List of publications

ORCID iD iconorcid.org/0000-0002-5574-8222
ResearcherID: K-6507-2014

Articles:

  1. 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 pp. 1644-1651.
  2. J. Szenajch, A. Szabelska-Beręsewicz, A. Świercz, J. Zyprych-Walczak, I. Siatkowski, M. Góralski, A. Synowiec, L. Handschuh, "Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells", Int. J. Mol. Sci. 21, 9218, 2020
  3. A. Martyna, M. Masłyk, M. Janeczko, E. Kochanowicz, B. Gielniewski, A. Swiercz, O.M. Demchuk, K. Kubiński, "Antifungal agent 4-AN changes the genome-wide expression profile, downregulates virulence-associated genes and induces necrosis in Candida albicans cells", Molecules 25(12), 2928, 2020 https://doi.org/10.3390/molecules25122928
  4. MJ. Smialek, E. Ilaslan, MP. Sajek, A. Swiercz, DM. Janecki, K. Kusz-Zamelczyk, T. Wozniak, M. Kotecki, L. Handschuh, M. Figlerowicz, J. Jaruzelska, "Characterization of RNP networks of PUM1 and PUM2 post-transcriptional regulators in TCam-2 cells, a human male germ cell model", Cells 9(4):984, 2020 doi: 10.3390/cells9040984
  5. 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(8): e0202355. 2018 https://doi.org/10.1371/journal.pone.0202355
  6. 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 (3), 2018, pp.799-812. doi:10.1016/j.ejor.2016.06.043
  7. A. Swiercz, chapter "Hyper-Heuristics and Metaheuristics for Selected Bio-Inspired Combinatorial Optimization Problems" in J. Del Ser Lorente (ed.) "Heuristics and Hyper-Heuristics - Principles and Applications", InTech, pp.3-20, 2017 DOI: 10.5772/intechopen.69225.
  8. M. Goralski, P. Sobieszczanska, A. Obrepalska-Steplowska, A. Swiercz, A. Zmienko, M. Figlerowicz, "A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly" Plant Methods, 12:28, 2016, doi:10.1186/s13007-016-0128-4.
  9. K. Klonowska, L. Handschuh, A. Swiercz, M. Figlerowicz, P. Kozlowski, "MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency", Oncotarget 7, 2016, pp.67266-67276, DOI: 10.18632/oncotarget.11646
  10. A. Swiercz, E.K. Burke, M. Cicheński, G. Pawlak, S. Petrovic, T. Zurkowski, J. Blazewicz, "Unified encoding for hyper-heuristics with application to bioinformatics" Central European Journal of Operations Research 22, 2014, pp.567-589. (DOI 10.1007/s10100-013-0321-8)
  11. D. Santoni, A. Świercz, A. Żmienko, M. Kasprzak, M. Błażewicz, 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 2, 2014, pp.155-165.
  12. 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, pp.9-20.
  13. D. Kowalczykiewicz, A Swiercz, L. Handschuh, K. Lesniak, M. Figlerowicz, J. Wrzesinski, "Characterization of Sus scrofa small non-coding RNAs present in both female and male gonads", PLOS ONE,9(11): e113249, 2014, DOI: 10.1371/journal.pone.0113249.
  14. 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, pp.25-34.
  15. J. Blazewicz, E.K. Burke, G. Kendall, W. Mruczkiewicz, C. Oguz, A. Swiercz, "A hyper-heuristic approach to sequencing by hybridization of DNA sequences" Annals of Operations Research 207(1), 2013, pp. 27-41. (DOI: 10.1007/s10479-011-0927-y)
  16. J. Blazewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek, A. Swiercz, "Highly efficient parallel approach to the next-generation DNA sequencing", in Proceedings of PPAM'11, Lecture Notes in Computer Science 7204, 2012, pp.262-271.
  17. J. Gracz, A. Świercz, T. Twardowski, "Computational analysis of alternative spliced genes on maize chromosome 1" BioTechnologia 93, 2012, pp.41-47. pdf
  18. J. Blazewicz, M. Bryja, M. Figlerowicz, P. Gawron, M. Kasprzak, E. Kirton, D. Platt, J. Przybytek, A. Swiercz, L. Szajkowski, "Whole genome assembly from 454 sequencing output via modified DNA graph concept" Computational Biology and Chemistry 33 no.3 , 2009, pp. 224-230.
  19. M. Kasprzak, A. Swiercz, "Sekwencjonowanie i asemblacja DNA - podejścia, modele grafowe, algorytmy" Kosmos, 58 no. 1-2, 2009, pp. 17-28. pdf
  20. J. Blazewicz, M. Bryja, M. Figlerowicz, P. Gawron, M. Kasprzak, D. Platt, J. Przybytek, A. Swiercz, L. Szajkowski, "A new algorithm for genome assembly from short reads", in Proceedings of IT 2008, A. Stepnowski, M. Moszynski, T. Kochanski, J. Dabrowski (eds.), Gdansk: IEEE Computer Society 2008, pp. 455-458.
  21. J. Blazewicz, M. Kasprzak, A. Swiercz, M. Figlerowicz, P. Gawron, D. Platt, L. Szajkowski, "Parallel implementation of the novel approach to genome assembly", in Proceedings of SNPD 2008, R. Lee, P. Muenchaisri, W. Dosch (eds.), Los Alamitos: IEEE Computer Society, 2008, 732-737.
  22. J. Błażewicz, F. Glover, M. Kasprzak, W.T. Markiewicz, C. Oğuz, D. Rebholz-Schuhmann, A. Świercz "Dealing with repetitions in sequencing by hybridization" Computational Biology and Chemistry 30, no. 5, 2006, pp. 313-320.
  23. J. Błażewicz, C. Oğuz, A. Świercz, J. Węglarz "DNA sequencing by hybridization via genetic search" Operations Research 54, no. 6, 2006, pp. 1185-1192.
  24. J. Błażewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Świercz "Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries" Computational Biology and Chemistry 28, 2004, pp. 11-19.
  25. J. Błażewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Świercz "Tabu search method for isothermic DNA sequencing by hybridization" Proceedings of the RECOMB Abstracts, 2003, pp. 37-38.
  26. J. Błażewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Świercz "Tabu search method for DNA sequencing by hybridization with isothermic libraries" Proceedings of the ECCB Abstracts, 2003, pp. 517-518.
  27. J. Błażewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Świercz "Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries" Mathematical Biosciences Institute, Ohio State University, Report 11, 2003.

