their human targets. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2023;12:3. [PMID: 36644780 PMCID: PMC9823259 DOI: 10.1186/s43088-022-00330-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023]  Open
22
Monnens M, Halajian A, Littlewood DTJ, Briscoe AG, Artois T, Vanhove MP. Can avian flyways reflect dispersal barriers of clinostomid parasites? First evidence from the mitogenome of Clinostomum complanatum. Gene X 2023;851:146952. [DOI: 10.1016/j.gene.2022.146952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 09/08/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022]  Open
23
Olo Ndela E, Roux S, Henke C, Sczyrba A, Sime Ngando T, Varsani A, Enault F. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evol 2022;9:veac123. [PMID: 36694818 PMCID: PMC9865509 DOI: 10.1093/ve/veac123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]  Open
24
Rajasekaran S, Khan E, Ching SR, Khan M, Siddiqui J, Gradia DF, Lin C, Bouley SJ, Mercadante D, Manning AL, Gerber AP, Walker J, Miles W. PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. Nucleic Acids Res 2022;50:7048-7066. [PMID: 35736218 PMCID: PMC9262620 DOI: 10.1093/nar/gkac499] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022]  Open
25
Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2022;33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
26
Ender A, Grafl N, Kolberg T, Findeiß S, Stadler PF, Mörl M. Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes. RNA (NEW YORK, N.Y.) 2022;28:551-567. [PMID: 35022261 PMCID: PMC8925977 DOI: 10.1261/rna.078814.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
27
Yang B, Ye Z, Wang Y, Guo H, Lehmler HJ, Huang R, Song E, Song Y. Evaluation of Early Biomarkers of Atherosclerosis Associated with Polychlorinated Biphenyl Exposure: An in Vitro and in Vivo Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2022;130:37011. [PMID: 35349355 PMCID: PMC8963524 DOI: 10.1289/ehp9833] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
28
Rataj M, Vďačný P. Putative ITS2 secondary structure model and multi‐gene phylogenies of tetrahymenids (Ciliophora, Hymenostomatia) parasitizing planarians and crayfish worms. ZOOL SCR 2022. [DOI: 10.1111/zsc.12528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
29
Shatoff E, Bundschuh R. dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding. Bioinformatics 2022;38:687-693. [PMID: 34668517 DOI: 10.1093/bioinformatics/btab724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/15/2021] [Accepted: 10/15/2021] [Indexed: 02/03/2023]  Open
30
Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods Mol Biol 2022;2518:179-202. [PMID: 35666446 DOI: 10.1007/978-1-0716-2421-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
31
Steger G. Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. Methods Mol Biol 2022;2316:331-371. [PMID: 34845705 DOI: 10.1007/978-1-0716-1464-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
32
Pecina L, Vďačný P. DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
33
Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021;17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022]  Open
34
Serra F, Bottini S, Pratella D, Stathopoulou MG, Sebille W, El-Hami L, Repetto E, Mauduit C, Benahmed M, Grandjean V, Trabucchi M. Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding. Nucleic Acids Res 2021;49:e66. [PMID: 33823551 PMCID: PMC8216473 DOI: 10.1093/nar/gkab198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022]  Open
35
Meng F, Siu GKH, Mok BWY, Sun J, Fung KSC, Lam JYW, Wong NK, Gedefaw L, Luo S, Lee TMH, Yip SP, Huang CL. Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells. Cells 2021;10:1762. [PMID: 34359932 PMCID: PMC8307234 DOI: 10.3390/cells10071762] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022]  Open
36
Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN. DDX3 depletion represses translation of mRNAs with complex 5' UTRs. Nucleic Acids Res 2021;49:5336-5350. [PMID: 33905506 PMCID: PMC8136831 DOI: 10.1093/nar/gkab287] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]  Open
37
