dr Mateusz Banach

Doktor nauk technicznych – dziedzina: Informatyka, stopień naukowy nadany przez Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk w Warszawie w 2018 r. Tytuł zawodowy magistra (kierunek: Informatyka, specjalność: Informatyka Stosowana) uzyskał na Wydziale Fizyki, Astronomii i Informatyki Stosowanej Uniwersytetu Jagiellońskiego w Krakowie w 2009 r. Obecnie pracuje na stanowisku adiunkta. Członek Polskiego Towarzystwa Informatycznego (obecnie Oddziału Białostockiego) od 2016 r.

Dane kontaktowe i harmonogram zajęć

https://www.usosweb.uj.edu.pl/kontroler.php?_action=katalog2/osoby/pokazOsobe&os_id=2492

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Prowadzone zajęcia dydaktyczne

  • Telemedycyna z elementami symulacji medycznej (Wydział Lekarski, kierunek lekarski, II rok)
  • Informatyka i Statystyka Medyczna 2/2 (Wydział Lekarski, kierunek lekarsko-dentystyczny, III rok)
  • Informatyka – fakultet (Wydział Lekarski, kierunek dietetyka, II rok mgr)
  • Telemedicine with Elements of Medical Simulation (Szkoła Medyczna dla Obcokrajowców, kierunek lekarski, II rok)
  • Computer science and medical statistics (Szkoła Medyczna dla Obcokrajowców, kierunek lekarsko-dentystyczny, I rok)
  • Medical Informatics including biostatistics 2/2 (Szkoła Medyczna dla Obcokrajowców, kierunek lekarsko-dentystyczny, III rok)
  • Biochemistry with Elements of Chemistry (Szkoła Medyczna dla Obcokrajowców, kierunek lekarski, II rok)

Udział w projektach badawczych

  • 2018 – 2019: współpraca bilateralna pomiędzy Uniwersytetem Jagiellońskim – Collegium Medicum a Sorbonne Université (dawniej Université Pierre-et-Marie-Curie / Paris VI) w ramach grantu PHC Polonium nr 405111TL
  • 2012 – 2013: współpraca bilateralna pomiędzy Uniwersytetem Jagiellońskim – Collegium Medicum a Sorbonne Université (dawniej Université Pierre-et-Marie-Curie / Paris VI) w ramach grantu PHC Polonium nr 27748NE

Wykaz wybranych prac naukowych

Pełna i aktualna lista dorobku naukowego jest dostępna w witrynie Biblioteki Medycznej.

