Monographs and books chapters:
C. Jankowski, T. Kisiel, P. Lukasiak, S. Romaniuk, I. Witkowska, 2006, “Microsoft Technology for small Business Enterprises”, Executive MBA Thesis, Carlsson School of Managament, University of Minessota,
T. Kisiel, J. Krol, P. Lukasiak, D. Serafin, S. Szymankiewicz ”Eseje o przyszłości zarządzania” (in polish), red. P. Ploszajski, Fund. Rozw. Eduk. Men. SGH, Warsaw
P. Lukasiak, 2004, "Algorytmiczne aspekty przewidywania struktur bialek" (in polish), PhD thesis, Computer Science Faculty, Poznan University of Technology, Poznan.
J. Blazewicz, P.L. Hammer, P. Lukasiak, Logical Analysis of Data as a predictor of protein secondary structures, Bioinformatics of genome regulations and structure ed. Kolchanov, N., & Hofestaedt, 2003, Kluwer publisher
J. Blazewicz, P.L. Hammer, P. Lukasiak, 2001, Protein Secondary Structure Prediction using Logical Analysis of Data, Mathematics and Simulation with Biological, Economical and Musicoacoustical Applications, 202-207, WSES Press
Papers in journals from ISI list:
K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz, R.W. Adamiak, 2014, Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in Shi-Jie Chen, Donald H. Burke-Aguero (eds.) Methods in Enzymology: Computational Methods for Understanding Riboswitches 553, Elsevier, 3-34.
M. Antczak, T. Zok, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz, M. Szachniuk, 2014, RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research 42(W1), W368-W372
P. Lukasiak, M. Antczak, T. Ratajczak, J. M. Bujnicki, M. Szachniuk, R. W. Adamiak, M. Popenda, J. Blazewicz, 2013, RNAlyzer – novel approach for quality analysis of RNA structural models, Nucleic Acid Research, Nucleic Acid Research 41, pp. 5978-5990
J. Blazewicz, M. Borowski, W. Chaara, P. Kedziora, D. Klatzmann, P. Lukasiak, A. Six, P. Wojciechowski, 2012, GeVaDSs - decision support system for novel Genetic Vaccine development process, BMC Bioinformatics, 13:91
M. Popenda, M. Szachniuk, M. Antczak, K. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R. Adamiak, 2012, Automated 3D structure composition for large RNAs, Nucleic Acid Research, 40(14), e112
P. Lukasiak, J. Blazewicz, M. Milostan, 2010, Some operations research methods for analyzing protein sequences and structures, Annals of Operations Research, 175, pp. 9-35
N. Krasnogor, A.A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz, 2008, Web and Grid technologies in bioinformatics, computational and systems biology: a review, Current Bioinformatics, 3, pp. 10-31
J. Blazewicz, P. Lukasiak, S. Wilk, 2007, New machine learning methods for prediction of protein secondary structure, Control and Cybernetics, 36, pp.183-201
J. Blazewicz, P.L. Hammer, P. Lukasiak, 2005, Predicting secondary structures of proteins, IEEE Engineering in Medicine and Biology, 24, pp.88-94
J. Blazewicz, P. Lukasiak, M. Milostan, 2005, Application of tabu search strategy for finding low energy structure of protein, Artificial Intelligence in Medicine, 35, pp.135-145
Papers in peer reviewed journals:
M. Antczak, J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, G. Palik, 2011, DomAns - pattern based method for protein domain boundaries prediction and analysis, Foundations of Computing and Decision Sciences, 36, pp. 99-119
J. Sarzynska, A. Mickiewicz, M. Milostan, P. Lukasiak, J. Blazewicz, M. Figlerowicz, T. Kulinski, 2010, Flexibility of Dicer studied by implicit solvent molecular dynamics simulations, Computational Methods in Science and Technology, 16, pp. 97-104
J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, P. Jackowiak, 2009, Sequence Similarity Based Method For Protein Function Prediction, Foundations of Computing and Decision Sciences, 34, pp. 173-192
J. Blazewicz, P. Lukasiak, 2009System wspomagania wytwarzania i analizy szczepionek genetycznych, Kosmos, 58 (1-2), pp. 113-126
W. Jaskowski, J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, 2007, 3D-Judge - A Metaserver Approach to Protein Structure Prediction, Foundations of Computing and Decision Sciences, 32, pp. 3-14
J. Blazewicz, K. Dill, P. Lukasiak, M. Milostan, 2004, A tabu search strategy for finding low energy structures of proteins in HP-model, Computational Methods in Science and Technology 10, pp. 7-19.
