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

2021

  • Pigazzini, I., Fontana, F. A., & Walter, B. (2021, August). A study on correlations between architectural smells and design patterns. Journal of Systems and Software. Elsevier BV. http://doi.org/10.1016/j.jss.2021.110984
  • Vernet, M., Drozdowski, M., Pigné, Y., & Sanlaville, E. (2021, June). A theoretical and experimental study of a new algorithm for minimum cost flow in dynamic graphs. Discrete Applied Mathematics. Elsevier BV. http://doi.org/10.1016/j.dam.2019.12.012
  • Miskiewicz, J., Sarzynska, J., & Szachniuk, M. (2020, September 8). How bioinformatics resources work with G4 RNAs. Briefings in Bioinformatics. Oxford University Press (OUP). http://doi.org/10.1093/bib/bbaa201
  • Staron, M., Meding, W., Söder, O., & Ochodek, M. (2021). Improving Quality of Code Review Datasets – Token-Based Feature Extraction Method. Software Quality: Future Perspectives on Software Engineering Quality. Springer International Publishing. http://doi.org/10.1007/978-3-030-65854-0_7
  • Sterna, M. (2021, March). Late and early work scheduling: A survey. Omega. Elsevier BV. http://doi.org/10.1016/j.omega.2021.102453
  • Kaden, M., Bohnsack, K. S., Weber, M., Kudła, M., Gutowska, K., Blazewicz, J., & Villmann, T. (2021, April 27). Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences. Neural Computing and Applications. Springer Science and Business Media LLC. http://doi.org/10.1007/s00521-021-06018-2
  • Chen, X., Kovalev, S., Liu, Y., Sterna, M., Chalamon, I., & Błażewicz, J. (2021, February). Semi-online scheduling on two identical machines with a common due date to maximize total early work. Discrete Applied Mathematics. Elsevier BV. http://doi.org/10.1016/j.dam.2020.05.023
  • Ochodek, M., Kopczyńska, S., & Nawrocki, J. (2020). A Case Study on a Hybrid Approach to Assessing the Maturity of Requirements Engineering Practices in Agile Projects (REMMA). SOFSEM 2020: Theory and Practice of Computer Science. Springer International Publishing. http://doi.org/10.1007/978-3-030-38919-2_58
  • Czyzewski, M. A., Laskowski, A., & Wasik, S. (2020, December 1). Chessboard and Chess Piece Recognition With the Support of Neural Networks. Foundations of Computing and Decision Sciences. Walter de Gruyter GmbH. http://doi.org/10.2478/fcds-2020-0014
  • Ochodek, M., Kopczyńska, S., & Staron, M. (2020, July). Deep learning model for end-to-end approximation of COSMIC functional size based on use-case names. Information and Software Technology. Elsevier BV. http://doi.org/10.1016/j.infsof.2020.106310
  • Lehmann, T. P., Miskiewicz, J., Szostak, N., Szachniuk, M., Grodecka-Gazdecka, S., & Jagodziński, P. P. (2020, October 17). In Vitro and in Silico Analysis of miR-125a with rs12976445 Polymorphism in Breast Cancer Patients. Applied Sciences. MDPI AG. http://doi.org/10.3390/app10207275
  • Ochodek, M., Staron, M., Meding, W., & Bosch, J. (2020, November). LegacyPro—A DNA-Inspired Method for Identifying Process Legacies in Software Development Organizations. IEEE Software. Institute of Electrical and Electronics Engineers (IEEE). http://doi.org/10.1109/ms.2020.2971894
  • Sadaj, A., Ochodek, M., Kopczyńska, S., & Nawrocki, J. (2020). Maintainability of Automatic Acceptance Tests for Web Applications—A Case Study Comparing Two Approaches to Organizing Code of Test Cases. SOFSEM 2020: Theory and Practice of Computer Science. Springer International Publishing. http://doi.org/10.1007/978-3-030-38919-2_37
