Marta Kasprzak - Publications from the years 2001-2005

Articles:

16. J. Blazewicz, P. Formanowicz, M. Jaroszewski, M. Kasprzak, W.T. Markiewicz, "Simplified partial digest method for DNA restriction maps construction", in Currents in Computational Molecular Biology, N. El-Mabrouk, T. Lengauer, D. Sankoff (eds.), Montreal: Les Publications CRM, 2001, pp. 9-10.
17. J. Blazewicz, P. Formanowicz, M. Kasprzak, M. Jaroszewski, W.T. Markiewicz, "Construction of DNA restriction maps based on a simplified experiment", Bioinformatics 17, 2001, pp. 398-404. Download full text
18. J. Blazewicz, P. Formanowicz, M. Kasprzak, K. Michalak, P. Wierzejewski, "Clustal W algorithm for multiple sequence alignment revisited", Foundations of Computing and Decision Sciences 26, 2001, pp. 189-196.
19. J. Blazewicz, P. Formanowicz, M. Kasprzak, D. Kobler, "On the recognition of de Bruijn graphs and their induced subgraphs", Discrete Mathematics 245, 2002, pp. 81-92. Abstract or Download full text
20. J. Blazewicz, P. Formanowicz, F. Guinand, M. Kasprzak, "A heuristic managing errors for DNA sequencing", Bioinformatics 18, 2002, pp. 652-660. Download full text
21. J. Blazewicz, M. Kasprzak, W. Kuroczycki, "Hybrid genetic algorithm for DNA sequencing with errors", Journal of Heuristics 8, 2002, pp. 495-502. Abstract
22. J. Blazewicz, P. Formanowicz, M. Kasprzak, P. Schuurman, G.J. Woeginger, "DNA sequencing, Eulerian graphs, and the exact perfect matching problem", in Lecture Notes in Computer Science 2573, Graph-Theoretic Concepts in Computer Science, L. Kucera (ed.), Berlin: Springer-Verlag, 2002, pp. 13-24.
23. J. Blazewicz, M. Kasprzak, "Complexity of DNA sequencing by hybridization", Theoretical Computer Science 290, 2003, pp. 1459-1473. Abstract or Download full text
24. J. Blazewicz, M. Kasprzak, "O zlozonosci zagadnien sekwencjonowania lancuchow DNA", Pro Dialog 16, 2003, pp. 139-151. Streszczenie
25. J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz, "Tabu search method for isothermic DNA sequencing by hybridization", in Currents in Computational Molecular Biology, R. Spang, P. Beziat, M. Vingron (eds.), Berlin, 2003, pp. 37-38.
26. M. Szachniuk, R.W. Adamiak, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, J. Blazewicz, "A combinatorial analysis of 2D NMR spectra of RNA duplexes", in Currents in Computational Molecular Biology, R. Spang, P. Beziat, M. Vingron (eds.), Berlin, 2003, pp. 345-346.
27. M. Kasprzak, "Two approaches to the common superstring problem", Foundations of Computing and Decision Sciences 28, 2003, pp. 113-123. Abstract
28. J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz, "Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries", Computational Biology and Chemistry 28, 2004, pp. 11-19.
29. R.W. Adamiak, J. Blazewicz, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, M. Szachniuk, "An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes", Journal of Computational Biology 11, 2004, pp. 163-179. Download full text
30. M. Kasprzak, "An algorithm for isothermic DNA sequencing", Bulletin of the Polish Academy of Sciences. Technical Sciences 52, 2004, pp. 31-35. Download full text
31. J. Blazewicz, F. Glover, M. Kasprzak, "DNA sequencing - tabu and scatter search combined", INFORMS Journal on Computing 16, 2004, pp. 232-240. Abstract
32. J. Blazewicz, E. Burke, M. Jaroszewski, M. Kasprzak, B. Paliswiat, P. Pryputniewicz, "On the complexity of the double digest problem", Control and Cybernetics 33, 2004, pp. 133-140. Download full text
33. J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, "Sequencing by hybridization with isothermic oligonucleotide libraries", Discrete Applied Mathematics 145, 2004, 40-51. Abstract or Download full text
34. M. Kasprzak, "On the link between DNA sequencing and graph theory", Computational Methods in Science and Technology 10, 2004, 39-47.
35. J. Blazewicz, M. Figlerowicz, P. Jackowiak, D. Janny, D. Jarczynski, M. Kasprzak, M. Nalewaj, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera, "Parallel DNA sequence assembly", in Proceedings of ENC 2004, R. Baeza-Yates, J.L. Marroquin, E. Chavez(eds.), Los Alamitos: IEEE Computer Society, 2004, 378-382.
36. J. Blazewicz, M. Figlerowicz, P. Formanowicz, M. Kasprzak, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera, M. Wiktorczyk, "Assembling the SARS-CoV genome - new method based on graph theoretical approach", Acta Biochimica Polonica 51, 2004, 983-993. Abstract or Download full text
37. J. Blazewicz, P. Formanowicz, M. Kasprzak, "Selected combinatorial problems of computational biology", European Journal of Operational Research 161, 2005, 585-597. Abstract
38. J. Blazewicz, F. Glover, M. Kasprzak, "Evolutionary approaches to DNA sequencing with errors", Annals of Operations Research 138, 2005, 67-78. Abstract
39. J. Blazewicz, M. Kasprzak, "Combinatorial optimization in DNA mapping - a computational thread of the Simplified Partial Digest Problem", RAIRO - Operations Research 39, 2005, 227-241. Abstract or Download full text

Monographs and chapters:

2. J. Blazewicz, M. Kasprzak, "Determining genome sequences from experimental data using evolutionary computation", chapter 3 in Evolutionary Computation in Bioinformatics, G.B. Fogel, D.W. Corne (eds.), San Francisco: Morgan Kaufmann Publishers, 2003.
3. M. Kasprzak, Combinatorial models and methods for reading genomic sequences, Poznan: Wydawnictwo Politechniki Poznanskiej, Rozprawy nr 383, 2004.

Scientific reports:

12. M. Kasprzak, "ASSEMBL - opis programu i wyniki obliczen na procesorze Intel Pentium 4", Raport Poznanskiego Centrum Superkomputerowo-Sieciowego RA-002/2002, 2002.
13. J. Blazewicz (red.), "Bioportal. Algorytmy asemblacji lancuchow DNA", Raport Poznanskiego Centrum Superkomputerowo-Sieciowego RA-003/2002, 2002.
14. J. Blazewicz, M. Jaroszewski, M. Kasprzak, B. Paliswiat, P. Pryputniewicz, "On the complexity of the double digest problem", Laboratoire Leibniz-IMAG, Grenoble, Report 74, 2003.
15. J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz, "Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries", Mathematical Biosciences Institute, Ohio State University, Report 11, 2003.
16. J. Blazewicz (ed.), "ASM - DNA assembly application", Poznan Supercomputing and Networking Center, Report RA-001/2004, 2004.