Uniwersytet Jagielloński Collegium Medicum Zakład bioinformatyki i telemedycyny

Mateusz Banach, PhD

Received his PhD in technical sciences (discipline: Computer Science) from the Institute of Fundamental Technological Research of the Polish Academy of Sciences in Warsaw. Dissertation title: "Metody obliczeniowe jedno- i wielokryterialnej optymalizacji rojem cząstek. Zastosowanie w bioinformatyce" (Polish - original), "Computational methods of single and multiobjective particle swarm optimization. Application in bioinformatics" (English - translation), supervisor: prof. Irena Roterman-Konieczna. Received his MSc in Computer Science from the Faculty of Physics, Astronomy and Applied Computer Science of the Jagiellonian University in Kraków. Cooperates with the Department of Bioinformatics and Telemedicine of the Jagiellonian University – Medical College since 2009, where he is employed since 2013.

USOSweb profile (schedule and contact information)

Teaching courses

current
  • Telemedycyna z Elementami Symulacji Medycznej (pol)
  • Informatyka i Statystyka Medyczna (pol)
  • Technologia Informacyjna (pol)
  • Telemedicine with Elements of Medical Simulation (eng)
  • Medical Informatics Including Biostatistics (eng)
  • Biochemistry (eng)
previous
  • Techniki informatyczne w naukach medycznych i naukach o zdrowiu (pol)
  • Systemy Operacyjne (pol)

Research fields

  • Deterministic and non-deterministic optimization methods
  • Metaheurisic algorithms, in particular those based on particle swarm paradigm
  • Multiobjective, multimodal and dynamic optimization
  • Structural and functional analysis of proteins
  • Protein/water relation models
  • Quaternary protein structure prediction

Research projects

  1. 2019 – 2020: bilateral cooperation between Jagiellonian University – Medical College and Université Pierre-et-Marie-Curie (UPMC / Paris VI) – new edition
  2. 2012 – 2013: bilateral cooperation between Jagiellonian University – Medical College and Université Pierre-et-Marie-Curie (UPMC / Paris VI) under PHC Polonium grant from Égide nr. 27748NE

