Publications

Journal Articles

  • [DOI] N. Szostak, S. Wasik, and J. Blazewicz, “Understanding life: a bioinformatics perspective,” European Review, vol. 25, iss. 2, pp. 231-245, 2017.
    [Bibtex]
    @Article{Szostak2016,
    Title = {Understanding Life: A Bioinformatics Perspective},
    Author = {Szostak, N. and Wasik, S. and Blazewicz, J.},
    Journal = {{European Review}},
    Year = {2017},
    Month = {May},
    Number = {2},
    Pages = {231-245},
    Volume = {25},
    Doi = {10.1017/S1062798716000570},
    Owner = {swasik},
    Timestamp = {2016.01.12},
    Url = {https://doi.org/10.1017/S1062798716000570}
    }
  • [DOI] N. Szostak, J. Synak, M. Borowski, S. Wasik, and J. Blazewicz, “Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution,” PLOS ONE, 2017.
    [Bibtex]
    @Article{Szostak2017,
    Title = {Simulating the origins of life: {The} dual role of {RNA} replicases as an obstacle to evolution},
    Author = {Szostak, N. and Synak, J. and Borowski, M. and Wasik, S. and Blazewicz, J.},
    Journal = {{PLOS ONE}},
    Year = {2017},
    Doi = {10.1371/journal.pone.0180827},
    Owner = {swasik},
    Timestamp = {2017.07.06}
    }
  • [DOI] N. Szostak, S. Wasik, and J. Blazewicz, “Hypercycle,” PLOS Computational Biology, vol. 12, iss. 4, pp. 1-13, 2016.
    [Bibtex]
    @Article{Szostak2016a,
    Title = {Hypercycle},
    Author = {Szostak, Natalia AND Wasik, Szymon AND Blazewicz, Jacek},
    Journal = {{PLOS Computational Biology}},
    Year = {2016},
    Month = {04},
    Number = {4},
    Pages = {1-13},
    Volume = {12},
    Doi = {10.1371/journal.pcbi.1004853},
    Owner = {swasik},
    Publisher = {Public Library of Science},
    Timestamp = {2017.01.26},
    Url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004853}
    }
  • [DOI] T. Prejzendanc, S. Wasik, and J. Blazewicz, “Computer representations of bioinformatics models,” Current Bioinformatics, vol. 11, iss. 5, pp. 551-560, 2016.
    [Bibtex]
    @Article{Prejzendanc2016,
    Title = {Computer representations of bioinformatics models},
    Author = {Prejzendanc, T. and Wasik, S. and Blazewicz, J.},
    Journal = {{Current Bioinformatics}},
    Year = {2016},
    Number = {5},
    Pages = {551-560},
    Volume = {11},
    Doi = {10.2174/1574893610666150928193510},
    Owner = {swasik},
    Timestamp = {2016.01.12}
    }
  • [DOI] S. Wasik, F. Fratczak, J. Krzyskow, and J. Wulnikowski, “Inferring mathematical equations using crowdsourcing,” PLOS ONE, vol. 10(12), iss. e0145557, 2015.
    [Bibtex]
    @Article{Wasik2015,
    Title = {Inferring Mathematical Equations Using Crowdsourcing},
    Author = {Wasik, S. and Fratczak, F. and Krzyskow, J. and Wulnikowski, J.},
    Journal = {{PLOS ONE}},
    Year = {2015},
    Number = {e0145557},
    Volume = {10(12)},
    Doi = {10.1371/journal.pone.0145557},
    Owner = {swasik},
    Timestamp = {2016.01.12},
    Url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145557}
    }
  • [DOI] S. Wasik, P. Jackowiak, M. Figlerowicz, and J. Blazewicz, “Multi-agent model of hepatitis C virus infection,” Artificial Intelligence in Medicine, vol. 60, iss. 2, pp. 123-131, 2014.
    [Bibtex]
    @Article{Wasik2013,
    Title = {Multi-agent model of hepatitis {C} virus infection},
    Author = {Wasik, S. and Jackowiak, P. and Figlerowicz, M. and Blazewicz, J.},
    Journal = {{Artificial Intelligence in Medicine}},
    Year = {2014},
    Number = {2},
    Pages = {123-131},
    Volume = {60},
    Doi = {10.1016/j.artmed.2013.11.001},
    Owner = {Szymon Wasik},
    Timestamp = {2013.11.06},
    Url = {http://www.sciencedirect.com/science/article/pii/S093336571300153X}
    }
  • [DOI] S. Wasik, T. Prejzendanc, and J. Blazewicz, “ModeLang – a new approach for experts-friendly viral infections modeling,” Computational and Mathematical Methods in Medicine, vol. 2013, p. 8, 2013.
    [Bibtex]
    @Article{Wasik2013a,
    Title = {{ModeLang} - A new approach for experts-friendly viral infections modeling},
    Author = {Wasik, S. and Prejzendanc, T. and Blazewicz, J.},
    Journal = {{Computational and Mathematical Methods in Medicine}},
    Year = {2013},
    Pages = {8},
    Volume = {2013},
    Doi = {10.1155/2013/320715},
    Owner = {Szymon Wasik},
    Timestamp = {2013.11.14}
    }
  • [DOI] S. Wasik, P. Jackowiak, J. B. Krawczyk, P. Kedziora, P. Formanowicz, M. Figlerowicz, and J. Blazewicz, “Towards prediction of HCV therapy efficiency,” Computational and Mathematical Methods in Medicine, vol. 11(2), pp. 185-199, 2010.
    [Bibtex]
    @Article{Wasik2010,
    Title = {Towards prediction of {HCV} therapy efficiency},
    Author = {Wasik, S. and Jackowiak, P. and Krawczyk, J. B. and Kedziora, P. and Formanowicz, P. and Figlerowicz, M. and Blazewicz, J.},
    Journal = {{Computational and Mathematical Methods in Medicine}},
    Year = {2010},
    Pages = {185-199},
    Volume = {11(2)},
    Doi = {10.1080/17486700903170712},
    Owner = {Szymon Wasik},
    Timestamp = {2010.01.26},
    Url = {http://www.informaworld.com/10.1080/17486700903170712}
    }
  • [DOI] M. Popenda, M. Szachniuk, M. Blazewicz, S. Wasik, E. K. Burke, J. Blazewicz, and 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, vol. 11, p. 231, 2010.
    [Bibtex]
    @Article{Popenda2010,
    Title = {{RNA} {FRABASE} 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within {RNA} structures.},
    Author = {Popenda, Mariusz and Szachniuk, Marta and Blazewicz, Marek and Wasik, Szymon and Burke, Edmund K. and Blazewicz, Jacek and Adamiak, Ryszard W.},
    Journal = {{BMC Bioinformatics}},
    Year = {2010},
    Pages = {231},
    Volume = {11},
    __markedentry = {[Szymon Wasik:6]},
    Abstract = {Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl.RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.},
    Doi = {10.1186/1471-2105-11-231},
    Institution = {Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.},
    Keywords = {Databases, Nucleic Acid; Genomics, methods; Internet; Nucleic Acid Conformation; RNA, chemistry; Sequence Analysis, RNA; Software; User-Computer Interface},
    Language = {eng},
    Medline-pst = {epublish},
    Owner = {Szymon Wasik},
    Pii = {1471-2105-11-231},
    Pmid = {20459631},
    Timestamp = {2013.02.20},
    Url = {http://dx.doi.org/10.1186/1471-2105-11-231}
    }

