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ACHIEVEMENTS
ACHIEVEMENTS
We are proud of...
2016


  1. M. Milostan, P. Łukasiak (2016). DomGen-Graph based method for protein domain delineation, RAIRO-Oper. Res. 50 (2016) 363-374 (doi:10.1051/ro/2015040)

  2. J. Wiedemann, M. Milostan (2016). StructAnalyzer-a tool for sequence vs. structure similarity analysis, Acta Biochimica Polonica 63(4), 2016, 753-757

  3. M. Turkay, G. Felici, M. Szachniuk, P. Lukasiak (2016). Recent advances in operations research in computational biology, bioinformatics and medicine, RAIRO - Operations Research 50(2), 2016, 327-330 (doi:10.1051/ro/2015036).

  4. T. Prejzendanc, S. Wasik, J. Blazewicz (2016). Computer representations of bioinformatics models. Current Bioinformatics 11(5): 551-560. doi: 10.2174/1574893610666150928193510

  5. M. Antczak, M. Popenda, T. Zok, J. Sarzynska, T. Ratajczak, K. Tomczyk, R.W. Adamiak, M. Szachniuk (2016). New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure. Acta Biochimica Polonica doi: 10.18388/abp.2016_1329

  6. M. Chlopkowski, M. Antczak, M. Slusarczyk, A. Wdowinski, M. Zajaczkowski, M. Kasprzak (2016). High-order statistical compressor for long-term storage of DNA sequencing data. RAIRO Operations Research 50, pp. 351-361.

  7. N. Szostak, S. Wasik, J. Blazewicz (2016). Hypercycle. PLOS Comput Biol. 12:e1004853

  8. A. Mickiewicz, A. Rybarczyk, J. Sarzynska, M. Figlerowicz, J. Blazewicz (2016). AmiRNA Designer - new method of artificial miRNA design. Acta Biochimica Polonica 19.

  9. M. Marcinkowska-Swojak, L. Handschuh, P. Wojciechowski, M. Goralski, K. Tomaszewski, M. Kazmierczak, K. Lewandowski, M. Komarnicki, J. Blazewicz, M. Figlerowicz, P. Kozlowski (2016). A new MLPA-based method for the detection of acute myeloid leukemia-specific NPM1 mutations and simultaneous analysis of gene copy number alterations. Mutation Research. 786, pp.14-26

  10. M. Antczak, M. Kasprzak, P. Lukasiak, J. Blazewicz (2016). Structural alignment of protein descriptors – a combinatorial model. BMC Bioinformatics 17, pp. 383 doi:10.1186/s12859-016-1237-9

  11. A. Rybarczyk, P. Jackowiak, M. Figlerowicz, J. Blazewicz (2016). Computational prediction of non-enzymatic RNA degradation patterns. Acta biochimica Polonica

  12. P. Wojciechowski, W. Frohmberg, M. Kierzynka, P. Zurkowski, J. Blazewicz (2016). G-MAPSEQ – a new method for mapping reads to a reference genome. Foundations of Computing and Decision Sciences 41(2), pp. 123–142, doi: 10.1515/fcds-2016-0007

2015


  1. S. Wasik, F. Fratczak, J. Krzyskow, J. Wulnikowski (2015). Inferring Mathematical Equations Using Crowdsourcing. PLoS One 10(12):e0145557. doi: 10.1371/journal.pone.0145557. eCollection 2015.

  2. K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz, R.W. Adamiak (2015). Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in Shi-Jie Chen, Donald H. Burke-Aguero (eds.) Methods in Enzymology: Computational Methods for Understanding Riboswitches 553, 2015, pp. 3-34.

  3. M. Biesiada, K.J. Purzycka, M. Szachniuk, J. Blazewicz, R.W. Adamiak (2015). Automated RNA 3D structure prediction with RNAComposer: guidance for molecular biologists, in Doug Turner, David Mathews (eds.) Methods in Molecular Biology: RNA Structure Determination, Springer, Humana Press, 2015.

  4. M. Szachniuk (2015). Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms. Bulletin of the Polish Academy of Sciences Technical Sciences 63(1), pp. 329-338.

  5. M. Szachniuk, M.C. De Cola, G. Felici, D. de Werra, J. Blazewicz (2015). Optimal pathway reconstruction on 3D NMR maps. Discrete Applied Mathematics 182, pp. 134-149.