  • Komosinski, M., & Żok, T. (2020, March 1). Morality, protection, security and gain: lessons from a minimalistic, economically inspired multi-agent model. Foundations of Computing and Decision Sciences. Walter de Gruyter GmbH. http://doi.org/10.2478/fcds-2020-0002
  • Zok, T., Badura, J., Swat, S., Figurski, K., Popenda, M., & Antczak, M. (2020). New models and algorithms for RNA pseudoknot order assignment. International Journal of Applied Mathematics and Computer Science. http://doi.org/10.34768/AMCS-2020-0024
  • Ochodek, M., Staron, M., & Meding, W. (2019, December 9). On Identifying Similarities in Git Commit Trends—A Comparison Between Clustering and SimSAX. Software Quality: Quality Intelligence in Software and Systems Engineering. Springer International Publishing. http://doi.org/10.1007/978-3-030-35510-4_7
  • Pickerill, P., Jungen, H. J., Ochodek, M., Maćkowiak, M., & Staron, M. (2020, May 27). PHANTOM: Curating GitHub for engineered software projects using time-series clustering. Empirical Software Engineering. Springer Science and Business Media LLC. http://doi.org/10.1007/s10664-020-09825-8
  • Mayen, J. F. C., & Błażewicz, J. (2020, March 1). Recent Results on Computational Molecular Modeling of The Origins of Life. Foundations of Computing and Decision Sciences. Walter de Gruyter GmbH. http://doi.org/10.2478/fcds-2020-0003
  • Ochodek, M., Hebig, R., Meding, W., Frost, G., & Staron, M. (2019, November 14). Recognizing lines of code violating company-specific coding guidelines using machine learning. Empirical Software Engineering. Springer Science and Business Media LLC. http://doi.org/10.1007/s10664-019-09769-8
  • Gumna, J., Zok, T., Figurski, K., Pachulska-Wieczorek, K., & Szachniuk, M. (2020, October 1). RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis. (D. Barash, Ed.), Plos One. Public Library of Science (PLoS). http://doi.org/10.1371/journal.pone.0239287
  • Gryszczyńska, B., Budzyń, M., Formanowicz, D., Wanic-Kossowska, M., Formanowicz, P., Majewski, W., … Kasprzak, M. P. (2020, May 10). Selected Atherosclerosis-Related Diseases May Differentially Affect the Relationship between Plasma Advanced Glycation End Products, Receptor sRAGE, and Uric Acid. Journal of Clinical Medicine. MDPI AG. http://doi.org/10.3390/jcm9051416
  • Al-Sabbagh, K. W., Staron, M., Ochodek, M., Hebig, R., & Meding, W. (2020, October). Selective Regression Testing based on Big Data: Comparing Feature Extraction Techniques. 2020 IEEE International Conference on Software Testing, Verification and Validation Workshops (ICSTW). IEEE. http://doi.org/10.1109/icstw50294.2020.00058
  • Gutowska, K., Formanowicz, D., & Formanowicz, P. (2020). Systems Approach Based on Petri Nets as a Method for Modeling and Analysis of Complex Biological Systems Presented on the Example of Atherosclerosis Development Process. Advances in Intelligent Systems and Computing. Springer International Publishing. http://doi.org/10.1007/978-3-030-50936-1_49
  • Staron, M., Ochodek, M., Meding, W., & Soder, O. (2020, August). Using Machine Learning to Identify Code Fragments for Manual Review. 2020 46th Euromicro Conference on Software Engineering and Advanced Applications (SEAA). IEEE. http://doi.org/10.1109/seaa51224.2020.00085
  • Kudla, M., Gutowska, K., Synak, J., Weber, M., Bohnsack, K. S., Lukasiak, P., … Szachniuk, M. (2020, December 1). Virxicon: a lexicon of viral sequences. (Z. Lu, Ed.), Bioinformatics. Oxford University Press (OUP). http://doi.org/10.1093/bioinformatics/btaa1066

2020

