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ACHIEVEMENTS
ACHIEVEMENTS
We are proud of...
2009


  1. A. Sackmann, D. Formanowicz, P. Formanowicz, J. Blazewicz (2009). New insights into the human body iron metabolism analyzed by a Petri net based approach. Biosystems 96, pp. 104-113.

  2. J. Podkowinski, A. Zmienko, B. Florek, P. Wojciechowski, A. Rybarczyk, J. Wrzesinski, J. Ciesiolka, J. Blazewicz, A. Kondorosi, M. Crespi, A. Legocki (2009). Translational and structural analysis of the shortest legume enod40 gene in Lupinus luteus. Acta Biochimica Polonica 56, pp. 89-102.

  3. J. Blazewicz, M. Bryja, M. Figlerowicz, P. Gawron, M. Kasprzak, E. Kirton, D. Platt, J. Przybytek, A. Swiercz, L. Szajkowski (2009). Whole genome assembly from 454 sequencing output via modified DNA graph concept. Computational Biology and Chemistry 33, pp. 224-230.

  4. J. Blazewicz, D. Formanowicz, P. Formanowicz, A. Sackmann, M. Sajkowski (2009). Modeling the process of human body iron homeostasis using a variant of timed Petri nets. Discrete Applied Mathematics 157, pp. 2221-2231.

  5. M. Figlerowicz, P. Jackowiak, M. Alejska, N. Malinowska, A. Kowala-Piaskowska, P. Kedziora, P. Formanowicz, J. Blazewicz, M. Figlerowicz (2009). Two types of viral quasispecies identified in children suffering from chronic hepatitis C. Journal of Hepatology 55, pp. 27.

  6. J. Blazewicz, D. Formanowicz, P. Formanowicz (2009). Zastosowanie sieci Petriego do modelowania procesow biologicznych. Kosmos 58, pp. 79-88.

  7. J. Blazewicz, P. Lukasiak (2009). System wspomagania wytwarzania i analizy szczepionek genetycznych. Kosmos 58, pp. 113-126.

  8. J. Blazewicz, E. Burke, M. Kasprzak, A. Kovalev, M.Y. Kovalyov (2009). On the approximability of the Simplified Partial Digest Problem. Discrete Applied Mathematics 157, pp. 3586-3592.

  9. J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, P. Jackowiak (2009). Sequence Similarity Based Method For Protein Function Prediction. Foundations of Computing and Decision Sciences 34, pp. 173-192.

  10. J. Blazewicz, P. Formanowicz, P. Wojciechowski (2009). Some remarks on evaluation of quality of the multiple sequence alignment based on BAliBASE benchmark. International Journal of Applied Mathematics and Computer Science 19, pp. 675-678.

  11. M. Kasprzak, A. Swiercz (2009). Sekwencjonowanie i asemblacja DNA – podejscia, modele grafowe, algorytmy. Kosmos 58, pp. 17-28.

2008


  1. J. Blazewicz, M. Kasprzak (2008). Graph reduction and its application to DNA sequence assembly. Bulletin of the Polish Academy of Sciences. Technical Sciences 56, pp. 65-70.

  2. N. Krasnogor, A.A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz (2008). Web and Grid technologies in bioinformatics, computational and systems biology: a review. Current Bioinformatics 3, pp. 10-31.

  3. M. Stobiecki, M. Borowski, K. Rosiak, P. Kachlicki, D. Muth, J. Blazewicz (2008). Plant phenolic secondary metabolites mass spectra database. Acta Biochimica Polonica 55, Suppl.2, P3.9.

  4. J. Blazewicz, M. Kasprzak, B. Leroy-Beaulieu, D. de Werra (2008). Finding Hamiltonian circuits in quasi-adjoint graphs. Discrete Applied Mathematics 156, pp. 2573-2580.

  5. M. Popenda, M. Blazewicz, M. Szachniuk, R.W. Adamiak (2008). RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Research 36, D386-D391.

  6. J. Blazewicz, M. Kasprzak, A. Swiercz, M. Figlerowicz, P. Gawron, D. Platt, L. Szajkowski (2008). Parallel implementation of the novel approach to genome assembly. Proceedings of SNPD 2008,R. Lee, P. Muenchaisri, W. Dosch (eds.) Los Alamitos: IEEE Computer Society, pp. 732-737.

2007


  1. J. Blazewicz, K. Ecker, B. Hammer (ed.) (2007). ICOLE 2007, Lessach, Austria, Ifi Technical Series Ifi-07-03, Clausthal University of Technology.