J. Blazewicz, P.L. Hammer, P. Lukasiak, 2001, Protein prediction using Logical Analysis of Data, Computational Methods in Science and Technology, 7:8-26
Papers in peer reviewed international conferences proceedings:
M. Antczak, P. Lukasiak, K. Fidelis, A. Kryshtafovych, J. Blazewicz, „Protein structure quality assessment and modeling support techniques”, [in:] Machine Learning Reports (Proceedings of the ICOLE2011 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 18.09-24.09.2011), 2011, pp. 21.
M. Szachniuk , M. Popenda , M. Antczak , K. J. Purzycka, P. Lukasiak, N. Bartol , J. Blazewicz , R. W. Adamiak, RNAComposer and the art of composing RNA structures, [in:] Machine Learning Reports (Proceedings of the ICOLE2010 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 26.09-02.10.2010), 2011, pp. 26.
P. Lukasiak, K. Fidelis, M. Antczak, A. Kryshtafovych, J. Blazewicz, „Automated prediction of 3D structure of proteins based on descriptors approach”, [in:] Machine Learning Reports (Proceedings of the ICOLE2010 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 26.09-02.10.2010), 2010, pp. 19.
P. Lukasiak, M. Antczak, A. Hoffa, W. Biniecki, M. Wojciechowski, ProDomAn-Protein Domains Analysis platform, [in:] Technical Report Series (Proceedings of the ICOLE2009 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 25.05-29.05.2009), 2009, pp. 60.
M. Milostan, J. Sarzynska, A. Mickiewicz, M. Antczak, P. Lukasiak, J. Blazewicz, „Protein structure modelling–case study”, [in:] Technical Report Series (Proceedings of the ICOLE2009 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 25.05-29.05.2009), 2009, pp. 47.
M. Antczak, R. Adamiak, P. Lukasiak, M. Popenda, M. Szachniuk, G. Palik, J. Blazewicz, „3D–RNA–Pred: An Automatic Construction of Three–Dimensional RNA Structures”, [in:] Technical Report Series (Proceedings of the ICOLE2008 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 09.06-13.06.2008), 2008, pp. 46.
J. Blazewicz, P. Lukasiak, M. Antczak, M. Milostan, G. Palik, „Domain Analysis Server (DomAnS)–Protein domains prediction algorithm (DomAn)”, [in:] Technical Report Series (Proceedings of the ICOLE2007 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 27.05-02.06.2007), 2007, pp. 18.
M. Milostan, J. Blazewicz, P. Lukasiak, M. Antczak, „Graph clustering approach for protein domain decomposition”, [in:] Technical Report Series (Proceedings of the ICOLE2007 – German - Polish Workshop on Computational Biology, Perspectives of Bioinformatics, Operations Research and Machine Learning, Lessach, Austria, 27.05-02.06.2007), 2007, pp. 22.
