References
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Blazewicz, J. and Kasprzak, M. (2012). Complexity issues in computational biology, Fundamenta Informaticae 118(4): 385-401, DOI: 10.3233/FI-2012-721.
- Chanfreau, G. (2015). Two degrading decades for RNA, RNA 21(4): 584-585, DOI: 10.1261/rna.050146.115.
- Deutscher, M. (2003). Degradation of stable RNA in bacteria, Journal of Biological Chemistry 278(46): 45041-45044, DOI: 10.1074/jbc.R300031200.
- 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.
- 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.
- Garey, M. and Johnson, D. (1979). Computers and Intractability. A Guide to the Theory of NP-Completeness,W.H. Freeman & Co., New York, NY.
- Glover, F. (1990). Tabu search: A tutorial, Interfaces 20: 74-94, DOI: 10.1287/inte.20.4.74.
- 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.
- Glover, F. and Laguna, M. (1997). Tabu Search, Kluwer Academic Publishers, Norwell, MA.
- 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.
- 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.
- 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.
- 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.
- Kierzek, R. (1992). Hydrolysis of oligoribonucleotides: influence of sequence and length, Nucleic Acids Research20(19): 5073-5077, DOI: 10.1093/nar/20.19.5073.
- Kierzek, R. (2001). Nonenzymatic cleavage of oligoribonucleotides, Methods in Enzymology 341: 657-675.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.