Department of Biomedical Engineering   
Group of Bioinformatics and Biophysics of Nanopores
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Publications
  1. Wojciechowski JW, Kotulska M, PATH - prediction of amyloidogenicity by threading and machine learning. Scientific Reports. 2020, vol. 10, art. 7721, s. 1-9. doi: doi.org/10.1038/s41598-020-64270-3

  2. Unold O., Gabor M., Dyrka W (2020) Unsupervised Grammar Induction for Revealing the Internal Structure of Protein Sequence Motifs. In: Michalowski M., Moskovitch R. (eds) Artificial Intelligence in Medicine. AIME 2020. Lecture Notes in Computer Science, vol 12299, pp. 299-309. Springer, Cham. doi: 10.1007/978-3-030-59137-3_27

  3. Kobielarz MJ, Kozuń MM, Gąsior-Głogowska ME, Chwiłkowska A, Mechanical and structural properties of different types of human aortic atherosclerotic plaques. Journal of the Mechanical Behavior of Biomedical Materials. 2020, vol. 109, art. 103837, s. 1-12. doi: 10.1016/j.jmbbm.2020.103837

  4. Kulbacka J, Choromańska A, Drąg-Zalesińska M, Nowak PM, Baczyńska D, Kotulska M, Bednarz-Misa I, Saczko J, Chwiłkowska A, Proapoptotic activity induced by photodynamic reaction with novel cyanine dyes in caspase-3-deficient human breast adenocarcinoma cell lines (MCF/ WT and MCF/DX). Photodiagnosis and Photodynamic Therapy. 2020, vol. 30, art. 101775, s. 1-8.

  5. Kulbacka J, Kasztelanic R, Kotulska M, Pysz D, Stępniewski G, Stępień R, Saczko J, Miklavčič D, Buczyński R, Ultrathin glass fiber microprobe for electroporation of arbitrary selected cell groups. Bioelectrochemistry. 2020, vol. 135, art. 107545, s. 1-12. doi: 10.1016/j.bioelechem.2020.107545

  6. Dyrka W, Pyzik M, Coste F, Talibart H, Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ. 2019, vol. 7, art. e6559, s. 1-35. doi: 10.7717/peerj.6559

  7. Bujok J, Gąsior-Głogowska ME, Marszałek M, Trochanowska-Pauk N, Zigo F, Pavľak A, Komorowska M, Walski TJ. Applicability of FTIR-ATR method to measure carbonyls in blood plasma after physical and mental stress. Biomed Research International. 2019, vol. 2019, art. 2181370, s. 1-9. doi: 10.1155/2019/2181370

  8. Mączyńska J, Choromańska A, Kutkowska J, Kotulska M, Zalewski M, Zalewski J, Kulbacka J, Saczko J, Effect of electrochemotherapy with betulinic acid or cisplatin on regulation of heat shock proteins in metastatic human carcinoma cells in vitro. Oncology Reports. 2019, vol. 41, nr 6, s. 3444-3454. doi: 10.3892/or.2019.7103

  9. Hatt M, Laurent B, Ouahabi A, Fayad H, Tan S, Li L, Lu W, Jaouen V, Tauber C, Czakon J, Drapejkowski F, Dyrka W, Camarasu-Pop S, Cervenansky F, Girard P, Glatard T, Kain M, Yao Y, Barillot C, Kirov A, Visvikis D, The first MICCAI challenge on PET tumor segmentation. Medical Image Analysis. 2018, vol. 44, s. 177-195. doi: 10.1016/j.media.2017.12.007

  10. Konopka BM, Lwow F, Owczarz M, Łaczmański Ł, Exploratory data analysis of a clinical study group: Development of a procedure for exploring multidimensional data. PLoS ONE. 2018, vol. 13, nr 8, art. e0201950, s. 1-21. doi: 10.1371/journal.pone.0201950

  11. Rorbach G, Unold O, Konopka BM, Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods. Scientific Reports. 2018, vol. 8, art. 7560, s. 1-13. doi: 10.1038/s41598-018-25578-3

  12. Weżgowiec JB, Kulbacka J, Saczko J, Rossowska J, Chodaczek G, Kotulska M, Biological effects in photodynamic treatment combined with electropermeabilization in wild and drug resistant breast cancer cells. Bioelectrochemistry. 2018, vol. 123, s. 9-18. doi: 10.1016/j.bioelechem.2018.04.008

  13. Kurczynska M, Kotulska M Automated method to differentiate between native and mirror protein models obtained from contact maps. PLoS ONE. 2018, vol. 13, nr 5, art. e0196993, s. 1-19. doi: 10.1371/journal.pone.0196993