Monographs:

  1. A. Świercz "Genome sequencing: algorithms for new approaches", Ph.D thesis, Poznan University of Technology, 2007.(pdf)

Reports and short papers:

  1. J. Blazewicz, M. Bryja, M. Figlerowicz, P. Gawron, M. Kasprzak, D. Platt, J. Przybytek, A. Swiercz, L. Szajkowski, "Whole genome assembly from 454 sequencing output", RECOMB2008 poster book, 2008, pp. 41-42.
  2. A. Swiercz, J. Blazewicz, M. Figlerowicz, P. Gawron, M. Kasprzak, "Reading a DNA sequence - from sequencing to assembling", TU Clausthal Technical Report Series IfI-08-03, 2008, pp.34-36.
  3. P. Gawron, J. Blazewicz, M. Figlerowicz, M. Kasprzak, A. Swiercz, "A new approach to DNA assembly", TU Clausthal Technical Report Series IfI-08-03, 2008, pp.37-38.
  4. A. Swiercz, J. Blazewicz, M. Figlerowicz, P. Gawron, M. Kasprzak, D. Platt, L. Szajkowski, "On the assembly of short DNA fragments", Book of abstracts ECCB'08, 2008, pp. 70-71
  5. A. Swiercz, "An application of hyperheuristics", in Proceedings of ICOLE'09, TU Clausthal Technical Report Series IfI-09-12, 2009, pp.79-83.
  6. H. Cwiek, A. Swiercz, P. Gawron, J. Blazewicz, "Introduction to microarray data analysis",in Proceedings of ICOLE'09, TU Clausthal Technical Report Series IfI-09-12, 2009, pp.84-88.
  7. A. Swiercz, J. Blazewicz, M. Figlerowicz, P. Gawron, M. Kasprzak, D. Platt, £. Szajkowski, "A new method for assembling of DNA sequences", in Proceedings of ECCO XXII, 2009, p.25.