Books

  • S. Wasik, Bioinformatyczne modele i algorytmy infekcji wirusowych (Bioinformatics models and algorithms of viral infections), Poznan, Poland: Nakom, 2012, vol. 10.
    [Bibtex]
    @Book{Wasik2012,
    Title = {Bioinformatyczne modele i algorytmy infekcji wirusowych ({Bioinformatics} models and algorithms of viral infections)},
    Author = {Szymon Wasik},
    Publisher = {Nakom},
    Year = {2012},
    Address = {Poznan, Poland},
    Month = {December},
    Series = {Poznan Monographs in Computing and Its Applications},
    Volume = {10},
    Owner = {Szymon Wasik},
    Timestamp = {2013.02.20}
    }

Thesis

  • S. Wasik, “Mathematical models of viral infections,” Master Thesis, 2008.
    [Bibtex]
    @MastersThesis{Wasik2008,
    Title = {Mathematical Models of Viral Infections},
    Author = {Szymon Wasik},
    School = {Poznan University of Technology},
    Year = {2008},
    Owner = {Szymon Wasik},
    Timestamp = {2013.02.20}
    }
  • S. Wasik, IntelliForest – a network-centric system for forest monitoring and protection, 2007.
    [Bibtex]
    @Misc{Wasik2007,
    Title = {{IntelliForest} - a network-centric system for forest monitoring and protection},
    Author = {Szymon Wasik},
    Note = {Bachelor Thesis},
    Year = {2007},
    Owner = {Szymon Wasik},
    School = {Poznan University of Technology},
    Timestamp = {2013.02.20}
    }

