Tabu Search for the RNA Partial Degradation Problem

Adachi, H. and Yu, Y. (2014). Purification of radiolabeled RNA products using denaturing gel electrophoresis, Current Protocols in Molecular Biology 105: 4.20.1-4.20.13, DOI: 10.1002/0471142727.mb0420s105.10.1002/0471142727.mb0420s105393401324510465Search in Google Scholar

Bibillo, A., Figlerowicz, M. and Kierzek, R. (1999). The non-enzymatic hydrolysis of oligoribonucleotides. VI: The role of biogenic polyamines, Nucleic Acids Research 27(19): 3931-3937, DOI: 10.1093/nar/27.19.3931.10.1093/nar/27.19.393114865710481033Search in Google Scholar

Bibillo, A., Figlerowicz, M., Ziomek, K. and Kierzek, R. (2000). The nonenzymatic hydrolysis of oligoribonucleotides. VII: Structural elements affecting hydrolysis, Nucleosides Nucleotides Nucleic Acids 19(5-6): 977-994, DOI: 10.1080/15257770008033037.10.1080/1525777000803303710893716Search in Google Scholar

Bilski, A. and Wojciechowski, J. (2016). Automatic parametric fault detection in complex analog systems based on a method of minimum node selection, International Journal of Applied Mathematics and Computer Science 26(3): 655-668, DOI: 10.1515/amcs-2016-0045. Fig. 7. Total computing time of tabu search for instances with false negatives and false positives. Fig. 8. Total computing time of both algorithms for instances with false negatives.Search in Google Scholar

Blazewicz, J., Figlerowicz, M., Kasprzak, M., Nowacka, M. and Rybarczyk, A. (2011). RNA partial degradation problem: Motivation, complexity, algorithm, Journal of Computational Biology 18(6): 821-834, DOI: 10.1089/cmb.2010.0153.10.1089/cmb.2010.015321563977Search in Google Scholar

Blazewicz, J., Formanowicz, P., Guinand, F. and Kasprzak, M. (2002). A heuristic managing errors for DNA sequencing, Bioinformatics 18(5): 652-660, DOI: 10.1093/bioinformatics/18.5.652.10.1093/bioinformatics/18.5.65212050060Search in Google Scholar

Blazewicz, J., Formanowicz, P., Kasprzak, M., Jaroszewski, M. and Markiewicz, W. (2001). Construction of DNA restriction maps based on a simplified experiment, Bioinformatics 17(5): 398-404, DOI: 10.1093/ bioinformatics/17.5.398.10.1093/bioinformatics/17.5.39811396417Search in Google Scholar

Blazewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W. and Weglarz, J. (1999). DNA sequencing with positive and negative errors, Journal of Computational Biology 6(1): 113-123, DOI: 10.1089/ cmb.1999.6.113.Search in Google Scholar

Blazewicz, J., Glover, F. and Kasprzak, M. (2005). Evolutionary approaches to DNA sequencing with errors, Annals of Operations Research 138(67): 67-78, DOI: 10.1007/s10479-005-2445-2.10.1007/s10479-005-2445-2Search in Google Scholar

Blazewicz, J. and Kasprzak, M. (2012). Complexity issues in computational biology, Fundamenta Informaticae 118(4): 385-401, DOI: 10.3233/FI-2012-721.10.3233/FI-2012-721Search in Google Scholar

Chanfreau, G. (2015). Two degrading decades for RNA, RNA 21(4): 584-585, DOI: 10.1261/rna.050146.115.10.1261/rna.050146.115437129125780149Search in Google Scholar

Deutscher, M. (2003). Degradation of stable RNA in bacteria, Journal of Biological Chemistry 278(46): 45041-45044, DOI: 10.1074/jbc.R300031200.10.1074/jbc.R30003120012941949Search in Google Scholar

Dutkiewicz, M. and Ciesiolka, J. (2005). Structural characterization of the highly conserved 98-base sequence at the 3’ end of HCV RNA genome and the complementary sequence located at the 5’ end of the replicative viral strand, Nucleic Acids Research 33(2): 693-703, DOI: 10.1093/nar/gki218.10.1093/nar/gki218Search in Google Scholar

Ender, C., Krek, A., Friedlander, M., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N. and Meister, G. (2008). A human snoRNA with microRNA-like functions, Molecular Cell 32(4): 519-528, DOI: 10.1016/j.molcel.2008.10.017.10.1016/j.molcel.2008.10.017Search in Google Scholar

Garey, M. and Johnson, D. (1979). Computers and Intractability. A Guide to the Theory of NP-Completeness,W.H. Freeman & Co., New York, NY.Search in Google Scholar

Glover, F. (1990). Tabu search: A tutorial, Interfaces 20: 74-94, DOI: 10.1287/inte.20.4.74.10.1287/inte.20.4.74Search in Google Scholar

Glover, F., Kelly, J. and Laguna, M. (1995). Genetic algorithms and tabu search: Hybrids for optimization, Computers and Operations Research 22(1): 111-134, DOI: 10.1016/0305-0548(93)E0023-M.10.1016/0305-0548(93)E0023-MSearch in Google Scholar

