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For: Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL. A folding algorithm for extended RNA secondary structures. Bioinformatics 2011;27:i129-36. [PMID: 21685061 PMCID: PMC3117358 DOI: 10.1093/bioinformatics/btr220] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
Number Cited by Other Article(s)
1
Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024;20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [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: 01/31/2024]
2
Kaloudas D, Pavlova N, Penchovsky R. GHOST-NOT and GHOST-YES: Two programs for generating high-speed biosensors with randomized oligonucleotide binding sites with NOT or YES Boolean logic functions based on experimentally validated algorithms. J Biotechnol 2023;373:82-89. [PMID: 37499876 DOI: 10.1016/j.jbiotec.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
3
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
4
An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms. Comput Biol Med 2022;145:105469. [DOI: 10.1016/j.compbiomed.2022.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
5
Flamm C, Hellmuth M, Merkle D, Nojgaard N, Stadler PF. Generic Context-Aware Group Contributions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:429-442. [PMID: 32750852 DOI: 10.1109/tcbb.2020.2998948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
6
De Bisschop G, Allouche D, Frezza E, Masquida B, Ponty Y, Will S, Sargueil B. Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Noncoding RNA 2021;7:71. [PMID: 34842779 PMCID: PMC8628965 DOI: 10.3390/ncrna7040071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023]  Open
7
Zhao Q, Zhao Z, Fan X, Yuan Z, Mao Q, Yao Y. Review of machine learning methods for RNA secondary structure prediction. PLoS Comput Biol 2021;17:e1009291. [PMID: 34437528 PMCID: PMC8389396 DOI: 10.1371/journal.pcbi.1009291] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
8
Stadler PF. Alignments of biomolecular contact maps. Interface Focus 2021;11:20200066. [PMID: 34123355 DOI: 10.1098/rsfs.2020.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 01/11/2023]  Open
9
Reinharz V, Sarrazin-Gendron R, Waldispühl J. Modeling and Predicting RNA Three-Dimensional Structures. Methods Mol Biol 2021;2284:17-42. [PMID: 33835435 DOI: 10.1007/978-1-0716-1307-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
10
Chillón I, Marcia M. The molecular structure of long non-coding RNAs: emerging patterns and functional implications. Crit Rev Biochem Mol Biol 2020;55:662-690. [PMID: 33043695 DOI: 10.1080/10409238.2020.1828259] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
11
Singh J, Hanson J, Paliwal K, Zhou Y. RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nat Commun 2019;10:5407. [PMID: 31776342 PMCID: PMC6881452 DOI: 10.1038/s41467-019-13395-9] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/01/2019] [Indexed: 01/03/2023]  Open
12
Antczak M, Zablocki M, Zok T, Rybarczyk A, Blazewicz J, Szachniuk M. RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. Bioinformatics 2019;35:152-155. [PMID: 29985979 PMCID: PMC6298044 DOI: 10.1093/bioinformatics/bty609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/06/2018] [Indexed: 01/23/2023]  Open
13
Zhang QL, Wang H, Zhu QH, Wang XX, Li YM, Chen JY, Morikawa H, Yang LF, Wang YJ. Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing. Front Genet 2019;10:877. [PMID: 31616471 PMCID: PMC6775235 DOI: 10.3389/fgene.2019.00877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 08/21/2019] [Indexed: 01/28/2023]  Open
14
RNApolis: Computational Platform for RNA Structure Analysis. FOUNDATIONS OF COMPUTING AND DECISION SCIENCES 2019. [DOI: 10.2478/fcds-2019-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
15
Mathews DH. How to benchmark RNA secondary structure prediction accuracy. Methods 2019;162-163:60-67. [PMID: 30951834 DOI: 10.1016/j.ymeth.2019.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/24/2019] [Accepted: 04/01/2019] [Indexed: 11/18/2022]  Open
16
Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH. Accelerated RNA secondary structure design using preselected sequences for helices and loops. RNA (NEW YORK, N.Y.) 2018;24:1555-1567. [PMID: 30097542 PMCID: PMC6191713 DOI: 10.1261/rna.066324.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
17
Tanzer A, Hofacker IL, Lorenz R. RNA modifications in structure prediction - Status quo and future challenges. Methods 2018;156:32-39. [PMID: 30385321 DOI: 10.1016/j.ymeth.2018.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]  Open
18
Guo QH, Sun LH. Combinatorics of Contacts in Protein Contact Maps. Bull Math Biol 2017;80:385-403. [PMID: 29230703 DOI: 10.1007/s11538-017-0380-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
19
Sloma MF, Mathews DH. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput Biol 2017;13:e1005827. [PMID: 29107980 PMCID: PMC5690697 DOI: 10.1371/journal.pcbi.1005827] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 11/16/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022]  Open
20
Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF. Recent advances in RNA folding. J Biotechnol 2017;261:97-104. [DOI: 10.1016/j.jbiotec.2017.07.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/02/2017] [Accepted: 07/04/2017] [Indexed: 12/23/2022]
