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For: Hamada M, Sato K, Asai K. Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics 2010;11:586. [PMID: 21118522 PMCID: PMC3003279 DOI: 10.1186/1471-2105-11-586] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 11/30/2010] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
2
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: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [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
3
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: 0.8] [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
4
Rangan R, Zheludev IN, Hagey RJ, Pham EA, Wayment-Steele HK, Glenn JS, Das R. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look. RNA (NEW YORK, N.Y.) 2020;26:937-959. [PMID: 32398273 PMCID: PMC7373990 DOI: 10.1261/rna.076141.120] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 05/11/2023]
5
Yu B, Lu Y, Zhang QC, Hou L. Prediction and differential analysis of RNA secondary structure. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0205-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
6
Rangan R, Zheludev IN, Das R. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.27.012906. [PMID: 32511306 PMCID: PMC7217285 DOI: 10.1101/2020.03.27.012906] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
7
Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017;5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
8
RNA secondary structure prediction from multi-aligned sequences. Methods Mol Biol 2015;1269:17-38. [PMID: 25577370 DOI: 10.1007/978-1-4939-2291-8_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
9
Iquebal MA, Ansari MS, Sarika, Dixit SP, Verma NK, Aggarwal RAK, Jayakumar S, Rai A, Kumar D. Locus minimization in breed prediction using artificial neural network approach. Anim Genet 2014;45:898-902. [PMID: 25183434 DOI: 10.1111/age.12208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 11/26/2022]
10
Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, Soreq H. Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PLoS Comput Biol 2014;10:e1003517. [PMID: 24651478 PMCID: PMC3961179 DOI: 10.1371/journal.pcbi.1003517] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/31/2014] [Indexed: 12/22/2022]  Open
11
3S: Shotgun secondary structure determination of long non-coding RNAs. Methods 2013;63:170-7. [DOI: 10.1016/j.ymeth.2013.07.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 11/22/2022]  Open
12
Hamada M. Fighting against uncertainty: an essential issue in bioinformatics. Brief Bioinform 2013;15:748-67. [PMID: 23803300 DOI: 10.1093/bib/bbt038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
13
Novikova IV, Hennelly SP, Tung CS, Sanbonmatsu KY. Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol 2013;425:3731-46. [PMID: 23467124 DOI: 10.1016/j.jmb.2013.02.030] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 01/19/2023]
14
Puton T, Kozlowski LP, Rother KM, Bujnicki JM. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res 2013;41:4307-23. [PMID: 23435231 PMCID: PMC3627593 DOI: 10.1093/nar/gkt101] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
15
Hamada M, Asai K. A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). J Comput Biol 2012;19:532-49. [PMID: 22313125 DOI: 10.1089/cmb.2011.0197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
16
Hajiaghayi M, Condon A, Hoos HH. Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinformatics 2012;13:22. [PMID: 22296803 PMCID: PMC3347993 DOI: 10.1186/1471-2105-13-22] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 02/01/2012] [Indexed: 01/21/2023]  Open
17
Sato K, Kato Y, Hamada M, Akutsu T, Asai K. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. ACTA ACUST UNITED AC 2011;27:i85-93. [PMID: 21685106 PMCID: PMC3117384 DOI: 10.1093/bioinformatics/btr215] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
18
Hamada M, Wijaya E, Frith MC, Asai K. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. ACTA ACUST UNITED AC 2011;27:3085-92. [PMID: 21976422 DOI: 10.1093/bioinformatics/btr537] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
19
Hamada M, Kiryu H, Iwasaki W, Asai K. Generalized centroid estimators in bioinformatics. PLoS One 2011;6:e16450. [PMID: 21365017 PMCID: PMC3041832 DOI: 10.1371/journal.pone.0016450] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 12/22/2010] [Indexed: 11/27/2022]  Open
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