Publications

2015

  • Zmienko A, Samelak-Czajka A, Goralski M, Sobieszczuk-Nowicka E, Kozlowski P, Figlerowicz M. Selection of Reference Genes for qPCR- and ddPCR-Based Analyses of Gene Expression in Senescing Barley Leaves. PLoS One. 2015 Feb 27;10(2):e0118226. doi: 10.1371/journal.pone.0118226. eCollection 2015. PubMed PMID: 25723393; PubMed Central PMCID: PMC4344324.
  • Sobieszczuk-Nowicka E, Zmienko A, Samelak-Czajka A, Łuczak M, Pietrowska-Borek M, Iorio R, Del Duca S, Figlerowicz M, Legocka J. Dark-induced senescence of barley leaves involves activation of plastid transglutaminases. Amino Acids. 2015 Jan 13. [Epub ahead of print] PubMed PMID: 25583605.
  • Kubala S, Garnczarska M, Wojtyla Ł, Clippe A, Kosmala A, Żmieńko A, Lutts S, Quinet M. Deciphering priming-induced improvement of rapeseed (Brassica napus L.) germination through an integrated transcriptomic and proteomic approach. Plant Sci. 2015 Feb;231:94-113. doi: 10.1016/j.plantsci.2014.11.008. Epub 2014 Nov 29. PubMed PMID: 25575995.
  • Lewandowska MA, Czubak K, Klonowska K, Jozwicki W, Kowalewski J, Kozlowski P. The Use of a Two-Tiered Testing Strategy for the Simultaneous Detection of Small EGFR Mutations and EGFR Amplification in Lung Cancer. PLoS One. 2015 Feb 26;10(2):e0117983. 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) 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, 134-149 (SI), DOI: 10.1016/j.dam.2014.04.010
  • Zyprych-Walczak J, Szabelska A, Handschuh L, Górczak K, Klamecka K, Figlerowicz M, Siatkowski I, The impact of normalization methods on RNA-seq data analysis. BioMed Research International – in press
  • Janus P, Stokowy T, Jaksik R, Szoltysek K, Handschuh L, Podkowinski J, Widlak W, Kimmel M, Widlak P, 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
  • Gurda D, Handschuh L, Kotkowiak W, Jakubowski H, Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells. Amino Acids. 2015
  • Zmienko A, , Goralski M, Samelak-Czajka A, Sobieszczuk-Nowicka E, Figlerowicz M. (2015) Time course transcriptional profiling of senescing barley leaves. Genomics Data 4:78-81. doi:10.1016/j.gdata.2015.03.006
  • Klonowska K, Ratajska M, Czubak A, Kuzniacka A, Brozek I, Koczkowska M, Sniadecki M, Debniak J, Wydra D, Stukan M, Zmienko A, Finger II, Limon J, Kozlowski P. (2015) Analysis of large mutations in BARD1 gene in patients with breast and/or ovarian cancer. Scientific Reports in press.
  • M. Szachniuk, Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms, Bulletin of the Polish Academy of Sciences Technical Sciences 63(1), 2015, 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, 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. SzachniukRNApdbee - 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) 155-165.
  • A. Świercz, B. Bosak, M. Chłopkowski, 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.
  • 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. Cicheński, 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.
  • A. Swiercz, B. Bosak, M. Chłopkowski, A. Hoffa, M. Kasprzak, K. Kurowski, T. Piontek, J. Błazewicz, Preprocessing and storing high-throughput sequencing data, Computational Methods in Science and Technology 20, 2014, pp. 9-20
  • 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
  • Korfanty J, Stokowy T, Widlak P, Gogler-Piglowska A, Handschuh L, Podkowiński J, Vydra N, Naumowicz A, Toma-Jonik A, Widlak W, Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes. Int J Biochem Cell Biol. 2014 Dec;57:76-83
  • Kowalczykiewicz D, Świercz A, Handschuh L, Leśniak K, Figlerowicz M, Wrzesinski J, Characterization of Sus scrofa small non-coding RNAs present in both female and male gonads. PLoS One. 2014 Nov 21;9(11):e113249
  • Żmieńko A, Samelak A, Kozłowski P, Figlerowicz M. (2014) Copy number polymorphism in plant genomes. Theor Appl Genet. 127(1): 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, 2013, RNAlyzer – novel approach for quality analysis of RNA structural models, Nucleic Acid Research, Nucleic Acid Research 41, 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, 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
  • Kaźmierczak M, Luczak M, Lewandowski K, Handschuh L, Czyż A, Jarmuż M, Gniot M, Michalak M, Figlerowicz M, Komarnicki M, 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. 2013 Dec;30(4):725
  • Uszczyńska B, Zyprych-Walczak J, Handschuh L, Szabelska A, Kaźmierczak M, Woronowicz W, Kozłowski P, Sikorski MM, Komarnicki M, Siatkowski I, Figlerowicz M, Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure. Int J Mol Med. 2013 Sep;32(3):668-84

2012

  • J. Blazewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek, A. Świercz, "Highly efficient parallel approach to the next-generation DNA sequencing", Lecture Notes in Computer Science 7204 (2012) 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, e112 (doi:10.1093/nar/gks339).
  • M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R. Adamiak, 2012, Automated 3D structure composition for large RNAs, Nucleic Acid Research, 40(14), e112
  • J. Blazewicz, M. Borowski, W. Chaara, P. Kedziora, D. Klatzmann, P. Lukasiak, A. Six, P. Wojciechowski, 2012, GeVaDSs - decision support system for novel Genetic Vaccine development process, BMC Bioinformatics, 13:91
  • 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. Świercz, 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
  • Luczak M, Kaźmierczak M, Handschuh L, Lewandowski K, Komarnicki M, Figlerowicz M. Comparative proteome analysis of acute myeloid leukemia with and without maturation. J Proteomics. 2012 Oct 22;75(18):5734-48
  • Luczak M, Kaźmierczak M, Handschuh L, Lewandowski K, Komarnicki M, Figlerowicz M. Comparative proteomics in acute myeloid leukemia, Współczesna Onkologia/Contemporary Oncology 2012; 16 (2): 95–103
  • Kulik A, Anielska-Mazur A, Bucholc M, Koen E, Szymańska K, Żmieńko A, Krzywińska E, Wawer I, McLoughlin F, Ruszkowski D, Figlerowicz M, Testerink C, Skłodowska A, Wendehenne D, Dobrowolska G (2012) SNF1-related protein kinases type 2 are involved in plant responses to cadmium stress. Plant Physiol. 2012 160: 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) 821-834.
  • J. Blazewicz, P. Formanowicz, P.Kędziora, 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. Błażewicz, 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, 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
  • Schmidt MT, Handschuh L, Zyprych J, Szabelska A, Olejnik-Schmidt AK, Siatkowski I, Figlerowicz M, Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods. Acta Biochim Pol. 2011;58(4):573-80
  • A. Żmieńko, M. Guzowska-Nowowiejska, R. Urbaniak, W. Pląder, P. Formanowicz, M. Figlerowicz, A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants. Plant Methods 7, 29 (2011)
  • M. Łuczak, D. Formanowicz, E. Pawliczak, M. Wanic-Kossowska, A. Wykrętowicz, M. Figlerowicz, Chronic kidney disease-related atherosclerosis -proteomic studies of blood plasma. Proteome Science 9, 25 (2011).