  2. A. Kryshtafovych, A. Prlic, Z. Dmytriv, P. Daniluk, M. Milostan, V. Eyrich, T. Hubbard, K. Fidelis (2007). New tools and expanded data analysis capabilities at the protein structure prediction center. Proteins: Structure, Function, and Bioinformatics, doi:10.1002/prot.21653.

  3. D. Barthel, J.D. Hirst, J. Blazewicz, E.K. Burke, N. Krasnogor (2007). ProCKSI: A Decision Support System for Protein (Structure) Comparison, Knowledge, Similarity and Information. BMC Bioinformatics 8:416.

  4. J. Blazewicz, P. Lukasiak, S. Wilk (2007). New machine learning methods for prediction of protein secondary structure. Control and Cybernetics 36/1, pp. 183-201.

  5. M. Szachniuk, M. Popenda, S. Klemczak, J. Blazewicz (2007). Analiza trojwymiarowych widm MRJ w procesie okreslania struktury RNA. Research report RA-001/2007, Poznan. Supercomputing and Networking Center.

  6. J. Blazewicz, E. Burke, M. Kasprzak, A. Kovalev, M.Y. Kovalyov (2007). Simplified partial digest problem: enumerative and dynamic programming algorithms. IEEE/ACM Trans. on Computational Biology and Bioinformatics 4, pp. 668-680.

  7. D. Formanowicz, A. Sackmann, P. Formanowicz, J. Blazewicz (2007). Petri net based model of the body iron homeostasis. Journal of Biomedical Informatics 40/5, pp. 476-485.

  8. W. Jaskowski, J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor (2007). 3D-Judge - A Metaserver Approach to Protein Structure Prediction. Foundations of Computing and Decision Sciences 32/1, pp. 3-14.

  9. J. Blazewicz, P. Formanowicz, M. Kasprzak, P. Schuurman, G.J. Woeginger (2007). A polynomial time equivalence between DNA sequencing and the exact perfect matching problem. Discrete Optimization 4, pp. 154-162.

  10. A. Sackmann, D. Formanowicz, P. Formanowicz, I. Koch, J. Blazewicz (2007). An analysis of the Petri net based model of the human body iron homeostasis process. Computational Biology and Chemistry 31, pp. 1-10.

2006


  1. A. Spik, S. Oczkowski, A. Olszak, P. Formanowicz, J. Blazewicz, J. Jaruzelska (2006). Human fertility protein PUMILIO2 interacts in vitro with testis mRNA encoding Cdc42 effector 3 (CEP3). Reproductive Biology 6, pp. 103-113.

  2. J. Bacardit, M. Stout, J.D. Hirst, J. Blazewicz, N. Krasnogor (2006). Coordination number prediction using learning classifier systems: performance and interpretability. Proc. of the 2006 Genetic and Evolutionary Computation Conference (GECCO), ACM Press New York, NY, pp. 247-254.

  3. M. Stout, J. Bacardit, J.D. Hirst, J. Blazewicz, N. Krasnogor (2006). Prediction of residue exposure and contact number for simplified hp lattice model proteins using learning classifier systems. Proc. of the 7th International FLINS Conference on Applied Artificial Intelligence, World Scientific, pp. 601-608.

  4. J. Blazewicz, M. Kasprzak (2006). On the complexity of the DNA simplified partial digest problem. Proc. of the Twelfth Australasian Computing Theory Symposium (CATS 2006), pp. 93-100.

  5. A. Spik, S. Oczkowski, A. Olszak, M. Kotecki, P. Formanowicz, J. Blazewicz, J. Jaruzelska (2006). Candidate mRNAs interacting with fertility protein PUMILIO2 in the human germ line. Reproductive Biology 6, pp. 37-42.

  6. J. Blazewicz, C. Oguz, A. Swiercz, J. Weglarz (2006). DNA sequencing by hybridization via genetic search. Operations Research54/6, pp. 1185-1192.

  7. J. Blazewicz, B. Dziurdza, W.T. Markiewicz, C. Oguz (2006). The parallel genetic algorithm for designing DNA randomizations in a combinatorial protein experiment. Lecture Notes In Computer Science 3911, pp. 1097-1105.

  8. J. Blazewicz, F. Glover, M. Kasprzak, W.T. Markiewicz, C. Oguz, D. Rebholz-Schuhmann, A. Swiercz (2006). Dealing with repetitions in sequencing by hybridization. Computational Biology and Chemistry 30/5, pp 313-320.

  9. J. Blazewicz, P. Lukasiak, M. Milostan (2006). Some operations research methods for analyzing protein sequences and structures. 4OR: A Quarterly Journal of Operations Research4, pp. 91-123.

  10. J. Blazewicz, M. Kasprzak (2006). Computational complexity of isothermic DNA sequencing by hybridization. Discrete Applied Mathematics 154, pp. 718-729.

