Publications

2018

  • 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, pp. 799-812;

2017

  • A. Mickiewicz, J. Sarzyńska, M. Miłostan, A. Kurzyńska-Kokorniak, A. Rybarczyk, P. Łukasiak, T. Kuliński, M. Figlerowicz, J. Błażewicz, "Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA", Computational Biology and Chemistry 66, 2017, pp. 44-56;
  • A. Rybarczyk, P. Jackowiak, M. Figlerowicz, J. Blazewicz, "Computational prediction of nonenzymatic RNA degradation patterns", Acta Biochimica Polonica 63 (4), 2017, pp. 745-751;
  • N. Szostak, S. Wasik, J. Blazewicz, "Understanding Life: A Bioinformatics Perspective", European Review 25 (2), 2017, pp. 231-245;
  • 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 (2), 2017, pp. 401-415;
  • N. Szostak, J. Synak, M. Borowski, S. Wasik, J. Blazewicz, "Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution", PloS one 12 (7):e0180827, 2017;
  • J. Miskiewicz, K. Tomczyk, A. Mickiewicz, J. Sarzynska, M. Szachniuk, "Bioinformatics study of structural patterns in plant microRNA precursors",
    BioMed Research International vol. 2017, article ID 6783010, 8 pages,
    doi:10.1155/2017/6783010

2016

  • M. Marcinkowska-Swojak, L.Handschuh, P.Wojciechowski, M.Goralski, K.Tomaszewski, M.Kazmierczak, K.Lewandowski, M.Komarnicki, J.Blazewicz, M.Figlerowicz, P.Kozlowski, "Simultaneous detection of mutations and copy number variation of NPM1 in the acute myeloid leukemia using multiplex ligation-dependent probe amplification", Mutation Research 786, 2016, pp.14-26;
  • N. Szostak, S. Wasik, J Blazewicz,"Hypercycle",PLoS Comput Biol 12(4): e1004853, 2016, doi:10.1371/journal.pcbi.1004853;
  • P. Wojciechowski, W. Frohmberg, M. Kierzynka, P. Zurkowski, J. Blazewicz,"G-MAPSEQ–a new method for mapping reads to a reference genome",Foundations of Computing and Decision Sciences 41, 2016, pp. 123-142;
  • A. Mickiewicz, A. Rybarczyk, J. Sarzynska, M. Figlerowicz, J. Blazewicz, "AmiRNA Designer-new method of artificial miRNA design", Acta Biochimica Polonica 63, 2016, pp. 71-77;
  • T. Prejzendanc, S. Wasik, J. Blazewicz, Computer representations of bioinformatics models, Current Bioinformatics 11 (5), 2016, pp. 551-560;
  • A. Rybarczyk, P. Jackowiak, M. Figlerowicz, J. Blazewicz, "Computational prediction of nonenzymatic RNA degradation patterns", Acta Biochimica Polonica, 2016, pp. 1-15;
  • N. Szostak, S. Wasik, J. Blazewicz, Understanding Life: A Bioinformatics Perspective, European Review, 2016, pp. 1-15;
  • M. Biesiada, K.J. Purzycka, M. Szachniuk, J. Blazewicz, R.W. Adamiak, "Automated RNA 3D Structure Prediction with RNAComposer", RNA Structure Determination: Methods and Protocols, 2016, pp. 199-215;
  • M. Antczak, M. Kasprzak, P. Łukasiak, J. Błażewicz, "Structural alignment of protein descriptors - a combinatorial model", BMC Bioinformatics 17, 2016, pp.383, doi:10.1186/s12859-016-1237-9;
  • M. Antczak, M. Popenda, T. Zok, J. Sarzynska, T. Ratajczak, K. Tomczyk, R.W. Adamiak, M. Szachniuk, "New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure", Acta Biochimica Polonica 63(4), 2016, pp. 737-744,doi:10.18388/abp.2016_1329;

