Marta Kasprzak - List of publications in chronological order

Articles:

52. J. Blazewicz, E.K. Burke, M. Kasprzak, A. Kovalev, M.Y. Kovalyov, "The simplified partial digest problem: approximation and a graph-theoretic model", European Journal of Operational Research 208 (2011) 142-152. Abstract or Download full text — The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.ejor.2010.07.027
53. J. Blazewicz, M. Figlerowicz, M. Kasprzak, M. Nowacka, A. Rybarczyk, "RNA Partial Degradation Problem: motivation, complexity, algorithm", Journal of Computational Biology 18 (2011) 821-834. Abstract or Download full text — The final publication is available at Mary Ann Liebert, Inc. via http://online.liebertpub.com/doi/abs/10.1089/cmb.2010.0153
54. J. Blazewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek, A. Swiercz, "Highly efficient parallel approach to the next-generation DNA sequencing", Lecture Notes in Computer Science 7204 (2012) 262-271. Abstract or Download full text — The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-31500-8_27
55. J. Blazewicz, M. Kasprzak, "Reduced-by-matching graphs: toward simplifying Hamiltonian circuit problem", Fundamenta Informaticae 118 (2012) 225-244. Abstract or Download full text — The final publication is available at IOS Press via http://dx.doi.org/10.3233/FI-2012-711
56. J. Blazewicz, M. Kasprzak, "Complexity issues in computational biology", Fundamenta Informaticae 118 (2012) 385-401. Abstract or Download full text — The final publication is available at IOS Press via http://dx.doi.org/10.3233/FI-2012-721
57. J. Blazewicz, W. Frohmberg, P. Gawron, M. Kasprzak, M. Kierzynka, A. Swiercz, P. Wojciechowski, "DNA sequence assembly involving an acyclic graph model", Foundations of Computing and Decision Sciences 38 (2013) 25-34. Abstract or Download full text
58. D. Santoni, A. Swiercz, A. Zmienko, M. Kasprzak, M. Blazewicz, P. Bertolazzi, G. Felici, "An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana", OMICS: A Journal of Integrative Biology 18 (2014) 155-165. Abstract or Download full text — The final publication is available at Mary Ann Liebert, Inc. via http://online.liebertpub.com/doi/abs/10.1089/omi.2013.0050
59. A. Swiercz, B. Bosak, M. Chlopkowski, A. Hoffa, M. Kasprzak, K. Kurowski, T. Piontek, J. Blazewicz, "Preprocessing and storing high-throughput sequencing data", Computational Methods in Science and Technology 20 (2014) 9-20. Abstract or Download full text
60. M. Chlopkowski, M. Antczak, M. Slusarczyk, A. Wdowinski, M. Zajaczkowski, M. Kasprzak, "High-order statistical compressor for long-term storage of DNA sequencing data", RAIRO Operations Research 50 (2016) 351-361. Abstract or Download full text — The original publication is available at www.rairo-ro.org, with EDP Sciences as the copyright owner, via http://www.rairo-ro.org/articles/ro/abs/2016/02/ro150039-s/ro150039-s.html
61. M. Antczak, M. Kasprzak, P. Lukasiak, J. Blazewicz, "Structural alignment of protein descriptors − a combinatorial model", BMC Bioinformatics 17:383 (2016). Download full text
62. A. Rybarczyk, A. Hertz, M. Kasprzak, J. Blazewicz, "Tabu search for the RNA partial degradation problem", International Journal of Applied Mathematics and Computer Science 27 (2017) 401-415. Download full text
63. J. Blazewicz, M. Kasprzak, M. Kierzynka, W. Frohmberg, A. Swiercz, P. Wojciechowski, P. Zurkowski, "Graph algorithms for DNA sequencing - origins, current models and the future", European Journal of Operational Research 264 (2018) 799-812. Abstract or Download full text — The final publication is available at Elsevier via https://doi.org/10.1016/j.ejor.2016.06.043
64. M. Kasprzak, "Classification of de Bruijn-based labeled digraphs", Discrete Applied Mathematics 234 (2018) 86-92. Abstract or Download full text — The final publication is available at Elsevier via "https://doi.org/10.1016/j.dam.2016.10.014"
65. A. Swiercz, W. Frohmberg, M. Kierzynka, P. Wojciechowski, P. Zurkowski, J. Badura, A. Laskowski, M. Kasprzak, J. Blazewicz, "GRASShopPER − An algorithm for de novo assembly based on GPU alignments", PLoS ONE 13 (2018) e0202355. Abstract or Download full text
66. S. Swat, A. Laskowski, J. Badura, W. Frohmberg, P. Wojciechowski, A. Swiercz, M. Kasprzak, J. Blazewicz, "Genome-scale de novo assembly using ALGA", Bioinformatics 37 (2021) 1644-1651. Download full text
67. S. Swat, M. Kasprzak, "A heuristic approach to the treedepth decomposition problem for large graphs", Proceedings of the 47th International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2021), Lecture Notes in Computer Science 12911 (2021) 169-181. Download full text — The final publication is available at Springer via https://doi.org/10.1007/978-3-030-86838-3_13

Monographs and chapters:

4. M. Kasprzak, Wybrane algorytmy i modele grafowe w bioinformatyce, Poznan: Wydawnictwo Politechniki Poznanskiej, 2013.
   
5. J. Blazewicz, M. Kasprzak, N. Vlassis, "Ties between Graph Theory and Biology", section 13.2 in Handbook of Graph Theory (second edition), J.L. Gross, J. Yellen, P. Zhang (eds.), Chapman and Hall/CRC, 2013.
6. P. Formanowicz, M. Kasprzak, P. Wawrzyniak, "Labeled Graphs in Life Sciences - Two Important Applications", chapter 10 in Graph-Based Modelling in Science, Technology and Art, S. Zawislak, J. Rysinski (eds.), Springer, 2022.

Scientific reports: