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For: Sato K, Kato Y. Prediction of RNA secondary structure including pseudoknots for long sequences. Brief Bioinform 2021;23:6380459. [PMID: 34601552 PMCID: PMC8769711 DOI: 10.1093/bib/bbab395] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Omnes L, Angel E, Bartet P, Radvanyi F, Tahi F. A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification. PLoS One 2025;20:e0314837. [PMID: 40279361 PMCID: PMC12026937 DOI: 10.1371/journal.pone.0314837] [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: 11/18/2024] [Accepted: 03/04/2025] [Indexed: 04/27/2025]  Open
2
Yang J, Sato K, Loza M, Park SJ, Nakai K. RNA secondary structure prediction by conducting multi-class classifications. Comput Struct Biotechnol J 2025;27:1449-1459. [PMID: 40256169 PMCID: PMC12008525 DOI: 10.1016/j.csbj.2025.04.001] [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: 10/07/2024] [Revised: 03/29/2025] [Accepted: 04/01/2025] [Indexed: 04/22/2025]  Open
3
La Rosa M, Fiannaca A, Mendolia I, La Paglia L, Urso A. GL4SDA: Predicting snoRNA-disease associations using GNNs and LLM embeddings. Comput Struct Biotechnol J 2025;27:1023-1033. [PMID: 40160859 PMCID: PMC11952811 DOI: 10.1016/j.csbj.2025.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/04/2025] [Accepted: 03/08/2025] [Indexed: 04/02/2025]  Open
4
Kagaya Y, Zhang Z, Ibtehaz N, Wang X, Nakamura T, Punuru PD, Kihara D. NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation. Nat Commun 2025;16:881. [PMID: 39837861 PMCID: PMC11751094 DOI: 10.1038/s41467-025-56261-7] [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: 05/22/2024] [Accepted: 01/13/2025] [Indexed: 01/23/2025]  Open
5
Maghraby A, Alzalaty M. Genome-wide identification, characterization, and functional analysis of the CHX, SOS, and RLK genes in Solanum lycopersicum under salt stress. Sci Rep 2025;15:1142. [PMID: 39774029 PMCID: PMC11707246 DOI: 10.1038/s41598-024-83221-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 12/12/2024] [Indexed: 01/11/2025]  Open
6
Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. eLife 2024;13:RP98540. [PMID: 39625751 PMCID: PMC11614387 DOI: 10.7554/elife.98540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2024]  Open
7
Boon WX, Sia BZ, Ng CH. Prediction of the effects of the top 10 synonymous mutations from 26645 SARS-CoV-2 genomes of early pandemic phase. F1000Res 2024;10:1053. [PMID: 39268187 PMCID: PMC11391198 DOI: 10.12688/f1000research.72896.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2024] [Indexed: 09/15/2024]  Open
8
Fallah A, Havaei SA, Sedighian H, Kachuei R, Fooladi AAI. Prediction of aptamer affinity using an artificial intelligence approach. J Mater Chem B 2024;12:8825-8842. [PMID: 39158322 DOI: 10.1039/d4tb00909f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
9
Qi F, Chen J, Chen Y, Sun J, Lin Y, Chen Z, Kapranov P. Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae043. [PMID: 39317944 PMCID: PMC12016570 DOI: 10.1093/gpbjnl/qzae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2024] [Accepted: 06/05/2024] [Indexed: 09/26/2024]
10
Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589009. [PMID: 38645201 PMCID: PMC11030352 DOI: 10.1101/2024.04.11.589009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
11
Huang X, Du Z. Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs. PLoS One 2024;19:e0307541. [PMID: 39038036 PMCID: PMC11262651 DOI: 10.1371/journal.pone.0307541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024]  Open
12
Kolaitis A, Makris E, Karagiannis AA, Tsanakas P, Pavlatos C. Knotify_V2.0: Deciphering RNA Secondary Structures with H-Type Pseudoknots and Hairpin Loops. Genes (Basel) 2024;15:670. [PMID: 38927606 PMCID: PMC11203014 DOI: 10.3390/genes15060670] [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] [Received: 03/26/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]  Open
13
Maghraby A, Alzalaty M. Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress. Sci Rep 2024;14:7610. [PMID: 38556556 PMCID: PMC10982304 DOI: 10.1038/s41598-024-57376-5] [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: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]  Open
14
Gong T, Ju F, Bu D. Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials. Commun Biol 2024;7:297. [PMID: 38461362 PMCID: PMC10924946 DOI: 10.1038/s42003-024-05952-w] [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: 12/07/2023] [Accepted: 02/21/2024] [Indexed: 03/11/2024]  Open
15
Loyer G, Reinharz V. Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework. Bioinformatics 2024;40:btae022. [PMID: 38230755 PMCID: PMC10868335 DOI: 10.1093/bioinformatics/btae022] [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: 07/18/2023] [Revised: 11/30/2023] [Accepted: 01/12/2024] [Indexed: 01/18/2024]  Open
16
Rocca R, Grillone K, Citriniti EL, Gualtieri G, Artese A, Tagliaferri P, Tassone P, Alcaro S. Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. Eur J Med Chem 2023;261:115850. [PMID: 37839343 DOI: 10.1016/j.ejmech.2023.115850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
17
Ballarino M, Pepe G, Helmer-Citterich M, Palma A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Comput Struct Biotechnol J 2023;21:4706-4716. [PMID: 37841333 PMCID: PMC10568309 DOI: 10.1016/j.csbj.2023.09.041] [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: 08/12/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023]  Open
18
Sato K, Hamada M. Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery. Brief Bioinform 2023;24:bbad186. [PMID: 37232359 PMCID: PMC10359090 DOI: 10.1093/bib/bbad186] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]  Open
19
Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023;24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [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: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023]  Open
20
Makris E, Kolaitis A, Andrikos C, Moulos V, Tsanakas P, Pavlatos C. Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops. Biomolecules 2023;13:biom13020308. [PMID: 36830677 PMCID: PMC9953189 DOI: 10.3390/biom13020308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]  Open
21
Fukunaga T, Hamada M. LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods. BIOINFORMATICS ADVANCES 2022;2:vbac078. [PMID: 36699418 PMCID: PMC9710674 DOI: 10.1093/bioadv/vbac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
22
Bugnon LA, Edera AA, Prochetto S, Gerard M, Raad J, Fenoy E, Rubiolo M, Chorostecki U, Gabaldón T, Ariel F, Di Persia LE, Milone DH, Stegmayer G. Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches. Brief Bioinform 2022;23:6606044. [PMID: 35692094 DOI: 10.1093/bib/bbac205] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022]  Open
23
Moudgal N, Arhin G, Frank AT. Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure. J Phys Chem A 2022;126:2739-2745. [PMID: 35470661 DOI: 10.1021/acs.jpca.2c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
24
Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods. QRB DISCOVERY 2022. [PMID: 37529277 PMCID: PMC10392686 DOI: 10.1017/qrd.2022.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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