  • Bachosz, K., Zdarta, J., Marczak, Ł., Błażewicz, J., & Jesionowski, T. (2020, February). A highly effective approach to cofactor regeneration and subsequent membrane separation of bioconversion products: Kinetic parameters and effect of process conditions. Bioresource Technology Reports. Elsevier BV. http://doi.org/10.1016/j.biteb.2019.100365
  • Belter, A., Popenda, M., Sajek, M., Woźniak, T., Naskręt-Barciszewska, M. Z., Szachniuk, M., … Barciszewski, J. (2020, November 17). A new molecular mechanism of RNA circularization and the microRNA sponge formation. Journal of Biomolecular Structure and Dynamics. Informa UK Limited. http://doi.org/10.1080/07391102.2020.1844802
  • Formanowicz, D., Rybarczyk, A., Radom, M., & Formanowicz, P. (2020, May 9). A Role of Inflammation and Immunity in Essential Hypertension—Modeled and Analyzed Using Petri Nets. International Journal of Molecular Sciences. MDPI AG. http://doi.org/10.3390/ijms21093348
  • Formanowicz, D., Rybarczyk, A., Radom, M., Tanaś, K., & Formanowicz, P. (2020, November 13). A Stochastic Petri Net-Based Model of the Involvement of Interleukin 18 in Atherosclerosis. International Journal of Molecular Sciences. MDPI AG. http://doi.org/10.3390/ijms21228574
  • Marciniak, A., Jankowska, M. A., & Hoffmann, T. (2020). An Interval Difference Method of Second Order for Solving an Elliptical BVP. Parallel Processing and Applied Mathematics. Springer International Publishing. http://doi.org/10.1007/978-3-030-43222-5_36
  • Martyna, A., Masłyk, M., Janeczko, M., Kochanowicz, E., Gielniewski, B., Świercz, A., … Kubiński, K. (2020, June 25). Antifungal Agent 4-AN Changes the Genome-Wide Expression Profile, Downregulates Virulence-Associated Genes and Induces Necrosis in Candida albicans Cells. Molecules. MDPI AG. http://doi.org/10.3390/molecules25122928
  • Zmienko, A., Marszalek-Zenczak, M., Wojciechowski, P., Samelak-Czajka, A., Luczak, M., Kozlowski, P., … Figlerowicz, M. (2020, April 7). AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. The Plant Cell. Oxford University Press (OUP). http://doi.org/10.1105/tpc.19.00640
  • Smialek, M. J., Ilaslan, E., Sajek, M. P., Swiercz, A., Janecki, D. M., Kusz-Zamelczyk, K., … Jaruzelska, J. (2020, April 16). Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model. Cells. MDPI AG. http://doi.org/10.3390/cells9040984
  • Zok, T., Popenda, M., & Szachniuk, M. (2020, January 31). ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinformatics. Springer Science and Business Media LLC. http://doi.org/10.1186/s12859-020-3385-1
  • Chen, X., Wang, W., Xie, P., Zhang, X., Sterna, M., & Błażewicz, J. (2020, June). Exact and heuristic algorithms for scheduling on two identical machines with early work maximization. Computers & Industrial Engineering. Elsevier BV. http://doi.org/10.1016/j.cie.2020.106449
  • Chen, X., Liang, Y., Sterna, M., Wang, W., & Błażewicz, J. (2020, July). Fully polynomial time approximation scheme to maximize early work on parallel machines with common due date. European Journal of Operational Research. Elsevier BV. http://doi.org/10.1016/j.ejor.2019.12.003
  • Marciniak, A., & Jankowska, M. A. (2019, July 29). Interval methods of Adams-Bashforth type with variable step sizes. Numerical Algorithms. Springer Science and Business Media LLC. http://doi.org/10.1007/s11075-019-00774-y
  • Marciniak, A., & Jankowska, M. A. (2020, May). Interval versions for special kinds of explicit linear multistep methods. Results in Applied Mathematics. Elsevier BV. http://doi.org/10.1016/j.rinam.2020.100104