Publikacje w czasopismach
  1. Banach, M., Fabian, P., Stapor, K., Konieczny, L., Ptak-Kaczor, M., & Roterman, I. (2020). The Status of Edge Strands in Ferredoxin-Like Fold. Symmetry, Vol. 12(nr 6). https://doi.org/10.3390/sym12061032
  2. Banach, M., Fabian, P., Stapor, K., Konieczny, L., & Roterman, I. (2020). Structure of the Hydrophobic Core Determines the 3D Protein Structure-Verification by Single Mutation Proteins. Biomolecules, Vol. 10(nr 5). https://doi.org/10.3390/biom10050767
  3. Banach, M., Stapor, K., Konieczny, L., Fabian, P., & Roterman, I. (2020). Downhill, Ultrafast and Fast Folding Proteins Revised. International Journal of Molecular Sciences, Vol. 21(nr 20). https://doi.org/10.3390/ijms21207632
  4. Dułak, D., Gadzała, M., Banach, M., Konieczny, L., & Roterman, I. (2020). Alternative Structures of α-Synuclein. Molecules, Vol. 25(nr 3). https://doi.org/10.3390/molecules25030600
  5. Fabian, P., Banach, M., Stapor, K., Konieczny, L., Ptak-Kaczor, M., & Roterman, I. (2020). The Structure of Amyloid Versus the Structure of Globular Proteins. International Journal of Molecular Sciences, Vol. 21(nr 13). https://doi.org/10.3390/ijms21134683
  6. Fabian, P., Stapor, K., Banach, M., Ptak-Kaczor, M., Konieczny, L., & Roterman, I. (2020). Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy. Symmetry, Vol. 12(nr 2). https://doi.org/10.3390/sym12020273
  7. Banach, M., Konieczny, L., & Roterman, I. (2019). Symmetry and Dissymmetry in Protein Structure-System-Coding Its Biological Specificity. Symmetry, Vol. 11(nr 10), 1215. https://doi.org/10.3390/sym11101215
  8. Banach, M., Konieczny, L., & Roterman, I. (2019). The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules, Vol. 24(nr 23), 4395. https://doi.org/10.3390/molecules24234395
  9. Fabian, P., Stapor, K., Banach, M., Ptak-Kaczor, M., Konieczny, L., & Roterman, I. (2019). Different Synergy in Amyloids and Biologically Active Forms of Proteins. International Journal of Molecular Sciences, Vol. 20(nr 18), 4436. https://doi.org/10.3390/ijms20184436
  10. Gadzała, M., Dułak, D., Kalinowska, B., Baster, Z., Bryliński, M., Konieczny, L., Banach, M., & Roterman, I. (2019). The aqueous environment as an active participant in the protein folding process. Journal of Molecular Graphics & Modelling, Vol. 87, s. 227-239. https://doi.org/10.1016/j.jmgm.2018.12.008
  11. Ptak-Kaczor, M., Banach, M., Konieczny, L., & Roterman, I. (2019). Internal force field in selected proteins. Acta Biochimica Polonica, Vol. 66(nr 4, Part I), s. 451-458. https://doi.org/10.18388/abp.2019_2865
  12. Roterman, I., Dułak, D., Gadzała, M., Banach, M., & Konieczny, L. (2019). Structural analysis of the Aβ(1142) amyloid fibril based on hydrophobicity distribution. Journal of Computer-Aided Molecular Design, Vol. 33(nr 7), s. 665-675. https://doi.org/10.1007/s10822-019-00209-9
  13. Banach, M., Konieczny, L., & Roterman, I. (2018). Why do antifreeze proteins require a solenoid? Biochimie, Vol. 144, s. 74-84. https://doi.org/10.1016/j.biochi.2017.10.011
  14. Dułak, D., Banach, M., Gadzała, M., Konieczny, L., & Roterman, I. (2018). Structural analysis of the Aβ(15-40) amyloid fibril based on hydrophobicity distribution. Acta Biochimica Polonica, Vol. 65(nr 4), s. 595-604. https://doi.org/10.18388/abp.2018_2647
  15. Dułak, D., Gadzała, M., Banach, M., Ptak, M., Wiśniowski, Z., Konieczny, L., & Roterman, I. (2018). Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model. International Journal of Molecular Sciences, Vol. 19(nr 10 art. no. 2910), s. 1-29. https://doi.org/10.3390/ijms19102910
  16. Gadzała, M., Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2017). Determining protein similarity by comparing hydrophobic core structure. Heliyon, Vol. 3(nr 2 art. no. e00235), s. 1-32. https://doi.org/10.1016/j.heliyon.2017.e00235
  17. 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, Vol. 23(nr 7 art. no. 203), s. 1-16. https://doi.org/10.1007/s00894-017-3367-z
  18. Roterman, I., Banach, M., & Konieczny, L. (2017). Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. Entropy, Vol. 19(nr 4 art. no. 167), s. 1-19. https://doi.org/10.3390/e19040167
  19. Roterman, I., Banach, M., & Konieczny, L. (2017). Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals, Vol. 10(nr 4 art. nr 89), s. 1-15. https://doi.org/10.3390/ph10040089
  20. 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, Vol. 18(nr 3 art. no. 67), s. 1-21. https://doi.org/10.3390/e18030067