21
RNA structure prediction: from 2D to 3D. Emerg Top Life Sci 2017;1:275-285. [DOI: 10.1042/etls20160027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 07/27/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022]
22
Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences. Comput Biol Chem 2017;70:96-106. [PMID: 28844020 DOI: 10.1016/j.compbiolchem.2017.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/01/2017] [Accepted: 08/07/2017] [Indexed: 02/07/2023]
23
Regular Simple Queues of Protein Contact Maps. Bull Math Biol 2016;79:21-35. [PMID: 27844300 DOI: 10.1007/s11538-016-0212-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
24
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. Nucleic Acids Res 2016;44:W320-7. [PMID: 27235417 PMCID: PMC4987954 DOI: 10.1093/nar/gkw453] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 12/20/2022]  Open
25
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL. Predicting RNA secondary structures from sequence and probing data. Methods 2016;103:86-98. [PMID: 27064083 DOI: 10.1016/j.ymeth.2016.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/29/2016] [Accepted: 04/04/2016] [Indexed: 01/08/2023]  Open
26
zu Siederdissen CH, Prohaska SJ, Stadler PF. Algebraic Dynamic Programming over general data structures. BMC Bioinformatics 2015;16 Suppl 19:S2. [PMID: 26695390 PMCID: PMC4686793 DOI: 10.1186/1471-2105-16-s19-s2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
27
Waldispühl J, Reinharz V. Modeling and predicting RNA three-dimensional structures. Methods Mol Biol 2015;1269:101-21. [PMID: 25577374 DOI: 10.1007/978-1-4939-2291-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
28
Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak R, Blazewicz J, Szachniuk M. New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics 2015;16:276. [PMID: 26329823 PMCID: PMC4557229 DOI: 10.1186/s12859-015-0718-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/24/2015] [Indexed: 11/19/2022]  Open
29
Pietal MJ, Bujnicki JM, Kozlowski LP. GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. Bioinformatics 2015;31:3499-505. [PMID: 26130575 DOI: 10.1093/bioinformatics/btv390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 06/23/2015] [Indexed: 11/13/2022]  Open
30
Müller R, Nebel ME. Combinatorics of RNA Secondary Structures with Base Triples. J Comput Biol 2015;22:619-48. [PMID: 26098199 DOI: 10.1089/cmb.2013.0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
31
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL. Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA (NEW YORK, N.Y.) 2015;21:1110-1121. [PMID: 25904133 PMCID: PMC4436664 DOI: 10.1261/rna.047522.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
32
Chitsaz H, Aminisharifabad M. Exact Learning of RNA Energy Parameters From Structure. J Comput Biol 2015;22:463-73. [DOI: 10.1089/cmb.2014.0164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
33
Findeiß S, Wachsmuth M, Mörl M, Stadler PF. Design of transcription regulating riboswitches. Methods Enzymol 2014;550:1-22. [PMID: 25605378 DOI: 10.1016/bs.mie.2014.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
34
Chen WYC, Guo QH, Sun LH, Wang J. Zigzag stacks and m-regular linear stacks. J Comput Biol 2014;21:915-35. [PMID: 25455155 DOI: 10.1089/cmb.2014.0133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
35
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Res 2013;41:9999-10009. [PMID: 24005040 PMCID: PMC3905863 DOI: 10.1093/nar/gkt795] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
36
Rivas E. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol 2013;10:1185-96. [PMID: 23695796 PMCID: PMC3849167 DOI: 10.4161/rna.24971] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 12/31/2022]  Open
37
Chitsaz H, Forouzmand E, Haffari G. An efficient algorithm for upper bound on the partition function of nucleic acids. J Comput Biol 2013;20:486-94. [PMID: 23829650 DOI: 10.1089/cmb.2013.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
38
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: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
39
Reinharz V, Major F, Waldispühl J. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 2013;28:i207-14. [PMID: 22689763 PMCID: PMC3371858 DOI: 10.1093/bioinformatics/bts226] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
40
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y. DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. ACTA ACUST UNITED AC 2012;28:3218-24. [PMID: 23060618 DOI: 10.1093/bioinformatics/bts612] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
41
Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012;3:759-78. [PMID: 22991327 DOI: 10.1002/wrna.1134] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
42
Lorenz R, Bernhart SH, Höner zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Algorithms Mol Biol 2011;6:26. [PMID: 22115189 PMCID: PMC3319429 DOI: 10.1186/1748-7188-6-26] [Citation(s) in RCA: 3228] [Impact Index Per Article: 230.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 11/24/2011] [Indexed: 12/31/2022]  Open
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