  • Drozdowski, M., Singh, G., & Marszałkowski, J. M. (2020). Isoefficiency Maps for Divisible Computations in Hierarchical Memory Systems. Parallel Processing and Applied Mathematics. Springer International Publishing. http://doi.org/10.1007/978-3-030-43229-4_20
  • Chen, X., Kovalev, S., Sterna, M., & Błażewicz, J. (2020, January 30). Mirror scheduling problems with early work and late work criteria. Journal of Scheduling. Springer Science and Business Media LLC. http://doi.org/10.1007/s10951-020-00636-9
  • Synak, J., Rybarczyk, A., & Blazewicz, J. (2020, August 28). Multi-agent approach to sequence structure simulation in the RNA World hypothesis. (J.-L. E. Darlix, Ed.), Plos One. Public Library of Science (PLoS). http://doi.org/10.1371/journal.pone.0238253
  • Changaival, B., Danoy, G., Kliazovich, D., Guinand, F., Brust, M. R., Musial, J., … Bouvry, P. (2020, July 8). Ngap. Proceedings of the 2020 Genetic and Evolutionary Computation Conference Companion. ACM. http://doi.org/10.1145/3377929.3389941
  • Kopczyńska, S., Ochodek, M., & Nawrocki, J. (2019, August 3). On Importance of Non-functional Requirements in Agile Software Projects—A Survey. Integrating Research and Practice in Software Engineering. Springer International Publishing. http://doi.org/10.1007/978-3-030-26574-8_11
  • Miao, Z., Adamiak, R. W., Antczak, M., Boniecki, M. J., Bujnicki, J., Chen, S.-J., … Westhof, E. (2020, May 5). RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Rna. Cold Spring Harbor Laboratory. http://doi.org/10.1261/rna.075341.120
  • Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao, Y., … Miao, Z. (2019, December 4). RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Research. Oxford University Press (OUP). http://doi.org/10.1093/nar/gkz1108
  • Vellido, A., Gibert, K., Angulo, C., & Martín Guerrero, J. D. (Eds.). (2020). Advances in Self-Organizing Maps, Learning Vector Quantization, Clustering and Data Visualization. (A. Vellido, K. Gibert, C. Angulo, & J. D. Martín Guerrero, Eds.), Advances in Intelligent Systems and Computing. Springer International Publishing. http://doi.org/10.1007/978-3-030-19642-4
  • Wawrzyniak, J., Drozdowski, M., & Sanlaville, É. (2020, June). Selecting algorithms for large berth allocation problems. European Journal of Operational Research. Elsevier BV. http://doi.org/10.1016/j.ejor.2019.11.055
  • Jankowska, M. A., & Marciniak, A. (2020). The First Approach to the Interval Generalized Finite Differences. Parallel Processing and Applied Mathematics. Springer International Publishing. http://doi.org/10.1007/978-3-030-43222-5_34
  • Marszałkowski, J., Drozdowski, M., & Singh, G. (2020, October). Time–energy trade-offs in processing divisible loads on heterogeneous hierarchical memory systems. Journal of Parallel and Distributed Computing. Elsevier BV. http://doi.org/10.1016/j.jpdc.2020.05.015
  • Popenda, M., Miskiewicz, J., Sarzynska, J., Zok, T., & Szachniuk, M. (2019, October 7). Topology-based classification of tetrads and quadruplex structures. (A. Valencia, Ed.), Bioinformatics. Oxford University Press (OUP). http://doi.org/10.1093/bioinformatics/btz738
  • Szenajch, J., Szabelska-Beręsewicz, A., Świercz, A., Zyprych-Walczak, J., Siatkowski, I., Góralski, M., … Handschuh, L. (2020, December 3). Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. International Journal of Molecular Sciences. MDPI AG. http://doi.org/10.3390/ijms21239218
  • Wang, W., Chen, X., Musial, J., & Blazewicz, J. (2020). Two meta-heuristic algorithms for scheduling on unrelated machines with the late work criterion. International Journal of Applied Mathematics and Computer Science. http://doi.org/10.34768/AMCS-2020-0042