Conference Proceedings

  • S. Wasik, M. Antczak, J. Badura, A. Laskowski, M. Olszowy, T. Sternal, and K. Wedrowicz, “Optil.io Platform: Evaluation as a Service for Metaheuristics,” in Metaheuristics: Proceeding of the MIC and MAEB 2017 Conferences, Barcelona, Spain, 2017, pp. 225-227.
    [Bibtex]
    @InProceedings{Wasik2017,
    Title = {{Optil.io Platform: Evaluation as a Service for Metaheuristics}},
    Author = {Wasik, S. and Antczak, M. and Badura, J. and Laskowski, A. and Olszowy, M. and Sternal, T. and Wedrowicz, K.},
    Booktitle = {{Metaheuristics: Proceeding of the MIC and MAEB 2017 Conferences}},
    Year = {2017},
    Address = {Barcelona, Spain},
    Editor = {Duarte, A. and Viana, A. and Juan, A. and Melian, B. and Ramalhinho, H.},
    Month = {July},
    Organization = {{Universitat Pompeu Fabra}},
    Pages = {225-227},
    Publisher = {{Universitat Pompeu Fabra}},
    Owner = {swasik},
    Timestamp = {2017.07.06}
    }
  • [DOI] S. Wasik, M. Antczak, J. Badura, A. Laskowski, and T. Sternal, “Optil.io: Cloud Based Platform For Solving Optimization Problems Using Crowdsourcing Approach,” in Proceedings of the 19th ACM Conference on Computer Supported Cooperative Work and Social Computing Companion, San Francisco, CA, USA, 2016, pp. 433-436.
    [Bibtex]
    @InProceedings{Wasik2016,
    Title = {Optil.io: {Cloud Based Platform For Solving Optimization Problems Using Crowdsourcing Approach}},
    Author = {Wasik, S. and Antczak, M. and Badura, J. and Laskowski, A. and Sternal, T.},
    Booktitle = {Proceedings of the 19th {ACM Conference on Computer Supported Cooperative Work and Social Computing Companion}},
    Year = {2016},
    Address = {San Francisco, CA, USA},
    Organization = {ACM},
    Pages = {433-436},
    Publisher = {ACM Digital Library},
    Doi = {10.1145/2818052.2869098},
    Owner = {swasik},
    Timestamp = {2016.03.01},
    Url = {http://dl.acm.org/citation.cfm?id=2869098&CFID=757193601&CFTOKEN=64226357}
    }
  • J. Synak, N. Szostak, S. Wasik, and J. Blazewicz, “Application of chemical reaction simulation methods in order to verify rna world hypothesis,” in Machine Learning Reports 04/2015, 2015, p. 6.
    [Bibtex]
    @InProceedings{Synak2015,
    Title = {Application of chemical reaction simulation methods in order to verify RNA World hypothesis},
    Author = {Synak, J. and Szostak, N. and Wasik, S. and Blazewicz, J.},
    Booktitle = {{Machine Learning Reports} 04/2015},
    Year = {2015},
    Note = {ISSN:1865-3960 http://www.techfak.uni-bielefeld.de/~fschleif/mlr/mlr_04_2015.pdf},
    Pages = {6},
    Series = {Machine Learning Reports},
    Owner = {Szymon Wasik},
    Timestamp = {2016.02.23},
    Url = {http://www.techfak.uni-bielefeld.de/~fschleif/mlr/mlr_04_2015.pdf}
    }
  • S. Wasik, “Two crowdsourcing approaches for solving optimization problems,” in Machine Learning Reports 04/2015, 2015, p. 16.
    [Bibtex]
    @InProceedings{Wasik2015a,
    Title = {Two crowdsourcing approaches for solving optimization problems},
    Author = {Wasik, S.},
    Booktitle = {{Machine Learning Reports} 04/2015},
    Year = {2015},
    Note = {ISSN:1865-3960 http://www.techfak.uni-bielefeld.de/~fschleif/mlr/mlr_04_2015.pdf},
    Pages = {16},
    Series = {Machine Learning Reports},
    Owner = {Szymon Wasik},
    Timestamp = {2016.02.23},
    Url = {http://www.techfak.uni-bielefeld.de/~fschleif/mlr/mlr_04_2015.pdf}
    }
  • S. Wasik, P. Jackowiak, M. Figlerowicz, and J. Blazewicz, “Modeling HCV infection using multi-agent simulation,” in Machine Learning Reports 01/2011, 2011, pp. 37-41.
    [Bibtex]
    @InProceedings{Wasik2011,
    Title = {Modeling {HCV} infection using multi-agent simulation},
    Author = {Wasik, S. and Jackowiak, P. and Figlerowicz, M. and Blazewicz, J.},
    Booktitle = {{Machine Learning Reports} 01/2011},
    Year = {2011},
    Note = {ISSN:1865-3960 http://www.techfak.uni-bielefeld.de/$\tilde{ }$fschleif/mlr/mlr\_01\_2011.pdf},
    Pages = {37-41},
    Series = {Machine Learning Reports},
    Owner = {Szymon Wasik},
    Timestamp = {2011.02.10}
    }

