List of publications
orcid.org/0000-0002-5574-8222
ResearcherID: K-6507-2014
Articles:
- 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.
- 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
- 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
- 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
- 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
- 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
- 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.
- 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.
- 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
- 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)
- 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.
- 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.
- 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.
- 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.
- 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)
- 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.
- J. Gracz, A. Świercz, T. Twardowski,
"Computational analysis of alternative spliced genes on maize chromosome 1"
BioTechnologia 93, 2012, pp.41-47. pdf
- 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.
- M. Kasprzak, A. Swiercz,
"Sekwencjonowanie i asemblacja DNA - podejścia, modele grafowe, algorytmy" Kosmos, 58 no. 1-2, 2009, pp. 17-28. pdf
- 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.
- 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.
- 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.
- J. Błażewicz, C. Oğuz, A. Świercz, J. Węglarz
"DNA sequencing by hybridization via genetic search"
Operations Research 54, no. 6, 2006, pp. 1185-1192.
- 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.
- 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.
- 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.
- 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:
- A. Świercz "Genome sequencing: algorithms for new approaches",
Ph.D thesis, Poznan University of Technology, 2007.(pdf)
Reports and short papers:
- 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.
- 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.
- 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.
- 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
- A. Swiercz, "An application of hyperheuristics", in Proceedings of ICOLE'09, TU Clausthal Technical Report Series IfI-09-12, 2009, pp.79-83.
- 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.
- 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.