  6. T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk (2015). Building the library of RNA 3D nucleotide conformations using clustering approach, International Journal of Applied Mathematics and Computer Science, 2015, 25(3), pp. 689-700 (doi:10.1515/amcs-2015-0050.

  7. 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 (2015). RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures, RNA 21(6), pp. 1-19.

  8. A. Rybarczyk, N. Szostak, M. Antczak, T. Zok, M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk, New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics, 2015, 16(1), pp. 276 (doi:10.1186/s12859-015-0718-6).

  9. P. Lukasiak, M. Antczak, T. Ratajczak, M. Szachniuk, M. Popenda, R.W. Adamiak, J. Blazewicz, RNAssess - a web server for quality assessment of RNA 3D structures, Nucleic Acids Research, 2015, 43(W1), pp. W502-506 (doi:10.1093/nar/gkv557).

  10. M. Chlopkowski, M. Antczak, M. Slusarczyk, A. Wdowinski, M. Zajaczkowski, M. Kasprzak, High-order statistical compressor for long-term storage of DNA sequencing data, RAIRO - Operations Research, 2015, 10 (doi:10.1051/ro/2015039).

  11. M. Turkay, G. Felici, M. Szachniuk, P. Lukasiak, Recent advances in operations research in computational biology, bioinformatics and medicine, RAIRO - Operations Research 10, 2015, 1-3 (doi:10.1051/ro/2015036).

2014

  1. T. Zok, M. Popenda, M. Szachniuk (2013). MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research 22(3), pp. 457-474.

  2. J. Blazewicz, M. Szachniuk, N. Szostak, G-W. Weber (2014). Historic Venue for a Young Group of an Emerging Field. IFORS News 8(3), pp.9.

  3. N. Szostak, F. Royo, A. Rybarczyk, M. Szachniuk, J. Blazewicz, A. del Sol, J.M. Falcon-Perez (2014). Sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biology 11(7), 2014, 836-844 (doi:10.4161/rna.29305).

  4. D. Santoni, A. Świercz, A. Żmienko, M. Kasprzak, M. Błażewicz, P. Bertolazzi, G. Felici (2014). 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, pp.155-165.

  5. M. Antczak, T. Zok, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz, M. Szachniuk (2014). RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Research 2014, W368-W372. (doi:10.1093/nar/gku330)

  6. M. Szachniuk, M.C. De Cola, G. Felici, J. Blazewicz (20134). The Orderly Colored Longest Path Problem - a survey of applications and new algorithms. RAIRO Operations Research 48(1), pp. 25-51 (doi:10.1051/ro/2013046).

  7. S. Wasik, P. Jackowiak, M. Figlerowicz, J. Blazewicz (2014). Multi-agent model of hepatitis c virus infection.
    Artificial intelligence in medicine 60, pp.123-131.

  8. P. Wojciechowski, P. Formanowicz, J Blazewicz (2014). Reference alignment based methods for quality evaluation of multiple sequence alignment - a survey. Current Bioinformatics 9, pp. 44-56.

  9. A. Swiercz, B. Bosak, M. Chłopkowski, A. Hoffa, M. Kasprzak, K. Kurowski, T. Piontek, J. Błazewicz (2014). Preprocessing and storing high-throughput sequencing data. Computational Methods in Science and Technology 20, pp. 9-20.

  10. G-W. Weber, J. Blazewicz, M. Rauner, M. Türkay (2014). Recent advances in computational biology, bioinformatics, medicine, and healthcare by modern OR. CEJOR 22, pp. 427-430.

  11. A. Swiercz, E.K. Burke, M. Cicheński, G. Pawlak, S. Petrovic, T. Zurkowski, J. Blazewicz (2014). Unified encoding for hyper-heuristics with application to bioinformatics. CEJOR 22, pp.567-589.

2013


  1. S. Wasik, T. Prejzendanc, J. Blazewicz (2013). Modelang -- a new approach for experts-friendly viral infections modeling. Computational and Mathematical Methods in Medicine 2013, pp. 1-8.