2015

  • A. Zmienko, A. Samelak-Czajka,M. Goralski,E. Sobieszczuk-Nowicka, P. Kozlowski, M. Figlerowicz, "Selection of Reference Genes for qPCR- and ddPCR-Based Analyses of Gene Expression in Senescing Barley Leaves", PLoS One 10 (2): e0118226, 2015, doi:10.1371/journal.pone.0118226. eCollection 2015. PubMed PMID: 25723393; PubMed Central PMCID: PMC4344324;
  • E. Sobieszczuk-Nowicka, A. Zmienko, A. Samelak-Czajka, M. Łuczak, M. Pietrowska-Borek, R. Iorio, S. Del Duca, M. Figlerowicz, J. Legocka, "Dark-induced senescence ofbarley leaves involves activation of plastid transglutaminases", Amino Acids, 2015, [Epub ahead of print] PubMed PMID: 25583605;
  • S. Kubala, M. Garnczarska, L. Wojtyla, A. Clippe, A. Kosmala, A.Zmienko, S. Lutts, M. Quinet, "Deciphering priming-induced improvement of rapeseed (Brassica napus L.)germination through an integrated transcriptomic and proteomic approach", Plant Sci 231, 2015, pp. 94-113, doi: 10.1016/j.plantsci.2014.11.008, PubMed PMID: 25575995;
  • M.A. Lewandowska, K. Czubak, K. Klonowska, W. Jozwicki, J. Kowalewski, P. Kozlowski, "The Use of a Two-Tiered Testing Strategy for the Simultaneous Detection of Small EGFR Mutations and EGFR Amplification in Lung Cancer", PLoS One 10(2):e0117983, 2015, doi:10.1371/journal.pone.0117983. eCollection 2015;
  • K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz, R.W. Adamiak, "Automated 3D RNA structure prediction using the RNAComposer method for riboswitches", Methods in Enzymology: Computational Methods for Understanding Riboswitches 553, 2014, pp. 3-34, doi:10.1016/bs.mie.2014.10.050;
  • M. Szachniuk, M.C. De Cola, G. Felici, D. de Werra, J. Blazewicz, "Optimal pathway reconstruction on 3D NMR maps", DISCRETE APPLIED MATHEMATICS 182, 2015, pp. 134-149 (SI), doi:10.1016/j.dam.2014.04.010;
  • J. Zyprych-Walczak,A. Szabelska, L. Handschuh, K. Górczak, K. Klamecka, M. Figlerowicz, I. Siatkowski, "The impact of normalization methods on RNA-seq data analysis", BioMed Research International – in press, 2015;
  • P. Janus, T. Stokowy,R. Jaksik, K. Szoltysek, L. Handschuh,J. Podkowinski, W. Widlak, M. Kimmel, P. Widlak, "Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock", Mol Genet Genomics, 2015;
  • D. Gurda, L. Handschuh, W. Kotkowiak, H. Jakubowski, "Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells", Amino Acids, 2015;
  • A. Zmienko,M. Goralski, A. Samelak-Czajka, E. Sobieszczuk-Nowicka, M. Figlerowicz, "Time course transcriptional profiling of senescing barley leaves", Genomics Data 4, 2015, pp: 78-81, doi:10.1016/j.gdata.2015.03.006;
  • K. Klonowska, M. Ratajska, K. Czubak, A. Kuzniacka, I. Brozek, M. Koczkowska, M. Sniadecki, J. Debniak, D. Wydra, M. Stukan, A. Zmienko, I.I. Finger, J. Limon, P. Kozlowski, "Analysis of large mutations in BARD1 gene in patients with breast and/or ovarian cancer", Scientific Reports - in press, 2015;
  • M. Szachniuk, "Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms", Bulletin of the Polish Academy of Sciences Technical Sciences 63(1), 2015, pp. 329-338, doi:10.1515/bpasts-2015-0037;
  • Z. Miao, R.W. Adamiak, M.-F. Blanchet, M. Boniecki, J.M. Bujnicki, S.-J. Chen, C. Cheng, G. Chojnowski, F.-C. Chou, P. Cordero, J.A. Cruz, A, Ferre-D'Amare, R. Das, F. Ding, N.V. Dokholyan, S. Dunin-Horkawicz, W. Kladwang, A. Krokhotin, G. Lach, M. Magnus, F. Major, T.H. Mann, B. Masquida, D. Matelska, M. Meyer, A. Peselis, M. Popenda, K.J. Purzycka, A. Serganov, J. Stasiewicz, M. Szachniuk, A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, T. Zok, E. Westhof, "RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures", RNA 21(6), 2015, pp. 1-19, doi:10.1261/rna.049502.114;
  • T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk, "Building the library of RNA 3D nucleotide conformations using clustering approach", International Journal of Applied Mathematics and Computer Science, 2015
  • P. Lukasiak, M. Antczak, T. Ratajczak, M. Szachniuk, M. Popenda, R.W. Adamiak, J. Blazewicz, "RNAssess - a webserver for quality assessment of RNA 3D structures", Nucleic Acids Research, 2015;