  14. Wozniak PP, Pelc J, Skrzypecki M, Vriend G, Kotulska M Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinformatics. 2018, vol. 34, nr 21, s. 3675–3683. doi: 10.1093/bioinformatics/bty416

  15. Konopka BM, Marta Marciniak, Dyrka W Quantiprot - a Python package for quantitative analysis of protein sequences. BMC Bioinformatics. 2017, vol. 18, art. 339, s. 1-6. doi: 10.1186/s12859-017-1751-4

  16. Wozniak PP, Vriend G, Kotulska M, Correlated mutations select misfolded from properly folded proteins. Bioinformatics. 2017 Jan 17. doi: 10.1093/bioinformatics/btx013.

  17. Wozniak PP, Konopka BM, Xu J, Vriend G, Kotulska M, Forecasting residue–residue contact prediction accuracy. Bioinformatics. 2017 Nov 1. doi: 10.1093/bioinformatics/btx416.

  18. Burdukiewicz M, Sobczyk P, Rödiger S, Duda-Madej A, Mackiewicz P, Kotulska M, Amyloidogenic motifs revealed by n-gram analysis. Scientific Reports. 2017 Oct 11. doi: 10.1038/s41598-017-13210-9

  19. Kurczynska M, Konopka BM, Kotulska M, Role of bioinformatics in the study of ionic channels. Advances in Anatomy, Embryology and Cell Biology. 2017, vol. 227, s. 17-39. doi: 10.1007/978-3-319-56895-9_2

  20. Kurczynska M, Konopka BM, Kotulska M, Role of bioinformatics in the study of ionic channels. Advances in Anatomy, Embryology and Cell Biology. 2017, vol. 227, s. 17-39. doi: 10.1007/978-3-319-56895-9_2

  21. Kulbacka J , Paczuska J, Rembiałkowska N, Saczko J, Kiełbowicz Z, Kinda W, Liszka B, Kotulska M, Kos B, Miklavčič D, Tozon N, Čemažar M, Electrochemotherapy combined with standard and CO2 laser surgeries in canine oral melanoma. Slovenian Veterinary Research. 017: 54 (4): 181-6. doi: 10.26873/SVR-322-2017

  22. Dyrka W, Kurczynska M, Konopka BM, Kotulska M, Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics. Proteins: Structure, Function and Bioinformatics. 2016, vol. 84, nr 2, s. 217-231. doi: 10.1002/prot.24967.

  23. Kulbacka J, Pucek AJ, Kotulska M, Dubińska-Magiera M, Rossowska J, Rols M, Wilk K, Electroporation and lipid nanoparticles with cyanine IR-780 and flavonoids as efficient vectors to enhanced drug delivery in colon cancer. Bioelectrochemistry 110 (2016) 19–31. doi: 10.1016/j.bioelechem.2016.02.013.

  24. Kulbacka J, Pucek A, Wilk KA, Dubińska-Magiera M, Rossowska J, Kulbacki M, Kotulska M, The effect of millisecond pulsed electric fields (msPEF) on intracellular drug transport with negatively charged large nanocarriers made of solid lipid nanoparticles (SLN): in vitro study. Journal of Membrane Biology. 2016 May 12. doi: 10.1007/s00232-016-9906-1.

  25. Lamacchia M, Dyrka W, Breton A, Saupe SJ, Paoletti M, Overlapping Podospora anserina transcriptional responses to bacterial and fungal non self indicate a multilayered innate immune response. Frontiers in Microbiology 2016, 7:471.

  26. Kurczynska M, Kania E, Konopka BM, Kotulska M, Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps. J Mol Model. 2016 May;22(5):111. doi: 10.1007/s00894-016-2975-3

  27. Wozniak PP, Nebel J-C, Kotulska M, Databases of Peptides Susceptible to Aggregation as a Tool for Studying Mechanisms of Diseases of Civilization, ACIIDS 2016, part I, Lecture Notes in Artificial Intelligence LNCS/LNAI 9621, Chapter 30, 978-3-662-49380-9, 417955_1_En, 14-16 March 2016.