  • Kadziński, M., Badura, J., & Figueira, J. R. (2020, June). Using a segmenting description approach in multiple criteria decision aiding. Expert Systems with Applications. Elsevier BV. http://doi.org/10.1016/j.eswa.2020.113186

2019

  • D. Formanowicz, J.B. Krawczyk, B. Perek, P. Formanowicz, A Control-Theoretic Model of Atherosclerosis. International Journal of Molecular Sciences - 2019, vol. 20, iss. 3, s. 785-1-785-20
  • A. Kozak, T. Głowacki, P. Formanowicz, A method for constructing artificial DNA libraries based on generalized de Bruijn sequences. Discrete Applied Mathematics - 2019, vol. 259, s. 127-144
  • N.S. Labib, G. Danoy, J. Musiał, M.R. Brust, P. Bouvry, A Multilayer Low-Altitude Airspace Model for UAV Traffic Management. Proceedings of the 9th ACM Symposium on Design and Analysis of Intelligent Vehicular Networks and Applications DIVANet '19: ACM, 2019 - s. 57-63
  • B. Gryszczyńska, M. Budzyń, D. Formanowicz, P. Formanowicz , Zbigniew Krasiński, N. Majewska, M. Iskra, M.P. Kasprzak, Advanced Oxidation Protein Products and Carbonylated Proteins Levels in Endovascular and Open Repair of an Abdominal Aortic Aneurysm: The Effect of Pre-, Intra-, and Postoperative Treatment. BioMed Research International - 2019, vol. 2019, s. 7976043-1-7976043-9
  • K. Wiatr, P. Piasecki, Ł. Marczak, P. Wojciechowski, M. Kurkowiak, R. Płoski, M. Rydzanicz, L. Handschuh, J. Jungverdorben, O. Brüstle, M. Figlerowicz, M. Figiel, Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse. Molecular Neurobiology - 2019, vol. 56, iss. 12, s. 8168-8202
  • J. Błażewicz, X. Chen, R.C.T. Lee, B.M.T. Lin, F. Lin, E. Pesch, M. Sterna, Z. Wang, Clarification of lower bounds of two-machine flowshop scheduling to minimize total late work. Engineering Optimization - 2019, vol. 51, no. 7, s. 1279-1280
  • J. Musiał, E. Kieffer, M. Guzek, G. Danoy, S.S. Wagle, P. Bouvry, J. Błażewicz, Cloud Brokering with Bundles: Multi-objective Optimization of Services Selection. Foundations of Computing and Decision Sciences - 2019, vol. 44, no. 4, s. 407-426
  • J. Błażewicz, K.H. Ecker, E. Pesch, G. Schmidt, M. Sterna, J. Węglarz, Handbook on Scheduling : from Theory to Practice. Springer International Publishing, International Handbooks on Information Systems, 2019 - 833 s.
  • K. Świtońska, W. Szlachcic, L. Handschuh, P. Wojciechowski, Ł. Marczak, M. Stelmaszczuk, M. Figlerowicz, M. Figiel, Identification of altered developmental pathways in human juvenile HD iPSC with 71Q and 109Q using transcriptome profiling. Frontiers in Cellular Neuroscience - 2019, vol. 12
  • S. Halali, M. Staron, M. Ochodek, W. Meding, Improving Defect Localization by Classifying the Affected Asset Using Machine Learning. W: Software Quality: The Complexity and Challenges of Software Engineering and Software Quality in the Cloud : 11th International Conference, SWQD 2019, Vienna, Austria, January 15–18, 2019, Proceedings / red. Dietmar Winkler, Stefan Biffl, Johannes Bergsmann - Cham, Switzerland : Springer, 2019 - s. 106-122
  • A. Marciniak, M. Jankowska, Interval methods of Adams-Bashforth type with variable step sizes. Numerical Algorithms - 2019, in press, in press, s. 1-28
  • A. Marciniak, B. Szyszka, Interval Runge-Kutta Methods with Variable Step Sizes. Computational Methods in Science and Technology - 2019, vol. 25, no. 1, s. 17-30
  • A. Marciniak, Nakao's method and an interval difference scheme of second order for solving the elliptic BVP. Computational Methods in Science and Technology - 2019, vol. 25, no. 2, s. 81-97