Abstracts in conference proceedings:
P. Lukasiak, M. Antczak, T. Ratajczak, J. Blazewicz, Quality evaluation of biomolecules, EURO XXVI 1-4 July 2013, Rzym, Włochy
M. Milostan, P. Lukasiak, J. Blazewicz, Graph clustering and biomolecules, EURO XXVI 1-4 July 2013, Rzym, Włochy
M. Antczak, P. Lukasiak, K. Fidelis, J. Blazewicz, Novel approach to model quality assessment of proteins, EURO XXVI 1-4 July 2013, Rzym, Włochy
P. Lukasiak, M. Wojciechowski, T. Ratajczak, K. Hasinski, B. Monastyrsky, A. Krysthafovych, K. Fidelis, SphereGrinder – estimating similarity of structures on a local scale, Critical Assessment of Techniques for Protein Structure Prediction, 10th Meeting, December, 2012, Gaeta, Włochy, , pp. 274.
P. Lukasiak, Quality assessment methodologies in analysis of structural models, 25th European Conference on Operational Research, EURO XXV 8-11 July 2012, Wilno, Litwa, p. 80
M. Antczak, P. Lukasiak, J. Blazewicz, K. Fidelis, Protein structure quality assessment and modeling support framework, 25th European Conference on Operational Research, EURO XXV 8-11 July 2012, Wilno, Litwa, p. 80
P. Lukasiak, The novel approach for building models of protein structure, European Chapter on Combinatorial Optimization (ECCO) XXII, April 26-28, 2012 Antalya, Turcja, p. 6
J. Blazewicz, M. Popenda, M. Antczak, M. Szachniuk, P. Lukasiak, R.W. Adamiak, N. Bartol, K. Purzycka, The tool for automatic prediction of RNA tertiary structures European Chapter on Combinatorial Optimization (ECCO) XXV, April 26-28, 2012 Antalya, Turcja, p. 6
P. Lukasiak, K. Fidelis, M. Wojciechowski, M. Antczak, Quality assessment of protein 3D model, 24th European Conference on Operational Research, EURO XXIV 30 May – 01 June 2011, Amsterdam, Holandia, p. 26
M. Antczak, P. Lukasiak, J, Blazewicz, K, Fidelis, Quality assessment of protein structure models with using systematic evaluation of local sequence-structure compatibility, 24th European Conference on Operational Research, EURO XXIV 30 May – 01 June 2011, Amsterdam, Holandia, p. 24
P. Lukasiak, K. Fidelis, J. Blazewicz, A new approach for measuring and visualizing quality of 3D protein models, 24th European Conference on Operational Research, EURO XXIV 11-14 July 2010, Lizbona, Portugalia, p. 12
M. Milostan. P. Lukasiak, J. Blazewicz, Insights into Protein-RNA complex modeling on example of Dicer-Like proteins, 24th European Conference on Operational Research, EURO XXIV 11-14 July 2010, Lizbona, Portugalia, p. 34.
K. Fidelis, P. Lukasiak, M. Antczak, W. Biniecki, Assessment of protein structure models by systematic evaluation of local sequence-structure compatibility, 24th European Conference on Operational Research, EURO XXIV 11-14 July 2010, Lizbona, Portugalia, p. 34.