  28. Dyrka W, Kurczynska M, Konopka BM, Kotulska M, Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics, Proteins. 2016 Feb;84(2):217-31. doi: 10.1002/prot.24967

  29. Daskalov A, Dyrka W, Saupe SJ, Theme and variations: evolutionary diversification of the HET-s functional amyloid motif, Scientific Reports 2015, 5:12494

  30. Wozniak PP, Kotulska M, AmyLoad - website dedicated to amyloidogenic protein fragments. Bioinformatics. 2015 doi: 10.1093/bioinformatics/btv375

  31. Zulpo M, Kotulska M, Comparative modeling of hypothetical amyloid pores based on cylindrin. Journal of Molecular Modeling. 2015, 21(6): 2691

  32. Kurczynska M, Kotulska M, Ion Move Brownian Dynamics (IMBD) - Simulations of Ion Transport. Acta of Bioengineering and Biomechanics. 2014, 16(4): 105-114

  33. Wozniak PP, Kotulska M, Characteristics of protein residue-residue contacts and their application in contact prediction. J Mol Model. 2014 Nov;20(11):2497. doi: 10.1007/s00894-014-2497-9.

  34. Kulbacka J, Daczewska M, Dubinska-Magiera M, Choromanska A, Rembialkowska N, Surowiak P, Kulbacki M, Kotulska M, Saczko J, Doxorubicin delivery enhanced by electroporation to gastrointestinal adenocarcinoma cells with P-gp overexpression, Bioelectrochemistry, 2014, doi: 10.1016/j.bioelechem.2014.03.013. [Epub ahead of print]

  35. Gasior P, Kotulska M, FISH Amyloid - a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids, BMC Bioinformatics, 2014, 15:54, doi: 10.1186/1471-2105-15-54

  36. Konopka BM, Ciombor M, Kurczynska M, Kotulska M, Automated procedure for contact-map-based protein structure reconstruction, Journal of Membrane Biology, 2014, DOI 10.1007/s00232-014-9648-x

  37. Kotulska M and Unold O, On the amyloid datasets used for training PAFIG - how (not) to extend the experimental dataset of hexapeptides, BMC Bioinformatics [e-published], 2013, vol. 14, nr 351, pp. 1-8.

  38. Dyrka W, Nebel J-C, and Kotulska M, Probabilistic grammatical model for helix-helix contact site classification, Algorithms for Molecular Biology [e-published], 2013, vol. 8, nr 31, pp. 1-26

  39. Cichowski W and Kurczynska M, Ion current analyser v.2.0 (ICA) - narzedzie do analizy wynikow symulacji transportu jonow przez nanopory, Otwarta Innowacja, 2013, nr 1/2, pp. 16-25

  40. Kotulska M, Kulbacka J, and Saczko J, Advances in photodynamic therapy assisted by electroporation, Current Drug Metabolism, 2013, vol. 14, nr 3, pp. 309-318

  41. Kulbacka J, Kotulska M, Rembialkowska N, Choromanska A, Kaminska I, Garbiec A, Rossowska J, Daczewska M, Jachimska B, and Saczko J, Cellular stress induced by photodynamic reaction with CoTPPS and MnTMPyPCl5 in combination with electroporation in human colon adenocarcinoma cell lines (LoVo and LoVoDX), Cell Stress & Chaperones, 2013, pp. 1-13

  42. Stanislawski J, Kotulska M, and Unold O, Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides, BMC Bioinformatics, 2013, vol. 14, [art.] 21, pp. 1-19

  43. Wezgowiec J, Derylo M B, Teissie J, Orio J, Rols M-P, Kulbacka J, Saczko J, and Kotulska M, Electric field-assisted delivery of photofrin to human breast carcinoma cells, Journal of Membrane Biology, 2013, 246(10):725-735

  44. Wezgowiec J, Kotulska M, Saczko J, Derylo M B, Teissie J, Rols M-P, Orio J, Garbiec A, and Kulbacka J, Cyanines in photodynamic reaction assisted by reversible electroporation-in vitro study on human breast carcinoma cells, Photodiagnosis and Photodynamic Therapy, 2013, 10:490-502

  45. Dyrka W, Bartuzel MM, and Kotulska M, Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels, Proteins, 2013, Volume 81, Issue 10, pp. 1802-1822

  46. Kaminska I, Kotulska M, Stecka A, Saczko J, Drag-Zalesinska M, Wysocka T, Choromanska A, Skolucka N, Nowicki R, Marczak J, and Kulbacka J, Electroporation-induced changes in normal immature rat myoblasts (H9C2), General Physiology and Biophysics, 2012, vol. 31, pp. 19-25

  47. Konopka B, Nebel J-C, and Kotulska M, Quality assessment of protein model-structures based on structural and functional similarities, BMC Bioinformatics, 2012, vol. 13, pp. 1-18

  48. Kramar P, Delemotte L, Macek-Lebar A, Kotulska M, Tarek M, and Miklavcic D, Molecular-level characterization of lipid membrane electroporation using linearly rising current, Journal of Membrane Biology, 2012, vol. 245, nr 10, pp. 651-659

