Laboratory of

Algorithm Design and Programming Systems

Institute of Computing Science, Poznań University of Technology

Publications

Books and monographs

  • M. Drozdowski, Scheduling for Parallel Processing, Springer-Verlag, London, 2009
  • A. Marciniak, Selected Interval Methods for Solving the Initial Value Problem, Publishing House of Poznań University of Technology, Poznań, 2009
  • J. Błażewicz, K. Ecker, E. Pesch, G. Schmidt, J. Węglarz, Handbook on Scheduling, Springer Verlag, Berlin, New York, 2007
  • L. Madeyski, M. Ochodek, D. Weiss, J. Zendulka, Software Engineering in Progress, NAKOM, 2007
  • M. Sterna, Late Work scheduling in shop systems, Rozprawy nr 405, Wydawnictwo Politechniki Poznańskiej, Poznań, 2006
  • P. Formanowicz. Selected combinatorial aspects of biological sequence analysis, Publishing House of Poznan University of Technology, Poznań, 2005

Articles in journals

2016

  • X Chen, M Sterna, X Han, J Blazewicz, Scheduling on parallel identical machines with late work criterion: Offline and online cases, Journal of Scheduling 2016, pp. 1-8.
  • 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
  • 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 2016, doi:10.1016/j.ejor.2016.06.043
  • 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
  • MC Lopez-Loces, J Musial, JE Pecero, HJ Fraire-Huacuja, J Blazewicz, P Bouvry, Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs, International Journal of Applied Mathematics and Computer Science 26, 2016, pp. 391-406
  • J Blazewicz, N Cheriere, PF Dutot, J Musial, D Trystram, Novel dual discounting functions for the Internet shopping optimization problem: new algorithms, Journal of Scheduling 19, 2016, pp. 245-255
  • M Cichenski, F Jaehn, G Pawlak, E Pesch, G Singh, J Blazewicz, An integrated model for the transshipment yard scheduling problem, Journal of Scheduling 2016, doi:10.1007/s10951-016-0470-4
  • 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, Computer representations of bioinformatics models 11, 2016, pp. 551-560
  • A Mickiewicz, J Sarzyńska, M Miłostan, A Kurzyńska-Kokorniak, A Rybarczyk, P Łukasiak, T Kuliński, M Figlerowicza, 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 2016, DOI 10.1016/j.compbiolchem.2016.11.003

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 2015, doi:10.1016/bs.mie.2014.10.050
  • J. Blazewicz, E. Pesch, C. Phillips, D. Trystram, GC. Zhang, New Challenges in Scheduling Theory, RAIRO-Operations Research 49 (2), 2015, 335-337, DOI: 10.1051/ro/2014047
  • J. Blazewicz, A. Hertz, C. Picouleau, M. Widmer, Special Issue: Eighth International Colloquium on Graphs and Optimization (GO VIII), 2012 Foreword, DISCRETE APPLIED MATHEMATICS 182, 2015, 1-1 (SI), DOI: 10.1016/j.dam.2014.11.011
  • 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
  • J Blazewicz, S Kedad-Sidhoum, F Monna, G Mounié, D Trystram, A study of scheduling problems with preemptions on multi-core computers with GPU accelerators, Discrete Applied Mathematics 196, 2015, pp. 72-82
  • M Guzek, A Gniewek, P Bouvry, J Musial, J Blazewicz, Cloud Brokering: Current Practices and Upcoming Challenges, IEEE Cloud Computing 2, 2015, (2)
  • A.Rybarczyk, N.Szostak, M.Antczak, T.Zok, M.Popenda, R.Adamiak, J.Blazewicz, M.Szachniuk, New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics 16:276, 2015, DOI: 10.1186/s12859-015-0718-6
  • G Kendall, R Bai, J Błazewicz, PD Causmaecker, M Gendreau, R John, J Li, B McCollum, E Pesch, R Qu, N Sabar, GV Berghe, A Yee, Good Laboratory Practice for optimization research, Journal of the Operational Research Society 2015, doi: 10.1057/jors.2015.77
  • 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 the Clustering Approach, International Journal of Applied Mathematics and Computer Science 20, 2015, pp.689-700
  • 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, doi: 10.1093/nar/gkv557
  • J. Blazewicz, E. Pesch, D.Trystram, G.C. Zhang, New perspectives in scheduling theory, Journal of Scheduling 18, 2015, pp. 333-334.