Technical Reports

  • S. Wasik, F. Fratczak, J. Krzyskow, and J. Wulnikowski, “Eksperymentalna weryfikacja metod modelowania systemow dynamicznych z wykorzystaniem crowdsourcingu,” Institute of Computing Science, Poznan University of Technology, RB-7/16, 2016.
    [Bibtex]
    @TechReport{Wasik2016b,
    Title = {Eksperymentalna weryfikacja metod modelowania systemow dynamicznych z wykorzystaniem crowdsourcingu},
    Author = {Wasik, S. and Fratczak, F. and Krzyskow, J. and Wulnikowski, J.},
    Institution = {Institute of Computing Science, Poznan University of Technology},
    Year = {2016},
    Number = {RB-7/16},
    Owner = {swasik},
    Timestamp = {2016.03.18}
    }
  • S. Wasik, I. Bladek, T. Chojnacki, K. Miazga, J. Szwachla, and J. Blazewicz, “Platforma trochilus: opracowywanie metod estymacji parametrow systemow biologicznych z wykorzystaniem crowdsourcingu,” Institute of Computing Science, Poznan University of Technology, RB-5/16, 2016.
    [Bibtex]
    @TechReport{Wasik2016a,
    Title = {Platforma Trochilus: opracowywanie metod estymacji parametrow systemow biologicznych z wykorzystaniem crowdsourcingu},
    Author = {Wasik, S. and Bladek, I. and Chojnacki, T. and Miazga, K. and Szwachla, J. and Blazewicz, J.},
    Institution = {Institute of Computing Science, Poznan University of Technology},
    Year = {2016},
    Number = {RB-5/16},
    Owner = {swasik},
    Timestamp = {2016.03.18}
    }
  • S. Wasik, “Wst?pna implementacja modelu systemu crispr-cas,” Institute of Computing Science, Poznan University of Technology, RB-7/15, 2015.
    [Bibtex]
  • P. Gielda, W. Jaskowski, M. Kaczmarek, A. Krych, M. Nawrocki, M. Paszta, L. Piatkowski, J. Polak, M. Sobczak, B. Soltowski, M. Staszewski, W. Szymaniak, M. Ulatowski, and S. Wasik, “ITS Poznan – program funkcjonalno-uzytkowy,” Poznan University of Technology 2010.
    [Bibtex]
    @TechReport{Gielda2010,
    Title = {{ITS} {Poznan} - Program Funkcjonalno-Uzytkowy},
    Author = {Piotr Gielda and Wojciech Jaskowski and Mariusz Kaczmarek and Andrzej Krych and Mateusz Nawrocki and Maciej Paszta and Lukasz Piatkowski and Jan Polak and Mikolaj Sobczak and Blazej Soltowski and Michal Staszewski and Witold Szymaniak and Maciej Ulatowski and Szymon Wasik},
    Institution = {Poznan University of Technology},
    Year = {2010},
    Owner = {Szymon Wasik},
    Timestamp = {2014.01.15}
    }
  • S. Wasik, P. Jackowiak, J. Krawczyk, P. Kedziora, P. Formanowicz, M. Figlerowicz, and J. Blazewicz, “A certain model of HCV virus infection,” Institut fur Informatik, Technische Universitat Clausthal 2009.
    [Bibtex]
    @TechReport{Wasik2009,
    Title = {A certain model of {HCV} virus infection},
    Author = {Wasik, S. and Jackowiak, P. and Krawczyk, J. and Kedziora, P. and Formanowicz, P. and Figlerowicz, M. and Blazewicz, J.},
    Institution = {Institut fur Informatik, Technische Universitat Clausthal},
    Year = {2009},
    Month = {November},
    Note = {Proceedings of ICOLE'09: German-Polish Workshop on Computational Biology, Scheduling and Machine Learning, Lessach},
    Journal = {{TU Clausthal Technical Report Series}},
    Owner = {Szymon Wasik},
    Pages = {72-78},
    Timestamp = {2010.01.26},
    Url = {http://www.in.tu-clausthal.de/fileadmin/homes/techreports/ifi0912blazewicz.pdf},
    Volume = {Ifl-09-12}
    }