  49. Kulbacka J, Nowak M, Skołucka N, Saczko J, and Kotulska M, The influence of electroporation on in vitro photodynamic therapy of human breast carcinoma cells, Folia Biologica, 2011

  50. Skolucka N, Daczewska M, Saczko J, Chwilkowska A, Choromanska A, Kotulska M, Kaminska I, Kulbacka J, ETM study of electroporation influence on cell morphology in human malignant melanoma and human primary gingival fibroblast cells, Asian Pacific Journal of Tropical Biomedicine , 2011

  51. Kulbacka J, Pola A, Mosiadz D, Choromanska A, Nowak P, Kotulska M, Majkowski M, Hryniewicz-Jankowska A, Purzyc L, Saczko J, Cyanines as efficient photosensitizers in the photodynamic reaction: Photophysical properties and in vitro photodynamic activity, Biochemistry (Moscow), Vol. 76, issue 4, 2011.

  52. Dyrka W, Nebel JC, Kotulska M, Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence, T.M.H. Dijkstra et al. (Edpp.), PRIB 2010, Lecture Notes in Bioinformatics , 6282, 62–73, Springer 2010.

  53. Kotulska M, Basalyga J, Derylo MB, Sadowski P, Meta-stable pores at the onset of constant-current electroporation, Journal of Membrane Biology, 236(1), 37-41, 2010. (on-line)

  54. Saczko J, Nowak M, Skolucka N, Kulbacka J , Kotulska M , The effects of the electro-photodynamic in vitro treatment on human lung adenocarcinoma cells, Bioelectrochemistry,79(1), 90-4, 2010

  55. Kramar P, Miklavcic D, Kotulska M, Macek-Lebar AVoltage- and Current-Clamp Methods for Determination of Planar Lipid Bilayer Propertiepp. In ed. A. Iglic: "Advances in Planar Lipid Bilayers and Liposomes, Vol. 11, Burlington:Academic Press, 2010, pp. 29-69. Elsevier, ISBN: 978-0-12-381013-7

  56. Kotulska M, Dyrka W, Sadowski P, Fluorescent methods in evaluation of nanopore conductivity - computational validation, chapter in “Advanced electroporation techniques in biology and medicine”, edpp. Pakhomov A.G, Miklavcic D, Markov M.S, CRC, 2010.

  57. Skolucka N, Saczko J, Kotulska M, Kulbacka J, Elektroporacja i jej zastosowanie (Electroporation and its application) Polski Merkuriusz Lekarski, 28(168):501-4, 2010

  58. Dyrka W, Nebel JC., A stochastic context free grammar based framework for analysis of protein sequencepp. BMC Bioinformatics , 10:323, 2009 (on-line)

  59. Konopka B, Dyrka W, Nebel J-C, Kotulska M, Accuracy in predicting secondary structure of ionic channels, chapter in “Challenges in Computational Collective Intelligence”, edpp. N.T. Nguyen, R.Katarzyniak, A. Janiak, SCI 244, pp.315-326, Springer-Verlag Berlin Heidelberg, 2009 (book on-line).

  60. Dyrka W., Augousti A., Kotulska M., Ion flux through membrane channels - an enhanced algorithm for the Poisson-Nernst-Planck model, Journal of Computational Chemistry , 29/12 (2008), 1877-1888

  61. Kotulska M., Kubica K., Random processes in appearance and dynamics of an electropore in a lipid membrane, in: Advances in Planar Lipid Bilayers and Liposomes, vol. 7. ed. A. Leitmannova Liu, Elsevier (2008)

  62. Kotulska M., Electrochemotherapy in cancer treatment, Advances in clinical and experimental medicine, 16/5 (2007), 601-607

  63. Kotulska M., Electro-Nanopores in the Lipid Membrane and Their Application in Medicine, Prace Instytutu Biocybernetyki i Inżynierii Biomedycznej, Warsaw 2007.

  64. Kotulska M., Perspektywy terapii genowej wspomaganej elektroporacją o kontrolowanym rozmiarze i czasie życia elektropora, Proc. XV KbiIB (2007)

  65. Kotulska M., Natural fluctuations of an electropore show fractional Lévy stable motion, Biophysical Journal , 92 (2007) 2412-21 (pdf).

  66. Kotulska M., Kubica K., Koronkiewicz S., Kalinowski S., Modeling the induction of lipid membrane electropermeabilization, Bioelectrochemistry 70(1), (2007) 64-70, (pdf 165 kB).