2014

  • 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.
  • M. Szachniuk, M.C. De Cola, G. Felici, J. Blazewicz, The Orderly Colored Longest Path Problem - a survey of applications and new algorithms, RAIRO Operations Research 48(1), 2014, pp.25-51.
  • J.Błażewicz, P.Bouvry, M.Kovalyov, J.Musiał, Internet shopping with price sensitive discounts, 4OR-A Quarterly for Operations Research 12, 2014, pp. 35-48.
  • 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
  • M. Szachniuk, M.C. De Cola, G. Felici, D. de Werra, J. Blazewicz, Optimal pathway reconstruction on 3D NMR maps, Discrete Applied Mathematics 2014, doi:10.1016/j.dam.2014.04.010
  • J. Blazewicz, N. Cheriere, P.-F. Dutot, J. Musial, D. Trystram, Novel dual discounting functions for the Internet shopping optimization problem: new algorithms, Journal of Scheduling 2014, DOI. 10.1007/s10951-014-0390-0
  • J. Blazewicz, P. Bouvry, M.Y. Kovalyov, J. Musial , Erratum to: Internet shopping with price-sensitive discounts, 4OR-A Quarterly for Operations Research 12, 2014, pp 403-406
  • 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
  • M Antczak, T Zok, M Popenda, P Lukasiak, RW Adamiak, J Blazewicz, M Szachniuk, RNApdbee-a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acid Research 42, 2014, pp. W368-W372

2013

  • P. Lukasiak, M. Antczak, T. Ratajczak, J.M. Bujnicki, M. Szachniuk, M. Popenda, R. Adamiak, J. Blazewicz, RNAlyzer—novel approach for quality analysis of RNA structural models, Nucleic acids research 41 (12), 5978-5990
  • J. Nawrocki, J. Jurkiewicz, M. Ochodek, T. Głowacki, HAZOP-based identification of events in use cases; Empirical Soft. Eng.
  • M. Bender, J. Blazewicz, E. Pesch, D. Trystram, G.C.Zhang, New trends in scheduling, Journal of Scheduling 16, 2013, pp. 247-348
  • M. Szachniuk, M. Malaczynski, E. Pesch, E.K. Burke, J. Blazewicz, MLP accompanied beam search for the resonance assignment problem, Journal of Heuristics 19 (3), 443-464
  • D. Formanowicz, A. Kozak, T. Głowacki, M. Radom, P. Formanowicz, Hemojuvelin–hepcidin axis modeled and analyzed using Petri nets, Journal of biomedical informatics 46 (6), 1030-1043
  • 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), 27-41
  • W. Frohmberg, M. Kierzynka, J. Blazewicz, P. Gawron, P. Wojciechowski, G-DNA–a highly efficient multi-GPU/MPI tool for aligning nucleotide reads, Bulletin PAS, TECHNICAL SCIENCES 61 (4)
  • A. Kozak, T. Głowacki, P. Formanowicz, On a generalized model of labeled graphs, Discrete Applied Mathematics 161 (13), 1818-1827
  • 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.
  • M. Kierzynka, J. Błażewicz, 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. Marszałkowski, M. Drozdowski, Optimization of column width in website layout for advertisement fit, European Journal of Operational Research vol. 226, 2013, 592-601,
  • T. Woźniak, R.W. Adamiak, Personalization of structural PDB files. Acta Biochim Pol. 2013;60(4):591-593
  • A. Kurzynska-Kokorniak, N. Koralewska, A. Tyczewska, T. Twardowski, M. Figlerowicz, A new short oligonucleotide-based strategy for the precursor-specific regulation of microRNA processing by Dicer, PLoS One, 2013, 8(10):e77703. DOI 10.1371/journal.pone.0077703.
  • A. Urbanowicz, D. Lewandowski, J. Jodynis-Liebert, C. Sadowski, M. Figlerowicz, Functional Insights into Recombinant TROSPA Protein from Ixodes ricinus. PLoS One 2013, 8(10):e76848. doi: 10.1371/journal.pone.0076848.
  • D. Lewandowski, A. Urbanowicz, M. Figlerowicz, Molecular interactions between Borrelia burgdorferi ticks and mammals, Postepy Mikrobiol. 2013 52 (1), 9-16
  • M. Nowacka, P.M. Strozycki, P. Jackowiak, A. Hojka-Osinska, M. Szymanski, M. Figlerowicz, Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions, Plant Molecular Biology, 2013, 83(3):191-204
  • 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., 2013, 32, 668-684
  • M. Marcinkowska-Swojak, B. Uszczynska, M. Figlerowicz, P. Kozlowski, An MLPA-based strategy for discrete CNV genotyping: CNV-miRNAs as an example. Hum Mutat., 2013, 34, 763-773.
  • M. Kaźmierczak, M. Luczak, K. Lewandowski, L. Handschuh, A. Czyż, M. Jarmuż, 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. Medical Oncology 2013, 30(4):725-734
  • J. Banasiak, W. Biała, A. Staszków, B. Swarcewicz, E. Kępczyńska, M. Figlerowicz, M. Jasiński, A Medicago truncatula ABC transporter belonging to subfamily G modulates the level of isoflavonoids, Journal of Experimental Botany, 2013, 64, (4) 1005-1015