M. Milostan, J. Blazewicz, P. Lukasiak, Role of graphs in protein structure analysis, 23rd European Conference on Operational Research, EURO XXIII 5-8 July 2009, Bonn, p. 57
P. Lukasiak, J. Blazewicz, A. Hoffa, M. Antczak, Bspred method . the new approach used for predicting binding sites, 23rd European Conference on Operational Research, EURO XXIII 5-8 July 2009, Bonn, p. 57
P. Lukasiak, J. Blazewicz, P. Wojciechowski, M. Borowski, P. Kedziora, Gevadss - system for development and standardized evaluation of novel genetic vaccines, 23rd European Conference on Operational Research, EURO XXIII 5-8 July 2009, Bonn, p. 82
M. Antczak, M. Milostan, P. Lukasiak, Doman2 - approach for predicting domains boundaries in proteins, 23rd European Conference on Operational Research, EURO XXIII 5-8 July 2009, Bonn, p. 82
P. Lukasiak, J. Blazewicz, D. Klatzmann, CompuVac - development and standardized evaluation of novel genetic vaccines, European Chapter on Combinatorial Optimization (ECCO) XXII, May 17-19, 2009 Jerusalem, Izrael, p. 16
P. Lukasiak, J. Blazewicz, M. Antczak, G. Palik, M. Milostan, OR approaches for domain prediction in proteins: methods, assessment, European Chapter on Combinatorial Optimization (ECCO) XXI, May 29-31, 2008 Dubrovnik, p. 34
P. Lukasiak, M. Milostan, J. Blazewicz, M. Antczak, G. Palik Protein structure analysis using OR approaches, Book of Abstracts of 22nd European Conference on Operational Research – EURO XXII, Praga, Czechy, 2007, p. 39
M. Milostan, P. Lukasiak, J. Blazewicz, Analysis of protein domains using graph clustering algorithms, Book of Abstracts of 22nd European Conference on Operational Research – EURO XXII, Praga, Czechy, 2007, p. 66
P. Lukasiak, DomAnS - approach for predicting domain boundaries in proteins, Book of Abstracts of European Chapter on Combinatorial Optimization – ECCO XX, 24-26 May, Limassol (Cypr), 2007, p. 17
J. Blazewicz, P. Lukasiak, M. Milostan, W. Jaskowski, 3D Judge - meta predictor for 3D protein structure, Critical Assessment of Techniques for Protein Structure Prediction, Seventh Meeting, November, 2006, Pacific Groove, California, USA, pp.82.
J. Blazewicz, P. Lukasiak, M. Antczak, M. Milostan, G. Palik, DomAnS method . the new approach used for predicting domains boundaries in proteins, Critical Assessment of Techniques for Protein Structure Prediction, Seventh Meeting, November, 2006, Pacific Groove, California, USA, pp.82.
P. Lukasiak, J. Blazewicz, Methods for structural analysis of protein modeling, Book of Abstracts of European Chapter on Combinatorial Optimization – ECCO XIX, May 26-28, 2005, Minsk (Białoruś), p. 17
P. Lukasiak, M. Milostan, Tabu search strategz in HP protein model, Managing and Mining Genome InformationŁ Frontiers in Bioinformatics, Abstracts of Dagstuhl Seminar on Scheduling in Computer and Manufacturing Systems, Dagstuhl, 30.10 – 4.11.2005,
J. Blazewicz, P.L. Hammer, P. Lukasiak, Rules generator for prediction of protein secondary structures, Currents in Molecular Biology, The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003, Berlin, Germany
J. Blazewicz, K. Dill, P. Lukasiak, M. Miłostan, A tabu search strategy for finding low energy structures of proteins in HP-model, Currents in Molecular Biology, The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003, Berlin, Germany
J. Blazewicz, P.L. Hammer, P. Lukasiak, Protein Secondary structure prediction based on binarization rules, Proc. of European Conference on Computational Biology, 2003, Paris, 169-170
J. Blazewicz, P.L. Hammer, P. Lukasiak, Logical Analysis of Data Approach to the prediction of protein secondary structures, Proc. of the Third International Conference on Bioinformatics of Genome Regulation and Structure, Nowosibirsk, Russia, 2002, 3:120-125
J. Blazewicz, P.L. Hammer, P. Lukasiak, Logical Analysis of Data as a machine learning approach for prediction of protein secondary structure, Proc. of Polish – German seminar “Perspectives of Structural and Computational Biology and Their Practical Applications”, 2002, Poznan, 43
J. Blazewicz, P.L. Hammer, P. Lukasiak, Protein secondary structure prediction, Proc. of World Scientific and Engineering Society International Conference, 2001, MCBC, Skiathos, Greece
J. Blazewicz, P.L. Hammer, P. Lukasiak, Prediction of protein structure using Logical Analysis of Data”, Proc. of European Chapter on Combinatorial Optimization XIV, 2001, Bonn, 56