Günzel C, Kühnl F, Arnold K, Findeiß S, Weinberg CE, Stadler PF, Mörl M. Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches. RNA Biol 2021;18:457-467. [PMID: 32882151 PMCID: PMC7971258 DOI: 10.1080/15476286.2020.1816336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023]  Open
38
Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021;49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022]  Open
39
Zheng X, Chen Y, Zhou Y, Shi K, Hu X, Li D, Ye H, Zhou Y, Wang K. Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton. PLANT PHYSIOLOGY 2021;185:179-195. [PMID: 33631798 PMCID: PMC8133545 DOI: 10.1093/plphys/kiaa003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/16/2020] [Indexed: 05/11/2023]
40
Pietrosanto M, Adinolfi M, Guarracino A, Ferrè F, Ausiello G, Vitale I, Helmer-Citterich M. Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments. NAR Genom Bioinform 2021;3:lqab007. [PMID: 33615214 PMCID: PMC7884220 DOI: 10.1093/nargab/lqab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/18/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022]  Open
41
Entzian G, Hofacker I, Ponty Y, Lorenz R, Tanzer A. RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes. Bioinformatics 2021;37:2126-2133. [PMID: 33538792 PMCID: PMC8352504 DOI: 10.1093/bioinformatics/btab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022]  Open
42
Bawm S, Sagara R, Kakisaka K, Thu MJ, Hmoon MM, Htun LL, Win MM, Nonaka N, Nakao R, Suzuki H, Katakura K. Identification, genetic variation, and structural analysis of 18S rRNA of Theileria orientalis and Theileria velifera-like isolates from Myanmar. Parasitol Int 2021;82:102299. [PMID: 33540120 DOI: 10.1016/j.parint.2021.102299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/25/2020] [Accepted: 01/29/2021] [Indexed: 12/30/2022]
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Stepanov VG, Fox GE. Expansion segments in bacterial and archaeal 5S ribosomal RNAs. RNA (NEW YORK, N.Y.) 2021;27:133-150. [PMID: 33184227 PMCID: PMC7812874 DOI: 10.1261/rna.077123.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
44
Obert T, Rurik I, Vd’ačný P. Diversity and Eco-Evolutionary Associations of Endosymbiotic Astome Ciliates With Their Lumbricid Earthworm Hosts. Front Microbiol 2021;12:689987. [PMID: 34220782 PMCID: PMC8250849 DOI: 10.3389/fmicb.2021.689987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022]  Open
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RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application. Genes (Basel) 2020;12:genes12010014. [PMID: 33374382 PMCID: PMC7823788 DOI: 10.3390/genes12010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022]  Open
46
Wang Y, Liu Y, Wang S, Liu Z, Gao Y, Zhang H, Dong L. ATTfold: RNA Secondary Structure Prediction With Pseudoknots Based on Attention Mechanism. Front Genet 2020;11:612086. [PMID: 33384721 PMCID: PMC7770172 DOI: 10.3389/fgene.2020.612086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 11/15/2022]  Open
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Chakraborty R, Hasija Y. Predicting MicroRNA Sequence Using CNN and LSTM Stacked in Seq2Seq Architecture. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:2183-2188. [PMID: 31443043 DOI: 10.1109/tcbb.2019.2936186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Kaur M, Kumar A, Siddaraju NK, Fairoze MN, Chhabra P, Ahlawat S, Vijh RK, Yadav A, Arora R. Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits. Sci Rep 2020;10:16332. [PMID: 33004825 PMCID: PMC7529745 DOI: 10.1038/s41598-020-73071-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]  Open
49
Medley JC, Panzade G, Zinovyeva AY. microRNA strand selection: Unwinding the rules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020;12:e1627. [PMID: 32954644 PMCID: PMC8047885 DOI: 10.1002/wrna.1627] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
50
Yang M, Woolfenden HC, Zhang Y, Fang X, Liu Q, Vigh ML, Cheema J, Yang X, Norris M, Yu S, Carbonell A, Brodersen P, Wang J, Ding Y. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Nucleic Acids Res 2020;48:8767-8781. [PMID: 32652041 PMCID: PMC7470952 DOI: 10.1093/nar/gkaa577] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/11/2020] [Accepted: 06/24/2020] [Indexed: 12/18/2022]  Open
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