  • M. Radom, M.A. Machnicka, J. Krwawicz, J.M. Bujnicki, P. Formanowicz, Petri net–based model of the human DNA base excision repair pathway. PLOS ONE - 2019, vol. 14, iss. 9, s. e0217913-1-e0217913-26
  • D. Kogut, K. Gutowska, A. Poterała-Hejmo, J. Śmieja, D. Formanowicz, P. Formanowicz, Petri nets and ODE as complementary tools in analysis of signaling pathways. Proceedings of 11th International Conference on Bioinformatics and Computational Biology / red. Oliver Eulenstein, Hisham Al-Mubaid, Qin Ding - [Manchester], United Kingdom : EasyChair, 2019 - s. 150-160
  • J. Carrascoza Mayen, J. Rydzewski, N. Szostak, J. Błażewicz, W. Nowak, Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinnello Ab Initio Simulations. Life - 2019, vol. 9, iss. 2, s. 46-1-46-18
  • M. Sajek, D. Janecki, M. J. Śmiałek, B. Ginter-Matuszewska, A. Spik, S. Oczkowski, Erkut Ilaslan, E. Kusz-Zamelczyk, M. Kotecki, J. Błażewicz, J. Jaruzelska, PUM1 and PUM2 exhibit different modes of regulation for SIAH1 that involve cooperativity with NANOS paralogues. Cellular and Molecular Life Sciences - 2019, vol. 76, iss. 1, s. 147-161
  • S. Wąsik, N. Szóstak, M. Kudła, M. Wachowiak, K. Krawiec, J. Błażewicz, Detecting Life Signatures with RNA Sequence Similarity Measures. Journal of Theoretical Biology - 2019, vol. 463, s. 110-120
  • M. Szachniuk, RNApolis: computational platform for RNA structure analysis. Foundations of Computing and Decision Sciences - 2019, vol. 44, no. 2, s. 241-257
  • M. Antczak, M. Zabłocki, T. Żok, A. Rybarczyk, J. Błażewicz, M. Szachniuk, RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. Bioinformatics - 2019, vol. 35, iss. 1, s. 152-155
  • K. Czerniachowska, Scheduling TV advertisements via genetic algorithm, European Journal of Industrial Engineering - 2019, vol. 13, no. 1, s. 81-116
  • K. Gutowska, D. Formanowicz, P. Formanowicz, Selected Aspects of Tobacco-Induced Prothrombotic State, Inflammation and Oxidative Stress: Modeled and Analyzed Using Petri Nets. Interdisciplinary Sciences: Computational Life Sciences - 2019, vol. 11, iss. 3, s. 373-386
  • M. Ochodek, M. Staron, W. Meding, Simsax: A measure of project similarity based on symbolic approximation method and software defect inflow. Information and Software Technology - 2019, vol. 115, s. 131-147
  • P. Jackowiak, A. Lis, M. Luczak, I. Stolarek, M. Figlerowicz, Functional characterization of RNA fragments using high-throughput interactome screening. Journal of Proteomics, 2019, 193, 173-183, doi: 10.1016/j.jprot.2018.10.007
  • M. Pokornowska, M.C. Milewski, K. Ciechanowska, A. Szczepańska, M. Wojnicka, Z. Radogostowicz, M. Figlerowicz, A. Kurzynska-Kokorniak, The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Cellular and Molecular Life Sciences 2019 Oct 26. doi: 10.1007/s00018-019-03344-6
  • T. Machałowski, M. Wysokowski, M.V. Tsurkan, R. Galli, C. Schimpf, D. Rafaja, E. Brendler, C. Viehweger, S. Żółtowska-Aksamitowska, I. Petrenko, K. Czaczyk, M. Kraft, M. Bertau, N. Bechmann, K. Guan, S. R. Bornstein, A. Voronkina, A. Fursov, M. Bejger, K. Biniek-Antosiak, W. Rypniewski, M. Figlerowicz, O. Pokrovsky, T. Jesionowski, H. Ehrlich, Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle. Molecules - 2019, vol. 24, iss. 20, s. 3736-1-3736-19
  • T. Machałowski, M. Wysokowski, S. Żółtowska-Aksamitowska, N. Bechmann, B. Binnewerg, M. Schubert, K. Guan, S.R. Bornstein, K. Czaczyk, O. Pokrovsky, M. Kraft, M. Bertau, C. Schimpf, D. Rafaja, M. Tsurkan, R. Galli, H. Meissner, I. Petrenko, A. Fursov, A. Voronkina, M. Figlerowicz, Y. Joseph, T. Jesionowski, H. Ehrlich, Spider Chitin. The biomimetic potential and applications of Caribena versicolor tubular chitin. Carbohydrate Polymers - 2019, vol. 226, s. 115301-1-115301-11