  11. M. Stout, J. Bacardit, J. D. Hirst, N. Krasnogor, J. Blazewicz (2006). From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems. Lecture Notes in Computer Science 3907, pp. 208-220.

2005


  1. J. Blazewicz, M. Kasprzak (2005). Combinatorial optimization in DNA mapping - a computational thread of the Simplified Partial Digest Problem. RAIRO - Operations Research 39, pp. 227-242.

  2. P. Formanowicz (2005). Selected combinatorial aspects of biological sequence analysis. Publishing House of Poznan University of Technology, Poznan.

  3. P. Formanowicz, L. Handschuh, R. Urbaniak, J. Blazewicz, M. Figlerowicz (2005). Projektowanie macierzy DNA. Na Pograniczu Chemii i Biologii XII, pp. 513-530.

  4. M. Figlerowicz, P. Formanowicz, P. Kedziora, M. Alejska, P. Jackowiak, J. Blazewicz, W. Sluzewski, M. Figlerowicz (2005). Znaczenie kliniczne zmian w populacji HCV w pierwszych tygodniach leczenia przewleklego zapalenia watroby typu C interferonem i rybawiryna. Przeglad Epidemiologiczny 59, pp. 581-590.

  5. P. Kedziora, M. Figlerowicz, P. Formanowicz, M. Alejska, P. Jackowiak, N. Malinowska, A. Fratczak, J. Blazewicz, M. Figlerowicz (2005). Computational methods in diagnostics of chronic hepatitis C. Bulletin of the Polish Academy of Sciences, Technical Sciences 53/3, pp. 273-281.

  6. J. Blazewicz, M. Borowski, P. Formanowicz, T. Glowacki (2005). On graph theoretical models for peptide sequence assembly. Foundations of Computing and Decision Sciences 30, pp. 183-191.

  7. J. Blazewicz, M. Borowski, P. Formanowicz, M. Stobiecki (2005). Tabu search method for determining sequences of amino acids in long polypeptides. Lecture Notes in Computer Science 3449, pp. 22-32.

  8. J. Blazewicz, M. Szachniuk, A. Wojtowicz (2005). RNA tertiary structure determination: NOE pathways construction by tabu search. Bioinformatics 21/10, pp. 2356-2361.

  9. J. Blazewicz, P.L. Hammer, P. Lukasiak (2005). Predicting secondary structures of proteins. IEEE Engineering in Medicine and Biology 24, pp. 88-94.

  10. J. Blazewicz, P. Lukasiak, M. Milostan (2005). Application of tabu search strategy for finding low energy structure of protein. Artificial Intelligence in Medicine 35, pp. 135-145.

  11. A. Urbanowicz, M. Alejska, P. Formanowicz, J. Blazewicz, M. Figlerowicz, J.J. Bujarski (2005). Homologous Crossovers among Molecules of Brome Mosaic Bromovirus RNA1 or RNA2 Segments in vivo. Journal of Virology 79/9, pp. 5732-5742.

  12. J. Blazewicz, P. Formanowicz (2005). Multistage isothermic sequencing by hybridization. Computational Biology and Chemistry 29, pp. 69-77.

  13. J. Blazewicz, F. Glover, M. Kasprzak (2005). Evolutionary approaches to DNA sequencing with errors. Annals of Operations Research 138, pp. 67-78.

  14. R.W. Adamiak, J. Blazewicz, Z. Gdaniec, L. Popenda, M. Szachniuk (2005). NMR Analysis of RNA Bulged Structures: Tabu Search Application in NOE Signal Assignment. Proc. of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, La Jolla, CA, pp. 172-178.

  15. J. Blazewicz, P. Formanowicz, M. Kasprzak (2005). Selected combinatiorial problems of computational biology. European Journal of Operational Research 161, pp. 585-597.

2004


  1. P. Formanowicz (2004). Resolving power of isithermic DNA sequencing chips. Bulletin of the Polish Academy of Sciences, Technical Sciences 52, pp. 231-237.

  2. M. Kasprzak (2004). An algorithm for isothermic DNA sequencing. Bulletin of the Polish Academy of Sciences, Technical Sciences 52, pp. 31-35.

  3. M. Kasprzak (2004). On the link between DNA sequencing and graph theory. Computational Methods in Science and Technology 10, pp. 39-47.

  4. M. Kasprzak (2004). Combinatorial models and methods for reading genomic sequences. Wydawnictwo Politechniki Poznanskiej, Rozprawy nr 383, Poznan.