  2. A. Swiercz, E.K. Burke, M. Cicheński, G. Pawlak, S. Petrovic, T. Zurkowski, J. Blazewicz (2013). Unified encoding for hyper-heuristics with application to bioinformatics. Central European Journal of Operations Research August 2013(doi:10.1007/s10100-013-0321-8)

  3. M. Kierzynka, J. Błażewicz, W. Frohmberg, P. Wojciechowski (2013). G-MSA - GPU-based, fast and accurate algorithm for multiple sequence alignment. Journal of Parallel and Distributed Computing 73, pp.32-41.

  4. J. Blazewicz, W. Frohmberg, P. Gawron, M. Kasprzak, M. Kierzynka, A. Swiercz, P. Wojciechowski (2013). DNA sequence assembly involving an acyclic graph model. Foundations of Computing and Decision Sciences 38, pp. 25-34.

  5. M. Szachniuk, M. Malaczynski, E. Pesch, E.K. Burke, J. Blazewicz (2013). MLP accompanied beam search for the resonance assignment problem. Journal of Heuristics 19(3), pp. 443-464.

  6. P. Lukasiak, M. Antczak, T. Ratajczak, J.M. Bujnicki, M. Szachniuk, M. Popenda, R.W. Adamiak, J. Blazewicz (2013). RNAlyzer – novel approach for quality analysis of RNA structural models. Nucleic Acids Research 41(12), pp. 5978-90.

  7. J. Błażewicz, E.K. Burke, G. Kendall, W. Mruczkiewicz, C. Oguz, A. Świercz (2013). A hyper-heuristic approach to sequencing by hybridization of DNA sequences. Annals of Operations Research 207(1), 2013, pp. 27-41.

  8. M. Kasprzak (2013). Wybrane algorytmy i modele grafowe w bioinformatyce. Poznan: Wydawnictwo Politechniki Poznanskiej, 2013.

  9. J. Blazewicz, M. Kasprzak, N. Vlassis (2013). Ties between Graph Theory and Biology. Section 13.2 in Handbook of Graph Theory (second edition), J.L. Gross, J. Yellen, P. Zhang (eds.), Chapman and Hall/CRC, 2013.

2012


  1. J. Błażewicz, E.K. Burke, G. Kendall, W. Mruczkiewicz, C. Oguz, A. Świercz (2012). A hyper-heuristic approach to sequencing by hybridization of DNA sequences. Annals of Operations Research 2012, DOI 10.1007/s10479-011-0927-y.

  2. J. Błażewicz, M. Borowski, W. Chaara, P. Kędziora, D. Klatzmann, P. Łukasiak, A. Six, P. Wojciechowski (2012). GeVaDSs - decision support system for novel Genetic Vaccine development process. BMC Bioinformatics, pp. 13:91.

  3. J. Błażewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek, A. Świercz (2012). Highly efficient parallel approach to the next-generation DNA sequencing. Lecture Notes in Computer Science 7204, pp. 262-271.

  4. M. Radom, A. Rybarczyk, R. Kottmann, P. Formanowicz, M. Szachniuk, F.O. Glöckner, D. Rebholz-Schuhmann, J. Błażewicz (2012). Poseidon: An information retrieval and extraction system for metagenomic marine science. Ecological Informatics 12, pp. 10-15.

  5. M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Łukasiak, N. Bartol, J. Błażewicz, R. Adamiak (2012). Automated 3D structure composition for large RNAs. Nucleic Acid Research 40(14), e112.

  6. J. Blazewicz, M. Kasprzak (2012). Reduced-by-matching graphs: toward simplifying Hamiltonian circuit problem. Fundamenta Informaticae 118, pp. 225-244.

  7. J. Blazewicz, M. Kasprzak (2012). Complexity issues in computational biology. Fundamenta Informaticae 118, pp. 385-401.

2011


  1. J. Błażewicz, E.K. Burke, M. Kasprzak, A. Kovalev, M. Kovalyov (2011). The Simplified Partial Digest Problem: approximation and a graph-theoretic model. European Journal of Operational Research 208, pp.142-152.

  2. J. Błażewicz, P. Formanowicz, P. Kędziora, P. Marciniak, P. Taront (2011). Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction. Annals of Operations Research 183, pp. 75-94.

  3. S. Bąk, J. Błażewicz, G. Pawlak, M. Płaza, E.K. Burke, G. Kendall (2011). A parallel branch and bound approach to the rectangular guillotine strip cutting problem. INFORMS Journal on Computing 23, pp. 15-25.