2012

  • J. Błażewicz, M. Borowski, W. Chaara, P. Kędziora, D. Klatzmann, P. Łukasiak, A. Six, P. Wojciechowski, GeVaDSs - decision support system for novel Genetic Vaccine development process, BMC Bioinformatics 2012, 13:91
  • J. Błażewicz, M.Kasprzak, Complexity issues in computational biology, Fundamenta Informaticae 118, 2012, pp. 385-401
  • J. Błażewicz, E.K. Burke, V.S. Gordon, M.Y. Kovalyov, Y. M. Shafransky, V.A. Strusevich, Editorial: new branches, old roots, Journal of Scheduling 15, 2012, pp. 399-401
  • R. Bai, J. Błażewicz, E.K. Burke, G. Kendall, B. McCollum, A simulated annealing hyper-heuristic methodology for flexible decision support, 4OR-A Quarterly Journal of Operations Research 10, 2012, pp. 43-66
  • J. Błażewicz, 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
  • J. Błażewicz, M. Kasprzak, Reduced-by-matching graphs: toward simplifying Hamiltonian circuit problem, Fundamenta Informaticae 118, 2012, pp. 225-244
  • M. Radom, A. Rybarczyk, R. Kottmann, P. Formanowicz, M. Szachniuk, F.O. Glöckner, D. Rebholz-Schuhmann, J. Błażewicz, Poseidon: An information retrieval and extraction system for metagenomic marine science, Ecological Informatics 12, 2012, pp. 10-15
  • J. Błażewicz, G. Pawlak, M. Tanaś, W. Wojciechowicz, New algorithms for coupled tasks scheduling- a survey, RAIRO - Operations Research 46, 2012, pp. 335-353
  • M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Łukasiak, N. Bartol, J. Błażewicz, R. Adamiak, Automated 3D structure composition for large RNAs, Nucleic Acid Research 40(14), 2012, e112

2011

  • J. Błażewicz, E.K. Burke, M. Kasprzak, A. Kovalev, M. Kovalyov, The Simplified Partial Digest Problem: approximation and a graph-theoretic model, European Journal of Operational Research 208, 2011, pp.142-152
  • J. Błażewicz, 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
  • S. Bąk, J. Błażewicz, G. Pawlak, M. Płaza, E.K. Burke, G. Kendall, A parallel branch and bound approach to the rectangular guillotine strip cutting problem, INFORMS Journal on Computing 23, 2011, pp. 15-25
  • 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
  • J. Błażewicz, T.C.E. Cheng, M. Machowiak, C. Oguz, Berth and quay crane allocation: a moldable task scheduling model, Journal of the Operational Research Society 62, 2011, pp. 1189-1197
  • D. Formanowicz, A. Sackmann, A. Kozak, J. Błażewicz, 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. Błażewicz, W. Frohmberg, M. Kierzynka, E. Pesch, P. Wojciechowski, Protein alignment algorithms with an efficient backtracking routine on multiple GPUs, BMC Bioinformatics 12, 2011, 181
  • J. Błażewicz, V. Boljuncic, S. Martello, J. Skorin-Kapov, Combinatorial Optimization Issues in Scheduling, Journal of Scheduling 14, 2011, pp. 221-223.
  • Y. Orlovicha, J. Błażewicz, A. Dolgui, G. Finke, V. Gordon, On the complexity of the independent set problem in triangle graphs, Discrete Mathematics 311, 2011, pp. 1670-1680
  • J. Błażewicz, 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 2011, DOI 10.1007/s10479-011-0927-y
  • J. Berlińska, M. Drozdowski, Scheduling divisible MapReduce computations, J. Parallel Distrib. Computing 71, 2011, pp. 450–459
  • M. Sterna, A survey of scheduling problems with late work criteria, Omega 39(2), 2011, 120-129
  • M. Antczak, J. Błażewicz, P. Lukasiak, M. Milostan, 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
  • B. Alchimowicz, J. Nawrocki, Generating syntax diagrams from regular expressions, Foundations of Computing and Decision Sciences 36, 2011, pp. 81-97
  • M. Ochodek, B. Alchimowicz, J. Jurkiewicz, J. Nawrocki, Improving the reliability of transaction identification in use cases, Information and Software Technology 53, 2011, pp. 885-897
  • M. Ochodek, J. Nawrocki, K. Kwarciak, Simplifying effort estimation based on Use Case Points, Information and Software Technology 53, 2011, pp. 200-213

