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For: Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R. RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinformatics 2017;33:2089-2096. [PMID: 28334186 PMCID: PMC5870858 DOI: 10.1093/bioinformatics/btx114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/22/2016] [Accepted: 02/23/2017] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
1
Gadekar V, Munk AW, Miladi M, Junge A, Backofen R, Seemann S, Gorodkin J. Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR Genom Bioinform 2024;6:lqae089. [PMID: 39131818 PMCID: PMC11310781 DOI: 10.1093/nargab/lqae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/26/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024]  Open
2
Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024;2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [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: 06/01/2024]
3
Genome-Wide RNA Secondary Structure Prediction. Methods Mol Biol 2023;2586:35-48. [PMID: 36705897 DOI: 10.1007/978-1-0716-2768-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
4
Sim M, Lee J, Kwon D, Lee D, Park N, Wy S, Ko Y, Kim J. Reference-based read clustering improves the de novo genome assembly of microbial strains. Comput Struct Biotechnol J 2022;21:444-451. [PMID: 36618978 PMCID: PMC9804104 DOI: 10.1016/j.csbj.2022.12.032] [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: 08/10/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]  Open
5
Ono Y, Katayama K, Onuma T, Kubo K, Tsuyuzaki H, Hamada M, Sato M. Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation. Nucleic Acids Res 2022;50:11229-11242. [PMID: 36259651 PMCID: PMC9638895 DOI: 10.1093/nar/gkac825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 12/04/2022]  Open
6
Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. Int J Mol Sci 2021;22:8719. [PMID: 34445436 PMCID: PMC8395733 DOI: 10.3390/ijms22168719] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023]  Open
7
Miladi M, Raden M, Will S, Backofen R. Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms Mol Biol 2020;15:19. [PMID: 33292340 PMCID: PMC7666477 DOI: 10.1186/s13015-020-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 10/16/2020] [Indexed: 12/14/2022]  Open
8
Chatterjee A, Mukherjee S, Basu B, Roy D, Basu R, Ghosh H, Mishra L, Bhattacharya M, Chakraborty N. Insight into the distinctive paradigm of Human Cytomegalovirus associated intrahepatic and extrahepatic cholestasis in neonates. Sci Rep 2020;10:15861. [PMID: 32985571 PMCID: PMC7522230 DOI: 10.1038/s41598-020-73009-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/18/2020] [Indexed: 01/15/2023]  Open
9
Müller T, Miladi M, Hutter F, Hofacker I, Will S, Backofen R. The locality dilemma of Sankoff-like RNA alignments. Bioinformatics 2020;36:i242-i250. [PMID: 32657398 PMCID: PMC7355259 DOI: 10.1093/bioinformatics/btaa431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
10
Mautner S, Montaseri S, Miladi M, Raden M, Costa F, Backofen R. ShaKer: RNA SHAPE prediction using graph kernel. Bioinformatics 2020;35:i354-i359. [PMID: 31510707 PMCID: PMC6612843 DOI: 10.1093/bioinformatics/btz395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
11
Berkemer SJ, Maier LK, Amman F, Bernhart SH, Wörtz J, Märkle P, Pfeiffer F, Stadler PF, Marchfelder A. Identification of RNA 3´ ends and termination sites in Haloferax volcanii. RNA Biol 2020;17:663-676. [PMID: 32041469 PMCID: PMC7237163 DOI: 10.1080/15476286.2020.1723328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
12
Miladi M, Sokhoyan E, Houwaart T, Heyne S, Costa F, Grüning B, Backofen R. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Gigascience 2019;8:giz150. [PMID: 31808801 PMCID: PMC6897289 DOI: 10.1093/gigascience/giz150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022]  Open
13
Crum M, Ram-Mohan N, Meyer MM. Regulatory context drives conservation of glycine riboswitch aptamers. PLoS Comput Biol 2019;15:e1007564. [PMID: 31860665 PMCID: PMC6944388 DOI: 10.1371/journal.pcbi.1007564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/06/2020] [Accepted: 11/25/2019] [Indexed: 12/13/2022]  Open
14
Eggenhofer F, Hofacker IL, Backofen R, Höner Zu Siederdissen C. CMV: visualization for RNA and protein family models and their comparisons. Bioinformatics 2019;34:2676-2678. [PMID: 29554223 PMCID: PMC6061798 DOI: 10.1093/bioinformatics/bty158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 03/13/2018] [Indexed: 11/14/2022]  Open
15
Aoki G, Sakakibara Y. Convolutional neural networks for classification of alignments of non-coding RNA sequences. Bioinformatics 2019;34:i237-i244. [PMID: 29949978 PMCID: PMC6022636 DOI: 10.1093/bioinformatics/bty228] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
16
Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J. Identification and characterization of novel conserved RNA structures in Drosophila. BMC Genomics 2018;19:899. [PMID: 30537930 PMCID: PMC6288889 DOI: 10.1186/s12864-018-5234-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/08/2018] [Indexed: 12/20/2022]  Open
17
Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. Genes (Basel) 2018;9:genes9120604. [PMID: 30518121 PMCID: PMC6315940 DOI: 10.3390/genes9120604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/03/2023]  Open
18
Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi. Sci Rep 2018;8:5563. [PMID: 29615754 PMCID: PMC5882874 DOI: 10.1038/s41598-018-23900-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/20/2018] [Indexed: 01/01/2023]  Open
19
Dotu I, Adamson SI, Coleman B, Fournier C, Ricart-Altimiras E, Eyras E, Chuang JH. SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data. PLoS Comput Biol 2018;14:e1006078. [PMID: 29596423 PMCID: PMC5892938 DOI: 10.1371/journal.pcbi.1006078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/10/2018] [Accepted: 03/05/2018] [Indexed: 12/02/2022]  Open
20
Smith MA, Seemann SE, Quek XC, Mattick JS. DotAligner: identification and clustering of RNA structure motifs. Genome Biol 2017;18:244. [PMID: 29284541 PMCID: PMC5747123 DOI: 10.1186/s13059-017-1371-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023]  Open
21
Kato Y, Gorodkin J, Havgaard JH. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots. BMC Genomics 2017;18:935. [PMID: 29197323 PMCID: PMC5712110 DOI: 10.1186/s12864-017-4309-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]  Open
22
Li X, Wong KC. Multiobjective Patient Stratification Using Evolutionary Multiobjective Optimization. IEEE J Biomed Health Inform 2017;22:1619-1629. [PMID: 29990162 DOI: 10.1109/jbhi.2017.2769711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
23
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J. The identification and functional annotation of RNA structures conserved in vertebrates. Genome Res 2017;27:1371-1383. [PMID: 28487280 PMCID: PMC5538553 DOI: 10.1101/gr.208652.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/04/2017] [Indexed: 01/15/2023]
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