  4. J. Błażewicz, M. Figlerowicz, M. Kasprzak, M. Nowacka, A. Rybarczyk (2011). RNA Partial Degradation Problem: motivation, complexity, algorithm. Journal of Computational Biology 18, pp. 821-834.

  5. D. Formanowicz, A. Sackmann, A. Kozak, J. Błażewicz, P. Formanowicz (2011). Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach. Bioprocess and Biosystems Engineering 34, pp. 581-595.

  6. J. Błażewicz, W. Frohmberg, M. Kierzynka, E. Pesch, P. Wojciechowski (2011). Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. BMC Bioinformatics 12, 181.

  7. Y. Orlovicha, J. Błażewicz, A. Dolgui, G. Finke, V. Gordon (2011). On the complexity of the independent set problem in triangle graphs. Discrete Mathematics 311, pp. 1670-1680.

  8. J. Błażewicz, E.K. Burke, G. Kendall, W. Mruczkiewicz, C. Oguz, A. Swiercz (2011). A hyper-heuristic approach to sequencing by hybridization of DNA sequences. Annals of Operations Research 2011, DOI 10.1007/s10479-011-0927-y.

  9. M. Antczak, J. Błażewicz, P. Lukasiak, M. Milostan, N. Krasnogor, G. Palik (2011). DomAns - pattern based method for protein domain boundaries prediction and analysis. Foundations of Computing and Decision Sciences 36, pp. 99-119.

2010


  1. P. Lukasiak, J. Blazewicz, M. Milostan (2010). Some operations research methods for analyzing protein sequences and structures. Annals of Operations Research 175, pp. 9-35.

  2. S. Wasik, P. Jackowiak, P. Kedziora, J. Krawczyk, P. Formanowicz, M. Figlerowicz, J. Blazewicz (2010). Towards prediction of HCV therapy efficiency. Computational and Mathematical Methods in Medicine, doi:10.1080/17486700903170712.

  3. J. Blazewicz, M. Borowski, P. Formanowicz, T. Glowacki (2010). Genetic and tabu search algorithms for peptide assembly problem. RAIRO - Operations Research 44.2, pp.153-166.

  4. J. Blazewicz, J. Musial, M. Kovalyov, A. Urbanski, A. Wojciechowski (2010). Internet Shopping Optimization problem. International Journal of Applied Mathematics and Computer Science 20 (2), pp. 385–39.

  5. J. Blazewicz, P. Formanowicz, P. Kedziora, P. Marciniak, P. Taront (2010). Adaptive memory programming: Local search parallel algorithms for phylogenetic tree construction. Annals of Operations Research 183 (1), pp.75-94.

  6. J. Blazewicz, K. Ecker, T. Kis, C.N. Potts, M. Tanas, J. Whitehead (2010). Scheduling of coupled tasks with unit processing times, Journal of Scheduling 13, pp. 453-461.

  7. J. Blazewicz, T.C.E. Cheng, M. Machowiak, C. Oguz (2010). Berth and quay crane allocation: a moldable task scheduling model. Journal of the Operational Research Society 62, pp. 1189–1197.

  8. S. Bak, J. Blazewicz, G. Pawlak, M. Plaza, E.K. Burke, G. Kendall (2010). A parallel branch and bound approach to the rectangular guillotine strip cutting problem. INFORMS J. on Computing 23.1, pp. 15-25.

  9. J. Blazewicz, V. Boljuncic, S. Martello, J. Skorin-Kapov (2010). Editorial. Combinatorial Optimization Issues in Scheduling. Journal of Scheduling 15(1).

  10. M. Bender, J. Blazewicz, E. Pesch, D. Trystram, G. Zhang (2010). New challenges in scheduling theory. Journal of Scheduling 13, pp. 451-452.

  11. M. Radom, R. Kottmann, A. Rybarczyk, P. Formanowicz, M. Szachniuk, F.O. Gloeckner, J. Blazewicz (2010). Cerberus: a new information retrieval tool for marine metagenomics. Foundations of Computing and Decision Sciences 35(2), pp. 107-126.

  12. M. Popenda, M. Szachniuk, M. Blazewicz, S. Wasik, E.K. Burke, J. Blazewicz, R.W. Adamiak (2010). RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics 11, pp. 231.