• Hennig EE, Mikula M, Goryca K, Paziewska A, Ledwon J, Nesteruk M, Woszczynski M, Walewska-Zielecka B, Pysniak K, Ostrowski J. Extracellular matrix and cytochrome P450 gene expression can distinguish steatohepatitis from steatosis in mice. J Cell Mol Med. 2014 Jun 9. doi: 10.1111/jcmm.12328.
  • Monika Markowska, Piotr Stępniak, Konrad Wojdan and Konrad Świrski - Smooth muscle contamination analysis in clinical oncology gene expression research, Acta Biochimica Polonica, 61(2), 333-340


  • Nesteruk M, Hennig EE, Mikula M, Karczmarski J, Dzwonek A, Goryca K, Rubel T, Paziewska A, Woszczynski M, Ledwon J, Dabrowska M, Dadlez M, Ostrowski J. Mitochondrial-related proteomic changes during obesity and fasting in mice are greater in the liver than skeletal muscles. Funct Integr Genomics. 2014 Mar;14(1):245-59. doi: 10.1007/s10142-013-0342-3. Epub 2013 Nov 1.
  • Piotr Stępniak, Matthew Maycock, Konrad Wojdan, Monika Markowska, Serhiy Perun, Aashish Srivastava, Lucjan S. Wyrwicz and Konrad Świrski: “Microarray Inspector: tissue cross contamination detection tool for microarray data“, Acta Biochimica Polonica, 60(4), 647-655
  • Piotr Stępniak, Konrad Wojdan, Joanna Chodzyńska, Lucjan Wyrwicz and Konrad Świrski: “Predictive systems in oncology based on real life patients records.”, Proceedings of the IADIS European Conference on Data Mining, Prague, Czech Republic, 22-24 July 2013
  • Martina Geier, Andreas Braun, Patrik Fladischer, Piotr Stepniak, Florian Rudroff, Christian Hametner, Marko D Mihovilovic, Anton Glieder: “Double site saturation mutagenesis of the human cytochrome P450 2D6 results in regioselective steroid hydroxylation.” FEBS Journal, 2013, DOI: 10.1111/febs.12270




  • K. Wojdan, K. Świrski, and M. Warchol: “Transition State Layer in the Immune Inspired Optimizer”, Trends in Applied Artificial Intelligence, Lecture Notes in Artificial Intelligence, vol. 6096, pp. 11–20, 2010
  • K. Wojdan, K. Swirski, and M. Warchol: “Transition States Handling in Self-Adaptive Steady State Optimizer of Industrial Processes”, Proceedings of the IASTED Conference on Modelling, Identification, and Control, Thailand, Phuket, ACTA Press 2010
  • Handschuh L, Lawenda M, Meyer N, Stepniak P, Figlerowicz M, Stroinski M, Weglarz J, Virtual laboratory and its application in genomics, in: editors: F. Davoli, N. Meyer, R. Pugliese and S. Zappatore (Eds), Remote Instrumentation and Virtual Laboratories. Service Architecture and Networking, Springer Science+Business Media, Publisher: Springer US, 2010 pp. 43-57. DOI 10.1007/978-1-4419-5597-5
  • Z.Szymański, S. Jankowski, M.Dwulit, L.S. Wyrwicz, J.Chodzyńska, “Pertinent Parameters Selection for Processing of Short Amino Acid Sequences” ,  seminar paper, Pattern Recognition in Information Systems - PRIS 2010 8-9 June, 2010, Portugal.
  • Wiśniowiecka-Kowalnik B, Nesteruk M, Peters SU, Xia Z, Cooper ML, Savage S, Amato RS, Bader P, Browning MF, Haun CL, Duda AW 3rd, Cheung SW, Stankiewicz P.Intragenic rearrangements in NRXN1 in three families with autism spectrum disorder, developmental delay, and speech delay. Am J Med Genet B Neuropsychiatr Genet. 2010; 153B(5):983-93.


  • K. Wojdan, K. Świrski, M. Warchoł, M. Maciorowski: “Conditioning of Model Identification Task in Immune Inspired Optimizer SILO”, book chapter “IAENG Transactions on Engineering Technologies Volume 3”, American Institute of Physics (AIP), November 2009
  • K. Wojdan, K. Świrski, M. Warchoł, M. Maciorowski: “Maintaining Good Conditioning of Model Identification Task in Immune Inspired On-line Optimizer of an Industrial Process”, Engineering Letters, Vol. 17/2, pp. 93-100, 2009
  • K. Wojdan, K. Świrski, M. Warchoł, M. Maciorowski: “Methods Providing Good Conditioning of Model Identification Task in Immune Inspired, Steady-State Controller of an Industrial Process”, Proc. of  International MultiConference of Engineers and Computer Scientists 2009 Vol II, IMECS 2009,  Hong Kong, 2009
  • Handschuh L., Lawenda M., Stępniak P., Figlerowicz M., Stroiński M., Węglarz J., New approach to Genomics Experiments – Taking Advantage of Virtual Laboratory System, Computational Methods in Science and Technology 15(1), 31-40 (2009)
  • Ruszczycki B., Burnett B., Zhao Z., Johnson, N. F. “Relating the microscopic rules in coalescence fragmentation models to the macroscopic cluster size distributions which emerge”, The European Physical Journal B (2009),Vol. 72, 289-302
  • Z. Zhao, A. Kirou, B. Ruszczycki and N. F. Johnson,” Dynamical Clustering as a Generator of Complex System Dynamics”, Mathematical Models and Methods in Applied Sciences, Vol. 19 (2009) pp. 1539-1565
  • Vissers LE, Bhatt SS, Janssen IM, Xia Z, Lalani SR, Pfundt R, Derwinska K, de Vries BB, Gilissen C, Hoischen A, Nesteruk M, Wisniowiecka-Kowalnik B, Smyk M, Brunner HG, Cheung SW, van Kessel AG, Veltman JA, Stankiewicz P (2009) Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture. Hum Mol Genet. 2009;18(19):3579-93. Epub 03.07.2009.