  21. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Sequence-to-Structure Relation in Proteins-Amyloidogenic Proteins with Chameleon Sequences. Journal of Proteomics and Bioinformatics, Vol. 9(nr 11), s. 264-275. https://doi.org/10.4172/jpb.1000415
  22. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Structural Role of Hydrophobic Core in Proteins-Selected Examples. Journal of Proteomics and Bioinformatics, Vol. 9(nr 11), s. 276-286. https://doi.org/10.4172/jpb.1000416
  23. 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, Vol. 17(nr 10 art. no. E1741), s. 1-21. https://doi.org/10.3390/ijms17101741
  24. 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, Vol. 18(nr 10 art. no. 351), s. 1-31. https://doi.org/10.3390/e18100351
  25. Banach, M., Prudhomme, N., Carpentier, M., Duprat, E., Papandreou, N., Kalinowska, B., Chomilier, J., & Roterman, I. (2015). Contribution to the prediction of the fold code: Application to immunoglobulin and flavodoxin cases. PLoS One, Vol. 10(nr 4 art. no. e0125098), s. 1-26. https://doi.org/10.1371/journal.pone.0125098
  26. 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, Vol. 17(nr 3), s. 1477-1507. https://doi.org/10.3390/e17031477
  27. 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, Vol. 351, s. 6-17. https://doi.org/10.1016/j.jtbi.2014.05.007
  28. 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, Vol. 94, s. 315-346. https://doi.org/10.1016/B978-0-12-800168-4.00008-1
  29. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2014). Hydrophobic core formation in protein complex of cathepsin. Journal of Biomolecular Structure & Dynamics, Vol. 32(nr 7), s. 1023-1032. https://doi.org/10.1080/07391102.2013.801784
  30. 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, Vol. 337, s. 15-23. https://doi.org/10.1016/j.jtbi.2013.07.016
  31. Banach, M., Prymula, K., Jurkowski, W., Konieczny, L., & Roterman, I. (2012). Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. Journal of Molecular Modeling, Vol. 18(nr 1), s. 229-237. https://doi.org/10.1007/s00894-011-1033-4
  32. Roterman, I., Konieczny, L., Banach, M., & Jurkowski, W. (2011). Intermediates in the protein folding process: A computational model. International Journal of Molecular Sciences, Vol. 12(nr 8), s. 4850-4860. https://doi.org/10.3390/ijms11084850
  33. Banach, M., Stąpor, K., & Roterman, I. (2009). Chaperonin structure—The large multi-subunit protein complex. International Journal of Molecular Sciences, Vol. 10(nr 3), s. 844-861. https://doi.org/10.3390/ijms10030844
Rozdziały w monografiach
  1. Banach, M., Konieczny, L., & Roterman, I. (2020). Anti-amyloid drug design. In From Globular Proteins to Amyloids. (p. s. 215-231). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00019-1
  2. Banach, M., Konieczny, L., & Roterman, I. (2020). Composite structures. In From Globular Proteins to Amyloids. (p. s. 117-133). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00011-7
  3. Banach, M., Konieczny, L., & Roterman, I. (2020). Ligand binding cavity encoded as a local hydrophobicity deficiency. In From Globular Proteins to Amyloids. (p. s. 91-93). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00009-9
  4. Banach, M., Konieczny, L., & Roterman, I. (2020). Local discordance. In From Globular Proteins to Amyloids. (p. s. 69). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00006-3
  5. Banach, M., Konieczny, L., & Roterman, I. (2020). Protein-protein interaction encoded as an exposure of hydrophobic residues on the surface. In From Globular Proteins to Amyloids. (p. s. 79-89). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00008-7
  6. Banach, M., Konieczny, L., & Roterman, I. (2020). Proteins structured as spherical micelles. In From Globular Proteins to Amyloids. (p. s. 55-68). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00005-1
  7. Banach, M., Konieczny, L., & Roterman, I. (2020). The active site in a single-chain enzyme. In From Globular Proteins to Amyloids. (p. s. 71-78). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00007-5
  8. Banach, M., Konieczny, L., & Roterman, I. (2020). The hypothetical amyloid transformation of transthyretin. In From Globular Proteins to Amyloids. (p. s. 233-240). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00020-8
  9. Banach, M., & Roterman, I. (2020). Amyloid as a ribbon-like micelle. In From Globular Proteins to Amyloids. (p. s. 177-191). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00016-6
  10. Banach, M., & Roterman, I. (2020). Amyloids identification based on fuzzy oil drop model. In From Globular Proteins to Amyloids. (p. s. 173-175). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00015-4