2010

  • P. Łukasiak, J. Błażewicz, M. Miłostan, Some operations research methods for analyzing protein sequences and structures, Annals of Operations Research 175, 2010, pp. 9-35
  • S. Wąsik, P. Jackowiak, P. Kędziora, J. Krawczyk, P. Formanowicz, M. Figlerowicz, J. Błażewicz, Towards prediction of HCV therapy efficiency, Computational and Mathematical Methods in Medicine 11, 2010, pp. 185-199
  • J. Błażewicz, M. Borowski, P. Formanowicz, T. Głowacki, Genetic and tabu search algorithms for peptide assembly problems, RAIRO - Operations Research 44, 2010, pp. 153-166
  • J. Błażewicz, J. Musiał, M. Kovalyov, A. Urbański, A. Wojciechowski, Internet Shopping Optimization problem, International Journal of Applied Mathematics and Computer Science 20, 2010, pp. 385-390
  • J. Błażewicz, K. Ecker, T. Kis, C.N. Potts, M. Tanas, J. Whitehead, Scheduling of coupled tasks with unit processing times, Journal of Scheduling 13, 2010, pp. 453-461
  • M. Bender, J. Błażewicz, E. Pesch, D. Trystram, G. Zhang, New challenges in scheduling theory, Journal of Scheduling 13, 2010, pp. 451-452
  • M. Figlerowicz, P. Jackowiak, P. Formanowicz, P. Kędziora, M. Alejska, N. Malinowska, J. Błażewicz, M. Figlerowicz, Hepatitis C virus quasispecies in chronically infected children subjected to interferon–ribavirin therapy, Archives of Virology 155, 2010, pp. 1977-1987
  • M. Popenda, M. Szachniuk, M. Błażewicz, S. Wasik, E.K. Burke, J. Błażewicz, R.W. Adamiak, RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics 11, 2010, p. 231
  • J. Berlińska, M. Drozdowski, Heuristics for multi-round divisible loads scheduling with limited memory, Parallel Computing 36, 2010, pp. 199–211
  • M. Drozdowski, L. Wielebski, Isoefficiency Maps for Divisible Computations, IEEE Transactions on Parallel and Distributed Systems 21, 2010, pp. 872-880
  • J. Sarzynska, A. Mickiewicz, M. Milostan, P. Lukasiak, J. Błażewicz, M. Figlerowicz, T. Kulinski, Flexibility of Dicer studied by implicit solvent molecular dynamics simulations, Computational Methods in Science and Technology 16, 2010, pp. 97-104
  • M. Radom, P. Formanowicz Algoritms for sequencing by hybridization problems bases on non-classical DNA chips, Przegląd Elektrotechniczny 9, 2010, pp. 97-100
  • M. Radom, R. Kottmann, A. Rybarczyk, P. Formanowicz, M. Szachniuk, F.O. Gloeckner, J. Błażewicz, Cerberus: a new information retrieval tool for marine metagenomics, Foundations of Computing and Decision Sciences 35, 2010, pp. 107-126
  • B. Alchimowicz, J. Jurkiewicz, M. Ochodek, J. Nawrocki, Building Benchmarks for Use Cases, Computing and Informatics 29, 2010, pp. 27-44
  • M. Ochodek, J. Nawrocki, Enhancing Use-Case-Based Effort Estimation with Transaction Types, Foundations of Computing and Decision Sciences 35, 2010, pp. 91-106
  • Ł. Olek, M. Ochodek, J. Nawrocki, Enhancing Use Cases with Screen Designs, A Comparison of Two Approaches, Computing and Informatics 29, 2010, pp. 3-25
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