  • K. Wojdan: “System optymalizacji bieżącej punktu pracy procesów technologicznych inspirowany działaniem układu immunologicznego”, PhD thesis, Politechnika Warszawska, Warszawa, 2008
  • S. Perun, J.Tatchen and C.M.Marian, “Singlet and Triplet Excited States and Intersystem Crossing in Free-Base Porphyrin: TDDFT and DFT/MRCI Study”, ChemPhysChem, 9 (2008) 282
  • Stępniak P., Handschuh L., Figlerowicz M., Mikromacierze DNA – analiza danych, Biotechnologia 4 (83) 2008, 68-87.
  • Andy Kirou, Blazej Ruszczycki, Markus Walser, Neil F. Johnson “Computational Modeling of Collective Human Behavior: The Example of Financial Markets”, ICCS ’08 Proceedings of the 8th international conference on Computational Science, Part I


  • K. Wojdan, K. Świrski, G. Jarmoszewicz, M. Warchoł: „ Zastosowanie systemu SILO do optymalizacji procesu spalania w elektrowni Newton”, PBEC 2007, Warszawa, December 2007
  • K. Wojdan, K. Świrski, T. Chomiak: „Immune Inspired System for Chemical Process Optimization using the example of a Combustion Process in a Power Boiler”, IEEE Proc. of 14th International Conference on Intelligent System Applications to Power Systems -ISAP 2007, Kaohsiung, Tajwan, November 2007
  • K. Wojdan, K. Świrski, M. Warchol, T. Chomiak: „New improvements of immune inspired optimizer SILO”, IEEE Proc. of 19th IEEE International Conference on Tools with Artificial Intelligence -ICTAI 2007, Patras, Greece, October 2007
  • K. Wojdan, K. Świrski: „Immune Inspired Optimizer of Combustion Process in Power Boiler”, New Trends in Applied Artificial Intelligence, Lecture Notes in Computer Science, wolumen  4570/2007, strony 1022-1031, czerwiec 2007
  • K. Wojdan, K. Świrski, M. Warchoł: „Zastosowanie optymalizatora opartego na teorii sztucznych systemów immunologicznych do sterowania procesem spalania w elektrowni”, Mat. konf. II konferencji Kontrola, Sterowanie i Automatyzacja Procesu Spalania w Kotle Energetycznym, Szczyrk, June 2007


  • S. Jankowski, K. Wojdan, Z. Szymanski, R. Kozłowski: “Approximation of HRPITS results for SI GaAs by large scale support vector machine algorithms”, XVIIIth IEEE-SPIE Symposium on Photonics, Electronics and Web Engineering, WILGA 2006, Proc. SPIE, 2006
  • K. Wojdan, K. Świrski, G. Jarmoszewicz: „Stochastic Immune Layer Optimizer: efficient tool for optimization of combustion process in a boiler”, Proc. of 1st IEEE International Conference on Bio-Inspired Models of Networks, Information and Computing Systems, Cavalese, Italy, December  2006
  • S. Perun, A. L. Sobolewski and W.Domcke, “Conical Intersections In Thymine”, J. Phys. Chem. A.,110(2006) 13238
  • S. Perun, A. L. Sobolewski and W.Domcke, “Role of Electron-Driven Proton-Transfer Processes in the Excited-State Deactivation of the Adenine-Thymine Base Pair”, J. Phys. Chem. A.,110 (2006) 9031
  • S. Perun, A. L. Sobolewski and W.Domcke, “Ab initio studies on photophysics of 2-Aminopurine“, Chem. Phys., 104 (2006) 1113


  • K. Wojdan, K. Świrski, G. Jarmoszewicz, T. Chomiak: „Sztuczny system immunologiczny jako optymalizator procesu spalania”, PBEC 2005, Warszawa, 2005
  • S. Perun, A. L. Sobolewski and W.Domcke, “Ab initio study on the photophysics of adenine”, J. Am. Chem. Soc., 127 (2005) 6257
  • S. Perun, A. L. Sobolewski and W.Domcke, “Photostability of 9H-adenine: mechanisms of the radiationless deactivation of the lowest excited singlet states”, Chem. Phys., 313 (2005) 107


  • C. Dedonder-Lardeux, Ch. Jouvet, S. Perun, and A. L. Sobolewski, “External electric field effect on excited states of indole: ab initio and molecular dynamics study”, Phys. Chem. Chem. Phys., 5 (2003) 5118