2014

  • M. Antczak, T. Zok, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz,M. Szachniuk, "RNApdbee - a webserver to derive secondary structures from pdb files ofknotted and unknotted RNAs", Nucleic Acids Research 42(W1), 2014, W368-W372, doi:10.1093/nar/gku330;
  • D. Santoni, A. Świercz, A. Żmieńko, 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, 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;
  • G.W. Weber, J. Blazewicz, M. Rauner, M. Türkay, "Recent advances in computational biology, bioinformatics, medicine, and healthcare by modern OR", CEJOR 22, 2014, pp. 427-430;
  • A. Swiercz, E.K. Burke, M. Cichenski, G. Pawlak, S. Petrovic, T. Zurkowski, J. Blazewicz, "Unified encoding for hyper-heuristics with application to bioinformatics", CEJOR 22, 2014, pp. 567-589;
  • S. Wasik, P. Jackowiak, M. Figlerowicz, J. Blazewicz, "Multi-agent model of hepatitis c virus infection", Artificial intelligence in medicine 60, 2014, pp. 123-131;
  • P. Wojciechowski, P. Formanowicz, J. Blazewicz, Reference alignment based methods for quality evaluation of multiple sequence alignment - a survey", Current Bioinformatics 9, 2014, pp. 44-56;
  • N.Szostak, F.Royo, A.Rybarczyk, M.Szachniuk, J.Blazewicz, A.del Sol, J.M.Falcon-Perez, "Sorting signal targeting mRNA into hepatic extracellular vesicles", RNA Biology 7, 2014, pp. 836-844;
  • J. Korfanty, T. Stokowy, P. Widlak, A. Gogler-Piglowska, L. Handschuh, J. Podkowiński, N. Vydra, A. Naumowicz, A. Toma-Jonik, W. Widlak, "Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes", Int J Biochem Cell Biol 57, 2014, pp. 76-83;
  • 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;
  • A. Zmieńko, A. Samelak, P. Kozłowski, M. Figlerowicz, "Copy number polymorphism in plant genomes", Theor Appl Genet. 127(1), 2014, pp. 1-18, doi: 10.1007/s00122-013-2177-7;

2013

  • P. Lukasiak, M. Antczak, T. Ratajczak, J. M. Bujnicki, M. Szachniuk, R. W. Adamiak, M. Popenda, J. Blazewicz, "RNAlyzer – novel approach for quality analysis of RNA structural models", Nucleic Acid Research 41, 2013, pp. 5978-5990;
  • M. Kierzynka, J. Blazewicz, W. Frohmberg, P. Wojciechowski, "G-MSA - GPU-based, fast and accurate algorithm for multiple sequence alignment", Journal of Parallel and Distributed Computing 73, 2013, pp.32-41;
  • 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;
  • P. Lukasiak, M. Antczak, T. Ratajczak, J. Bujnicki, M. Szachniuk, M. Popenda, R. Adamiak, J. Blazewicz, "RNAlyzer - novel approach for quality analysis of RNA structural models", Nucleic Acid Research 41, 2013, pp. 5978-5990;
  • J. Blazewicz, E.K. Burke, G. Kendall, W. Mruczkiewicz, C. Oguz, A. Świercz, "A hyper-heuristic approach to sequencing by hybridization of DNA sequences", Annals of Operations Research 207 (1), 2013, pp. 27-41;
  • S. Wasik, T. Prejzendanc, J. Blazewicz, "Modelang - a new approach for experts-friendly viral infections modeling", Computational and Mathematical Methods in Medicine, 2013, pp. 1-8;
  • W. Frohmberg, M. Kierzynka, J. Blazewicz, P. Gawron, and P. Wojciechowski, "G-DNA - a highly efficient multi-GPU/MPI tool for aligning nucleotide reads", Bulletin of the Polish Academy of Sciences-Technical Sciences 61(4), 2013, pp. 989–992:
  • M. Kaźmierczak, M. Luczak, K. Lewandowski, L. Handschuh, A. Czyz, M. Jarmuz, M. Gniot, M. Michalak, M. Figlerowicz, M. Komarnicki, "Esterase D and gamma 1 actin level might predict results of induction therapy in patients with acute myeloid leukemia without and with maturation", Med Oncol 4, 2013, pp. 725;
  • B. Uszczyńska, J. Zyprych-Walczak, L. Handschuh, A. Szabelska, M. Kaźmierczak, W. Woronowicz, P. Kozłowski, M.M. Sikorski, M. Komarnicki, I. Siatkowski, M. Figlerowicz, "Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure", Int J Mol Med. 3, 2013, pp. 668-684;