  11. Banach, M., & Roterman, I. (2020). Complexes AΒ(142) polypeptide with non-protein molecules. In From Globular Proteins to Amyloids. (p. s. 137-156). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00013-0
  12. Banach, M., & Roterman, I. (2020). Non-amyloid structure of the AΒ(142) polypeptide in presence of a permanent chaperone. In From Globular Proteins to Amyloids. (p. s. 135-136). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00012-9
  13. Banach, M., & Roterman, I. (2020). Solenoid—An amyloid under control. In From Globular Proteins to Amyloids. (p. s. 95-115). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00010-5
  14. Banach, M., & Roterman, I. (2020). Specificity of amino acid sequence and its role in secondary and supersecondary structure generation. In From Globular Proteins to Amyloids. (p. s. 207-214). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00018-X
  15. Banach, M., & Roterman, I. (2020). Structure of selected fragments of AΒ(142) in complex with other proteins. In From Globular Proteins to Amyloids. (p. s. 157-172). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00014-2
  16. Dułak, D., Gadzała, M., Banach, M., & Roterman, I. (2020). Analysis of alternative conformations of the AΒ(140) amyloid protein. In From Globular Proteins to Amyloids. (p. s. 193-206). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00017-8
  17. Banach, M., Konieczny, L., & Roterman, I. (2019). Fuzzy Oil Drop Model Application-From Globular Proteins to Amyloids. In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. From Bioinformatics to Molecular Quantum Mechanics. (p. s. 639-658). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-319-95843-9_19
  18. Banach, M., Konieczny, L., & Roterman, I. (2019). Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores. In Protein supersecondary structures. Methods and Protocols. (p. s. 347-378). Springer Science + Business Media. https://doi.org/10.1007/978-1-4939-9161-7_19
  19. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2018). Possible mechanism of amyloidogenesis of V domains. In Self-Assembled Molecules New Kind of Protein Ligands: Supramolecular Ligands. (p. s. 77-100). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-319-65639-7_5
  20. Roterman, I., Konieczny, L., Banach, M., Marchewka, D., Kalinowska, B., Baster, Z., Tomanek, M., & Piwowar, M. (2014). Simulation of the protein folding process. In Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: From bioinformatics to molecular quantum mechanics. (p. s. 599-638). Springer. https://doi.org/10.1007/978-3-642-28554-7_18
  21. Alejster, P., Banach, M., Jurkowski, W., Marchewka, D., & Roterman-Konieczna, I. (2013). Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins. In Identification of ligand binding site and protein-protein interaction area. (p. s. 55-86). Springer. https://doi.org/10.1007/978-94-007-5285-6_4
  22. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2013). Can the structure of the hydrophobic core determine the complexation site? In Identification of ligand binding site and protein-protein interaction area. (p. s. 41-54). Springer. https://doi.org/10.1007/978-94-007-5285-6_3
  23. Marchewka, D., Jurkowski, W., Banach, M., & Roterman-Konieczna, I. (2013). Prediction of protein-protein binding interfaces. In Identification of ligand binding site and protein-protein interaction area. (p. s. 105-134). Springer. https://doi.org/10.1007/978-94-007-5285-6_6
  24. Wiśniowski, Z., Banach, M., & Roterman, I. (2013). Antifreeze compounds to allow survival at temperatures below 0 C deg. In Manufacture Engineering, Quality and Production System II. (p. s. 32-38). Trans Tech Publications. https://doi.org/10.4028/www.scientific.net/AMR.711.32
  25. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Ligand-binding recognition. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 79-93). Woodhead Pub.
  26. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). The late-stage intermediate. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 21-37). Woodhead Pub.
  27. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Use of the fuzzy oil drop model to identify the complexation area in protein homodimers. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 95-122). Woodhead Pub.
  28. Banach, M., Marchewka, D., Piwowar, M., & Roterman-Konieczna, I. (2012). The divergence entropy characterizing the internal force field in proteins. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 55-77). Woodhead Pub.
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