Printing 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
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