  67. Kalinowski S., Koronkiewicz S., Kotulska M., Kubica K., Simulation of electroporated cell by chronopotentiometry, Bioelectrochemistry 70(1), (2007) 83-90

  68. Dyrka W, Nebel J-C: A probabilistic context-free grammar for the detection of binding sites from a protein sequence. BMC Systems Biology 2007 vol. 1, suppl. 1, http://www.biomedcentral.com/1752-0509/.

  69. Jafri M.S., Kotulska M., Modeling the Mechanism of Metabolic Oscillations in Ischemic Cardiac Myocytes, J. Theoretical Biology 242(4),(2006) 801-17

  70. Kotulska M., Kubica K., Structural and energetic model of the mechanisms for reduced self-diffusion in a lipid bilayer with increasing ionic strength, Physical Review E 72 (2005) 061903-09

  71. Kania M., Kotulska M., A system for modeling the cooperativity of ryanodine receptors in cardiac myocytes, Proc. 3rd IFMBE European Conference on Biomedical Engineering , EMBEC'05 (2005)

  72. Kotulska M., Kubica K., Modeling the Effect of Ionic Strength on Durability of Lipid Membrane in the Gel Phase, Acta Phypp. Pol. B 36 (2005) 1641-1651

  73. Kotulska M., 1/f noise in nanopores and its potential application in biosensors, Elektronika 8-9 (2004) 130

  74. Kotulska M., Koronkiewicz S., Kalinowski S., Self-similar processes and flicker noise from a fluctuating nanopore in a lipid membrane, Physical Review E 69 (2004), 031920-30

  75. Kotulska M., Jafri M. S. Modeling the Mechanism of Metabolic Oscillations in Metabolically Deprived Cardiac Myocytes, Proc. EMBS / BMES (2002), 2217-18

  76. Jellonek K., Kotulska M., New Concepts and Techniques in Education of Biomedical Engineers in Computer Science, Proc. IMEKO TC-1 (2002), 83-90

  77. Jellonek K., Kotulska M., Measuring and Diagnostic Systems in Biomedical Education, Engineering Science and Education Journal 11, (2002), 2-6

  78. Kotulska M.,Koronkiewicz S., Kalinowski S., Cholesterol Induced Changes in the Characteristics of the Time Series from Planar Lipid Bilayer Membrane During Electroporation, Acta Phypp. Pol. B (2002), 33, 1115-1124 (Abstract or gzipped PostScript).

  79. Jellonek K., Kotulska M., Measuring And Diagnostic Systems - Real and Virtual Measures in Biomedical Education, IEEE Proc.(2001).

  80. Jellonek K., Kotulska M., A Medical - Measuring Diagnostic System (MMDS) based on Cellular Telephone Functions, Proc. 11 IMEKO TC-4 (2001), 221-224

  81. Kotulska, M., Jurlewicz, A. How heterogenous strukture of tissue effects its dielectric characteristics, Acta Phypp. Pol. B 31 (2000), 1085-1096 (Abstract + gzipped PostScript).

  82. Kotulska, M., A comparison between deterministic and probabilistic approaches to the phenomenon of anomalous diffusion in tissue, Cellular & Molecular Biology Letters 4 (1999), 105-116

  83. Kotulska, M., Komputerowa analiza modelu zjawiska Maxwella-Wagnera w tkance, Materiałyy XI Konferencji Biocybernetyka i Inżynieria Biomedyczna , Warszawa 1999, 213-217.

  84. Kotulska, M. Weron, K. Continuous time random walk model of dielectric low frequency dispersion in tissue, Proc. SPIE , 37DP, Dielectric and Related Phenomena (1998), 56-63.

  85. Kotulska, M. Komputerowa analiza matematycznego modelu dielektrycznej dyspersji w tkance, Acta Bio-Opt. Inf. Med. , 4 (1998) 57-61.

  86. Kotulska, M, Weron, K. Probabilistic approach to the dielectric response of biological materials, Proc. SPIE, 3181, Dielectric and Related Phenomena (1997), 11-18

  87. Kotulska, M. Analiza odpowiedzi dielektrycznej tkanki w obszarze częstotliwości alfa-dyspersji, Materiały X Konferencji Biocybernetyka i Inżynieria Biomedyczna, Warszawa 1997, 361-365.

  88. Kotulska, M., Mikoda, J., Expert system for supporting therapy choice for non-Hodgkin lymphoma (in Polish) Materiały konferencji Inżynieria Wiedzy i Systemy Ekspertowe , Wrocław 1990, 140-143.

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