Glover, F. and Laguna, M. (1997). Tabu Search, Kluwer Academic Publishers, Norwell, MA.10.1007/978-1-4615-6089-0Search in Google Scholar

Haussecker, D., Huang, Y., Lau, A., Parameswaran, P., Fire, A. and Kay, M. (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing, RNA 16(4): 673-695, DOI: 10.1261/rna.2000810.10.1261/rna.2000810Search in Google Scholar

Jackowiak, P., Nowacka, M., Strozycki, P. and Figlerowicz, M. (2011). RNA degradome-ITS biogenesis and functions, Nucleic Acids Research 39(17): 7361-7370, DOI: 10.1093/nar/gkr450.10.1093/nar/gkr450Search in Google Scholar

Jankowiak, K., Lesicka, J., Pacak, A., Rybarczyk, A. and Szweykowska-Kulinska, Z. (2004). A comparison of roup II introns of plastid tRNALys UUU genes encoding maturase protein, Cellular and Molecular Biology Letters 9(2): 239-251.Search in Google Scholar

Jankowiak, K., Rybarczyk, A., Wyatt, R., Odrzykoski, I., Pacak, A. and Szweykowska-Kulinska, Z. (2005). Organellar inheritance in the allopolyploid moss rhizomnium pseudopunctatum, Taxon 54(2): 383-388, DOI: 10.2307/25065367.10.2307/25065367Search in Google Scholar

Kierzek, R. (1992). Hydrolysis of oligoribonucleotides: influence of sequence and length, Nucleic Acids Research20(19): 5073-5077, DOI: 10.1093/nar/20.19.5073.10.1093/nar/20.19.5073Search in Google Scholar

Kierzek, R. (2001). Nonenzymatic cleavage of oligoribonucleotides, Methods in Enzymology 341: 657-675.10.1016/S0076-6879(01)41183-9Search in Google Scholar

Kuppusamy, L. and Mahendran, A. (2016). Modelling DNA and RNA secondary structures using matrix insertion-deletion systems, International Journal of Applied Mathematics and Computer Science 26(1): 245-258, DOI: 10.1515/amcs-2016-0017.10.1515/amcs-2016-0017Search in Google Scholar

Nowacka, M., Jackowiak, P., Rybarczyk, A., Magacz, T., Strozycki, P., Barciszewski, J. and Figlerowicz, M. (2012). 2D-PAGE as an effective method of RNA degradome analysis, Molecular Biology Reports 39(1): 139-146, DOI: 10.1007/s11033-011-0718-1.10.1007/s11033-011-0718-1322184921559842Search in Google Scholar

Podkowinski, J., Zmienko, A., Florek, B., Wojciechowski, P., Rybarczyk, A., Wrzesinski, J., Ciesiolka, J., Blazewicz, J., Kondorosi, A., Crespi, M. and Legocki, A. (2009). Translational and structural analysis of the shortest legume ENOD40 gene in Lupinus luteus, Acta Biochimica Polonica 56(1): 89-102.10.18388/abp.2009_2520Search in Google Scholar

Rybarczyk, A., Jackowiak, P., Figlerowicz, M. and Blazewicz, J. (2016). Computational prediction of nonenzymatic RNA degradation patterns, Acta Biochimica Polonica 63(4): 745-751, DOI: 10.18388/abp.2016 1331.Search in Google Scholar

Rybarczyk, A., Szostak, N., Antczak, M., Zok, T., Popenda, M., Adamiak, R., Blazewicz, J. and Szachniuk, M. (2015). New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics 16: 276, DOI: 10.1186/s12859-015-0718-6.10.1186/s12859-015-0718-6455722926329823Search in Google Scholar

Szostak, N., Royo, F., Rybarczyk, A., Szachniuk, M., Blazewicz, J., del Sol, A. and Falcon-Perez, J. (2014). Sorting signal targeting mRNA into hepatic extracellular vesicles, RNA Biology 11(7): 836-844, DOI: 10.4161/rna.29305.10.4161/rna.29305417995824921245Search in Google Scholar

Yao, B., Hu, P., Zhang, M. and Jin, M. (2014). A support vector machine with the tabu search algorithm for freeway incident detection, International Journal of Applied Mathematics and Computer Science 24(2): 397-404, DOI: 10.2478/amcs-2014-0030.10.2478/amcs-2014-0030Search in Google Scholar

Zhang, S., Sun, L. and Kragler, F. (2009). The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation, Plant Physiology 150(1): 378-387, DOI: 10.1104/pp.108.134767.10.1104/pp.108.134767267574319261735Search in Google Scholar

Zok, T., Antczak, M., Riedel, M., Nebel, D., Villmann, T., Lukasiak, P., Blazewicz, J. and Szachniuk, M. (2015). Building the library of RNA 3D nucleotide conformations using the clustering approach, International Journal of Applied Mathematics and Computer Science 25(3): 689-700, DOI: 10.1515/amcs-2015-0050.10.1515/amcs-2015-0050Search in Google Scholar