  • Ł. Gutowski, K. Gutowska, M. Pioruńska-Stolzmann, P. Formanowicz, D. Formanowicz, Systems Approach to Study Associations between OxLDL and Abdominal Aortic Aneurysms. International Journal of Molecular Sciences - 2019, vol. 20, iss. 16, s. 3909-1-3909-16
  • B. Changaival, G. Danoy, D. Kliazovich, F. Guinand, M. R. Brust, J. Musiał, K. Lavangnananda, P. Bouvry, Toward real-world vehicle placement optimization in round-trip carsharing. GECCO '19 : proceedings of the Genetic and Evolutionary Computation Conference / red. Manuel López-Ibáñez - New York, USA : ACM, 2019 - s. 1138-1146
  • X. Chen, Z. Wang, E. Pesch, M. Sterna, J. Błażewicz, Two-machine flow-shop scheduling to minimize total late work: revisited. Engineering Optimization - 2019, vol. 51, no. 7, s. 1268-1278
  • S. Wąsik, M. Jaroszewski, M. Nowaczyk, N. Szostak, T. Prejzendanc, J. Błażewicz, VirDB: Crowdsourced Database for Evaluation of Dynamical Viral Infection Models. Current Bioinformatics - 2019, vol. 14, no. 8
  • S. Kopczyńska, J. Nawrocki, M. Ochodek, When NFR templates pay back? A study on evolution of catalog of NFR templates. Product-Focused Software Process Improvement : 20th International Conference, PROFES 2019, Barcelona, Spain, November 27–29, 2019 : Proceedings / red. Xavier Franch, Tomi Männistö, Silverio Martínez-Fernández: Springer International Publishing, 2019 - s. 145-160

2018

  • A. Swiercz, W. Frohmberg, M. Kierzynka, P. Wojciechowski, P. Zurkowski, J. Badura, A. Laskowski, M. Kasprzak, J. Blazewicz, GRASShopPER—An algorithm for de novo assembly based on GPU alignments. PLOS ONE 13(8): e0202355, 2018. https://doi.org/10.1371/journal.pone.0202355
  • J. Błażewicz, M. Kasprzak, M. Kierzynka, W. Frohmberg, A. Świercz, P. Wojciechowski, P. Żurkowski, Graph algorithms for DNA sequencing - origins, current models and the future, European Journal of Operational Research 264, 2018, pp. 799-812.
  • M. Maćkowiak, J. Nawrock, M. Ochodek, On some end-user programming constructs and their understandability, Journal of Systems and Software 142, 2018, pp. 206-222.

2017

  • A. Mickiewicz, J. Sarzyńsk, 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, A. Hertz, M. Kasprzak, J. Błażewicz, Tabu search for the RNA partial degradation problem, International Journal of Applied Mathematics and Computer Science 27, 2017, pp. 401-415.
  • N. Szostak, J. Synak, M. Borowski, S. Wąsik, J. Błażewicz, Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution, PLOS ONE 12, 2017.
  • N. Szostak, S. Wąsik, J. Błażewicz, Understanding Life: A Bioinformatics Perspective, European Review 25, 2017, pp. 1-15.
  • X. Chen, V. Chau, P. Xie, M. Sterna, J. Błażewicz, Complexity of late work minimization in flow shop systems and a particle swarm optimization algorithm for learning effect, Computers & Industrial Engineering 111, 2017, pp. 176-182.
  • M. Cicheński, F. Jaehn, G. Pawlak, E. Pesh, G. Singh, J. Błażewicz, An integrated model for the transshipment yard scheduling problem, Journal of Scheduling 20, 2017, 57-65.
  • J. Marszałkowski, D. Mokwa, M. Drozdowski, Ł. Rusiecki, H. Narożny, Fast algorithms for online construction of web tag clouds, Engineering Applications of Artificial Intelligence 64, 2017.
  • M. Drozdowski, F. Jaehn, R. Paszkowski, Scheduling Position-Dependent Maintenance Operations, Operations Research 65, 2017, pp. 1657 - 1677.