Publication list

Publications indexed by ISI Web of Science or PubMed
  1. Roterman, I., Banach, M., & Konieczny, L. (2018). Towards the design of anti-amyloid short peptide helices. Bioinformation, 14(01), 001–007. doi: 10.6026/97320630014001
  2. Banach, M., Konieczny, L., & Roterman, I. (2018). Why do antifreeze proteins require a solenoid? Biochimie, 144, 74–84. doi: 10.1016/j.biochi.2017.10.011
  3. Roterman, I., Banach, M., … Konieczny, L. (2017). Antifreeze proteins. Bioinformation, 13(12), 400–401. doi: 10.6026/97320630013400
  4. Roterman, I., Banach, M., & Konieczny, L. (2017). Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals, 10(4), 89. doi: 10.3390/ph10040089
  5. Kalinowska, B., Banach, M., Wiśniowski, Z., Konieczny, L., & Roterman, I. (2017). Is the hydrophobic core a universal structural element in proteins? Journal of Molecular Modeling, 23(7). doi: 10.1007/s00894-017-3367-z
  6. Roterman, I., Banach, M., & Konieczny, L. (2017). Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. Entropy, 19(4), 167. doi: 10.3390/e19040167
  7. Gadzała, M., Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2017). Determining protein similarity by comparing hydrophobic core structure. Heliyon, 3(2), e00235. doi: 10.1016/j.heliyon.2017.e00235
  8. Dygut, J., Kalinowska, B., Banach, M., Piwowar, M., Konieczny, L., & Roterman, I. (2016). Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. International Journal of Molecular Sciences, 17(10), 1741. doi: 10.3390/ijms17101741
  9. Roterman, I., Banach, M., Kalinowska, B., & Konieczny, L. (2016). Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. Entropy, 18(10), 351. doi: 10.3390/e18100351
  10. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes—An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins. Entropy, 18(3), 67. doi: 10.3390/e18030067
  11. Banach, M., Prudhomme, N., Carpentier, M., Duprat, E., Papandreou, N., Kalinowska, B., … Roterman, I. (2015). Contribution to the Prediction of the Fold Code: Application to Immunoglobulin and Flavodoxin Cases. PLOS ONE, 10(4), e0125098. doi: 10.1371/journal.pone.0125098
  12. Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2015). Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins. Entropy, 17(3), 1477–1507. doi: 10.3390/e17031477
  13. Banach, M., Konieczny, L., & Roterman, I. (2014). The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function. Journal of Theoretical Biology, 359, 6–17. doi: 10.1016/j.jtbi.2014.05.007
  14. Kalinowska, B., Banach, M., Konieczny, L., Marchewka, D., & Roterman, I. (2014). Intrinsically Disordered Proteins—Relation to General Model Expressing the Active Role of the Water Environment. Advances in Protein Chemistry and Structural Biology, 315–346. doi: 10.1016/b978-0-12-800168-4.00008-1
  15. Banach, M., Roterman, I., Prudhomme, N., & Chomilier, J. (2013). Hydrophobic core in domains of immunoglobulin-like fold. Journal of Biomolecular Structure and Dynamics, 32(10), 1583–1600. doi: 10.1080/07391102.2013.829756
  16. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2013). Structural role of exon-coded fragment of polypeptide chains in selected enzymes. Journal of Theoretical Biology, 337, 15–23. doi: 10.1016/j.jtbi.2013.07.016
  17. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2013). Hydrophobic core formation in protein complex of cathepsin. Journal of Biomolecular Structure and Dynamics, 32(7), 1023–1032. doi: 10.1080/07391102.2013.801784
  18. Roterman, I., Konieczny, L., Banach, M., & Jurkowski, W. (2011). Intermediates in the Protein Folding Process: A Computational Model. International Journal of Molecular Sciences, 12(8), 4850–4860. doi: 10.3390/ijms11084850
  19. Marchewka, D., Banach, M., & Roterman, I. (2011). Internal force field in proteins seen by divergence entropy. Bioinformation, 6(8), 300–302. doi: 10.6026/97320630006300
  20. Roterman, I., Konieczny, L., Jurkowski, W., Prymula, K., & Banach, M. (2011). Two-intermediate model to characterize the structure of fast-folding proteins. Journal of Theoretical Biology, 283(1), 60–70. doi: 10.1016/j.jtbi.2011.05.027
  21. Banach, M., Prymula, K., Jurkowski, W., Konieczny, L., & Roterman, I. (2011). Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. Journal of Molecular Modeling, 18(1), 229–237. doi: 10.1007/s00894-011-1033-4
  22. Banach, M., Prymula, K., Konieczny, L., & Roterman, I. (2011). Fuzzy oil drop model verified positively. Bioinformation, 5(9), 375–377. doi: 10.6026/97320630005375
  23. Banach, M., & Roterman, I. (2009). Recognition of protein complexation based on hydrophobicity distribution. Bioinformation, 4(3), 98–100. doi: 10.6026/97320630004098
  24. Banach, M., Stąpor, K., & Roterman, I. (2009). Chaperonin Structure - The Large Multi-Subunit Protein Complex. International Journal of Molecular Sciences, 10(3), 844–861. doi: 10.3390/ijms10030844
Chapters in collection series
  1. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2017). Possible Mechanism of Amyloidogenesis of V Domains. Self-Assembled Molecules – New Kind of Protein Ligands, 77–100. doi: 10.1007/978-3-319-65639-7_5
  2. Irena, R., Konieczny, L., Banach, M., Marchewka, D., Kalinowska, B., Baster, Z., … Piwowar, M. (2014). Simulation of the Protein Folding Process. Springer Series in Bio-/Neuroinformatics, 599–638. doi: 10.1007/978-3-642-28554-7_18
  3. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Can the Structure of the Hydrophobic Core Determine the Complexation Site? Focus on Structural Biology, 41–54. doi: 10.1007/978-94-007-5285-6_3
  4. Alejster, P., Banach, M., Jurkowski, W., Marchewka, D., & Roterman-Konieczna, I. (2012). Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins. Focus on Structural Biology, 55–86. doi: 10.1007/978-94-007-5285-6_4
  5. Marchewka, D., Jurkowski, W., Banach, M., & Roterman-Konieczna, I. (2012). Prediction of Protein-Protein Binding Interfaces. Focus on Structural Biology, 105–133. doi: 10.1007/978-94-007-5285-6_6
  6. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). The late-stage intermediate. Protein Folding in Silico, 21–37. doi: 10.1533/9781908818256.21
  7. Banach, M., Marchewka, D., Piwowar, M., & Roterman-Konieczna, I. (2012). The divergence entropy characterizing the internal force field in proteins. Protein Folding in Silico, 55–77. doi: 10.1533/9781908818256.55
  8. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Ligand-binding-site recognition. Protein Folding in Silico, 79–93. doi: 10.1533/9781908818256.79
  9. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Use of the “fuzzy oil drop” model to identify the complexation area in protein homodimers. Protein Folding in Silico, 95–122. doi: 10.1533/9781908818256.95
Complete publication list

Search results from the Medical College's Medical Library

Conference participation

  1. Cybernetic Modelling of Biological Systems, Kraków 2015, 14.05 – 15.05, poster
  2. 13th European Conference on Computational Biology, Strasbourg, 2014, 7.09 – 10.09, poster
  3. Modelowanie i Pomiary w Medycynie, Krynica Zdrój 2013, 19.05 – 23.05, referat
  4. Konferencja Użytkowników Komputerów Dużej Mocy, Zakopane 2013, 28.02 – 1.03, referat
  5. Konferencja Użytkowników Komputerów Dużej Mocy, Zakopane 2011, 9.03 – 11.03, poster
  6. Modeling & Design of Molecular Materials, Wrocław 2010, 4.07 – 8.07, poster
  7. Modelowanie Cybernetyczne Systemów Biologicznych, Kraków 2010, 21.05 – 22.05, referat
  8. VIII European Symposium of The Protein Society, Zürich 2009, 14.06 – 18.06, poster