  5. J. Blazewicz, M. Szachniuk, A. Wojtowicz (2004). Evolutionary approach to NOE Paths Assignment in RNA Structure Elucidation. Proc. of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, La Jolla, CA, pp. 206-213.

  6. J. Blazewicz, M. Szachniuk, A. Wojtowicz (2004). Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chain. Bulletin of the Polish Academy of Sciences, Technical Sciences 52/3, pp. 221-230.

  7. J. Blazewicz, M. Figlerowicz, P. Formanowicz, M. Kasprzak, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera, M. Wiktorczyk (2004). Assembling SARS-CoV genome - new method based on graph theoretic approach. Acta Biochimica Polonica51/4, pp. 983-993.

  8. J. Blazewicz, P.Formanowicz, M. Kasprzak, W.T. Markiewicz (2004). Sequencing by hybridization with isothermic oligonucleotide libraries. Discrete Applied Mathematics145, pp. 40-51.

  9. J. Blazewicz, M. Figlerowicz, P. Jackowiak, D. Janny, D. Jarczynski, M. Kasprzak, M. Nalewaj, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera (2004). Parallel DNA Sequence Assembly. Proc. ENC 2004, IEEE Computer Press, Alamitos, CA, pp. 378-382.

  10. J. Blazewicz, K. Dill, P. Lukasiak, M. Milostan (2004). A tabu search strategy for finding low energy structures of proteins in HP-model. Computational Methods in Science and Technology10, pp. 7-19.

  11. J. Blazewicz, P. Formanowicz, P. Kedziora, P. Wojciechowski (2004). Parallel algorithms for evolutionary history reconstruction. Lecture Notes in Computer Science3019, pp. 1138-1145.

  12. R.W. Adamiak, J. Blazewicz, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, M. Szachniuk (2004). An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes. Journal of Computational Biology 11, pp. 167-183.

  13. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Swiercz (2004). Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries. Computational Biology and Chemistry 28, pp. 11-19.

  14. J. Blazewicz, F. Glover, M. Kasprzak (2004). DNA sequencing - tabu and scatter search combined. INFORMS Journal on Computing 16, pp. 232-240.

  15. J. Blazewicz, E. Burke, M. Jaroszewski, M. Kasprzak, B. Paliswiat, M. Pryputniewicz (2004). On the complexity of the Double Digest Problem. Control and Cybernetics 33, pp. 133-140.

  16. M. Kasprzak (2004). ASM - DNA assembly application. Research report RA-001/2004. Poznan Supercomputing and Networking Center.

2003


  1. J. Blazewicz, M. Kasprzak (2003). Determining genome sequences from experimental data using evolutionary computation. Chapter 3 in Evolutionary Computation in Bioinformatics, G.B. Fogel, D.W. Corne (eds.), San Francisco: Morgan Kaufmann Publishers.

  2. J. Blazewicz, B. Dziurdza, W. T. Markiewicz (2003). Artificial evolution. An algorithm for an exploration of the amino acid sequences spaces. Foundations of Computing and Decision Sciences 28, pp. 195-209.

  3. M. Szachniuk, R.W. Adamiak, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, J. Blazewicz (2003). A combinatorial analysis of 2D NMR spectra of RNA duplexes. Currents in Computational Molecular Biology, Rainer Spang, Patricia Beziat, Martin Vingron (eds.), pp. 345-346.

  4. J. Blazewicz, M. Jaroszewski (2003). New algorithm for the Simplified Partial Digest Problem. Lecture Notes in Bioinformatics 2812, pp. 95-110.

  5. J. Blazewicz, P. Formanowicz, R. Urbaniak (2003). DNA based algorithms for some scheduling problems. Lecture Notes in Computer Science 2611, pp. 673-683.

  6. J. Blazewicz, M. Kasprzak (2003). Complexity of DNA sequencing by hybridization. Theoretical Computer Science 290, pp. 1459-1473.

  7. J. Blazewicz, P. Formanowicz, P. Kedziora, P. Wojciechowski (2003). Parallel implementation of algorithms for evolutionary history reconstruction on SUN Fire 6800 computer. Research Report RA-004/2003. Poznan Supercomputing and Networking Center.

  8. P. Formanowicz, K. Kwarciak (2003). Zastosowanie teorii jezykow formalnych do wykrywania genow kodujacych RNA. Research Report RB-038/03. Institute of Computing Science, Poznan University of Technology.

  9. J. Blazewicz, M. Jaroszewski, M. Kasprzak, B. Paliswiat, P. Pryputniewicz (2003). On the complexity of the double digest problem. Research Report 74. Laboratoire Leibniz-IMAG, Grenoble.

  10. J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz (2003). Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries. Research report 11. Mathematical Biosciences Institute, Ohio State University.