  • M. L. Espinouse, G. Pawlak, M. Sterna, Complexity of Scheduling Problem in Single-Machine Flexible Manufacturing System with Cyclic Transportation and Unlimited Buffers, Journal of Optimization Theory and Applications 173, 2017, pp. 1042-1054.
  • M. Sterna, K. Czerniachowska, Polynomial Time Approximation Scheme for Two Parallel Machines Scheduling with a Common Due Date to Maximize Early Work, Journal of Optimization Theory and Applications 174, 2017, pp. 927-944.
  • Z. Miao, R. Adamiak, M. Antczak, R. Batey, A. Becka, M. Biesiada, M. Boniecki, J. M. Bujnicki, S. J. Chen, C. Cheng, F. C. Chou, A. R. Ferre-D'Amare, R. Das, W. Dawson, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, K. Kappel, W. Kladwang, A. Krokhotin, G. Lach, F. Major, T. H. Mann, M. Magnus, K. Pachulska-Wieczorek, D. Patel, J. Piccirilli, M. Popenda, K. J. Purzycka, A. Ren, G. Rice, J. Santalucia, J. Sarzyńska, M. Szachniuk, A. Tandon, J. Trausch, S. Tian, J. Wang, K. Weeks, B. Williams, Y. Xiao, X. Xu, D. Zhang, T. Żok, E. Westhof RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA23, 2017, pp. 655-72.
  • J. Wiedemann, T. Żok, M. Miłostan, M. Szachniuk, LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics 18, 2016, pp. 456-469.
  • M. Antczak, M. Popenda, T. Żok, M. Żurkowski, R. W. Adamiak, M Szachniuk, New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, Bioinformatics 2017, pp. 1-9.
  • J. Miśkiewicz, K. Tomczyk, A. Mickiewicz, J. Sarzyńska, M. Szachniuk, Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors, BioMed Research International 2017, 6783010-1 - 6783010-8.
  • J. Musiał, M. C. Lopez-Loces, Trustworthy online shopping with price impact, Foundations of Computing and Decision Sciences 42, 2017, pp. 121-136.
  • N. Szostak, J. Synak, M. Borowski, S. Wąsik, J. Błażewicz, Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution, PLOS ONE 12, 2017.
  • S. Wąsik, M. Antczak, J. Badura, A. Laskowski, M. Olszowy, T. Sternal, K. Wędrowicz, Optil.io Platform: Evaluation as a Service for Metaheuristics, Metaheuristics: Proceeding of the MIC and MAEB 2017 Conferences, 2017, pp. 225-227.
  • M. Ochodek, A. Matysiak, P. Miklosik, S. Kopczyńska, Sketching Use-Case Scenarios Based on Use-Case Goals and Patterns, Software Engineering: Challenges and Solutions : Results of the XVIII KKIO 2016 Software Engineering Conference 2016 held at September 15-17 2016 in Wroclaw, Poland, 2017.

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, Current Bioinformatics 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
  • B. Alchimowicz, J. Nawrocki, The COCA quality model for user documentation, Software Quality Journal 24, 2016, pp. 205-230.
  • A. Rybarczyk, P. Jackowiak, M. Figlerowicz, J. Błażewicz, Computational prediction of non-enzymatic RNA degradation patterns, Acta Biochimica Polonica 63, pp. 2016, 745-751.
  • J. Musiał, M. C. Lopez-Loces, J. E. Pecero, H. J. Fraire-Huacuja, P. Bouvry, J. Błażewicz, Algorithms solving the Internet shopping optimization problem with price discounts, Bulletin of the Polish Academy of Sciences. Technical Sciences 64, 2016, pp. 505-516.
  • M. Antczak, M. Kasprzak, P. Łukasiak, J. Błażewicz, Structural alignment of protein descriptors – a combinatorial model, BMC Bioinformatics 17, 2016, pp. 383-1 - 383-14.
  • M. Turkay, G. Felici, M. Szachniuk, P. Łukasiak, Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine, RAIRO - Operations Research 50, 2016, pp. 327-330.
  • M. Antczak, M. Popenda, T. Żok, J. Sarzyńska, 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, 2016, pp. 737-744.
  • M. Ochodek, Functional size approximation based on use-case names, Information and Software Technology 80, 2016, pp. 73-88.

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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