2012

  • 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, pp. 262-271;
  • M. Popenda, M. Szachniuk, M. Antczak, K.J. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R.W. Adamiak, "Automated 3D structure composition for large RNAs", Nucleic Acids Research 40(14), 2012, doi:10.1093/nar/gks339;
  • M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R. Adamiak, "Automated 3D structure composition for large RNAs", Nucleic Acid Research 40(14), 2012, e112;
  • J. Blazewicz, M. Borowski, W. Chaara, P. Kedziora, D. Klatzmann, P. Lukasiak, A. Six, P. Wojciechowski, "GeVaDSs - decision support system for novel Genetic Vaccine development process", BMC Bioinformatics 13, 2012, pp. 91;
  • J. Blazewicz, M.Kasprzak, "Complexity issues in computational biology", Fundamenta Informaticae 118, 2012, pp. 385-401;
  • 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, pp. 262-271;
  • M. Radom, A. Rybarczyk, R. Kottmann, P. Formanowicz, M. Szachniuk, F.O. Glöckner, D. Rebholz-Schuhmann, J. Blazewicz, "Poseidon: An information retrieval and extraction system for metagenomic marine science", Ecological Informatics 12, 2012, pp. 10-15;
  • M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Łukasiak, N. Bartol, J. Blazewicz, R. Adamiak, "Automated 3D structure composition for large RNAs", Nucleic Acid Research 40(14), 2012, e112;
  • W. Frohmberg, M. Kierzynka J. Blazewicz, P. Wojciechowski, "G-PAS 2.0-an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs", Bulletin of the Polish Academy of Sciences-Technical Sciences 60, 2012, pp. 491-494;
  • M. Luczak, M. Kazmierczak, L. Handschuh, K. Lewandowski, M. Komarnicki, M. Figlerowicz, "Comparative proteome analysis of acute myeloid leukemia with and without maturation", J Proteomics 75 (18):5734-48, 2012;
  • M. Luczak, M. Kaźmierczak, L. Handschuh, K. Lewandowski, M. Komarnicki, M. Figlerowicz, "Comparative proteomics in acute myeloid leukemia", Współczesna Onkologia/Contemporary Oncology 16 (2), 2012, pp. 95–103;
  • A. Kulik, A. Anielska-Mazur, M. Bucholc, E. Koen, K. Szymanska, A. Zmienko, E. Krzywinska, I. Wawer, F. McLoughlin, D. Ruszkowski, M. Figlerowicz, C. Testerink, A. Sklodowska, D. Wendehenne, G. Dobrowolska, "SNF1-related protein kinases type 2 are involved in plant responses to cadmium stress", Plant Physiol. 160, 2012, pp. 868-883;

2011

  • J. Blazewicz, M. Figlerowicz, M. Kasprzak, M. Nowacka, A. Rybarczyk, "RNA Partial Degradation Problem: motivation, complexity, algorithm", Journal of Computational Biology 18, 2011, pp. 821-834;
  • J. Blazewicz, P. Formanowicz, P.Kedziora, P.Marciniak, P.Taront, "Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction", Annals of Operations Research 183, 2011, pp. 75-94;
  • J. Blazewicz, M. Figlerowicz, M. Kasprzak, M. Nowacka, A. Rybarczyk, "RNA Partial Degradation Problem: motivation, complexity, algorithm", Journal of Computational Biology 18, 2011, pp. 1-14;
  • D. Formanowicz, A. Sackmann, A. Kozak, J. Blazewicz, P. Formanowicz, "Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach", Bioprocess and Biosystems Engineering 34, 2011, pp. 581-595;
  • J. Blazewicz, W. Frohmberg, M. Kierzynka, E. Pesch, P. Wojciechowski, "Protein alignment algorithms with an efficient backtracking routine on multiple GPUs", BMC Bioinformatics 12, 2011, pp. 181;
  • M. Antczak, J. Blazewicz, P. Łukasiak, M. Miłostan, N. Krasnogor, G. Palik, "DomAns - pattern based method for protein domain boundaries prediction and analysis", Foundations of Computing and Decision Sciences 36, 2011, pp. 99-119;
  • M.T. Schmidt, L. Handschuh, J. Zyprych, A. Szabelska, A.K. Olejnik-Schmidt, I. Siatkowski, M. Figlerowicz, "Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods", Acta Biochim. Pol. 58 (4), 2011, pp. 573-580;
  • A. Zmienko, M. Guzowska-Nowowiejska, R. Urbaniak, W. Plader, P. Formanowicz, M. Figlerowicz, "A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants", Plant Methods 7, 2011, pp. 29;
  • M. Luczak, D. Formanowicz, E. Pawliczak, M. Wanic-Kossowska, A. Wykretowicz, M. Figlerowicz, "Chronic kidney disease-related atherosclerosis - proteomic studies of blood plasma", Proteome Science 9, 2011, pp. 25;.