Publications

  1. Badaczewska-Dawid A, Kmiecik S, Kolinski M, Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement. Briefings in Bioinformatics (accepted), 2020
  2. Dec R, Kolinski M, Kouza M, Dzwolak W, Rapid self-association of highly amyloidogenic H-fragments of insulin: Experiment and molecular dynamics simulations. International Journal of Biological Macromolecules 2020.
  3. Koliński, M., S. Kmiecik, R. Dec, M. Piejko, P. Mak, and W. Dzwolak, Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation. International Journal of Biological Macromolecules, 2020.
  4. Kurcinski, M., A. Badaczewska‐Dawid, M. Kolinski, A. Kolinski, and S. Kmiecik, Flexible docking of peptides to proteins using CABS‐dock. Protein Science, 2020. 29(1): p. 211-222.
  5. Dec, R., M. Koliński, and W. Dzwolak, Beyond amino acid sequence: disulfide bonds and the origins of the extreme amyloidogenic properties of insulin’s H‐fragment. The FEBS journal, 2019. 286(16): p. 3194-3205.
  6. Kmiecik, S., J. Wabik, M. Kolinski, M. Kouza, and A. Kolinski, Protein Dynamics Simulations Using Coarse-Grained Models, in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. 2019, Springer, Cham. p. 61-87.
  7. Blaszczyk, M., D. Gront, S. Kmiecik, M. Kurcinski, M. Kolinski, M.P. Ciemny, K. Ziolkowska, M. Panek, and A. Kolinski, Protein Structure Prediction Using Coarse-Grained Models, in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. 2019, Springer, Cham. p. 27-59.
  8. Szulczyk, D., M.A. Dobrowolski, P. Roszkowski, A. Bielenica, J. Stefańska, M. Koliński, S. Kmiecik, M. Jóźwiak, M. Wrzosek, and W. Olejarz, Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studies. European journal of medicinal chemistry, 2018. 156: p. 631-640.
  9. Sokołowska, B., T. Sadura-Sieklucka, L. Czerwosz, M. Hallay-Suszek, B. Lesyng, and K. Księżopolska-Orłowska, Estimation of Posturographic Trajectory Using k-Nearest Neighbors Classifier in Patients with Rheumatoid Arthritis and Osteoarthritis. Progress in Medical Research, 2018: p. 85-95.
  10. Sadura-Sieklucka, T., B. Sokołowska, A. Prusinowska, A. Trzaska, and K. Księżopolska-Orłowska, Benefits of wrist splinting in patients with rheumatoid arthritis. Reumatologia, 2018. 56(6): p. 362.
  11. Klemba, A., J.K. Purzycka-Olewiecka, G. Wcisło, A.M. Czarnecka, S. Lewicki, B. Lesyng, C. Szczylik, and C. Kieda, Surface markers of cancer stem-like cells of ovarian cancer and their clinical relevance. Contemporary Oncology, 2018. 22(1A): p. 48.
  12. Daniluk, P., G. Firlik, and B. Lesyng, Implementation of a maximum clique search procedure on CUDA. Journal of Heuristics, 2018: p. 1-25.
  13. Bielenica, A., A. Drzewiecka-Antonik, P. Rejmak, J. Stefańska, M. Koliński, S. Kmiecik, B. Lesyng, M. Włodarczyk, P. Pietrzyk, and M. Struga, Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper (II) complexes of 1, 3-disubstituted thiourea ligands. Journal of inorganic biochemistry, 2018. 182: p. 61-70.
  14. Niebroj-Dobosz, I., B. Sokołowska, A. Madej-Pilarczyk, M. Marchel, and I. Hausmanowa-Petrusewicz, Dysfunctional lamins as mediators of oxidative stress in Emery-Dreifuss muscular dystrophy. Folia neuropathologica, 2017. 55(3): p. 193-198.
  15. Gogolewski, K., W. Wronowska, A. Lech, B. Lesyng, and A. Gambin, Inferring molecular processes heterogeneity from transcriptional data. BioMed research international, 2017. 2017.
  16. Czerwosz, L., E. Szczepek, K. Nowiński, B. Sokołowska, J. Jurkiewicz, Z. Czernicki, and W. Koszewski, Discriminant analysis of intracranial volumetric variables in patients with normal pressure hydrocephalus and brain atrophy, in Current Concepts in Medical Research and Practice. 2017, Springer. p. 83-94.
  17. Troć, A., M. Zimnicka, M. Koliński, and W. Danikiewicz, Structural Elucidation of β‐Lactam Diastereoisomers through Ion Mobility Mass Spectrometry Studies and Theoretical Calculations. Journal of Mass Spectrometry, 2016. 51(4): p. 282-290.
  18. Pulawski, W., M. Jamroz, M. Kolinski, A. Kolinski, and S. Kmiecik, Coarse-grained simulations of membrane insertion and folding of small helical proteins using the CABS model. Journal of chemical information and modeling, 2016. 56(11): p. 2207-2215.
  19. Mielecki, M. and B. Lesyng, Cinnamic acid derivatives as inhibitors of oncogenic protein kinases–structure, mechanisms and biomedical effects. Current medicinal chemistry, 2016. 23(10): p. 954-982.
  20. Księżopolska-Orłowska, K., T. Sadura-Sieklucka, K. Kasprzak, E. Gaszewska, A. Rodkiewicz-Bogusławska, and B. Sokołowska, The beneficial effects of rehabilitation on hand function in patients with rheumatoid arthritis. Reumatologia, 2016. 54(6): p. 285.
  21. Kowalczyk, P., J. Jaworek, M. Kot, B. Sokolowska, A. Bielen, B. Janowska, J. Ciesla, G. Szparecki, B. Sados, and B. Tudek, Inflammation increases oxidative DNA Damage repair and stimulates preneoplastic changes in colons of newborn rats. Journal of Physiology and Pharmacology, 2016. 67(2): p. 277-286.
  22. Kmiecik, S., D. Gront, M. Kolinski, L. Wieteska, A.E. Dawid, and A. Kolinski, Coarse-grained protein models and their applications. Chemical Reviews, 2016. 116(14): p. 7898-7936.
  23. Dziubiński, M. and B. Lesyng, Toward the identification of molecular cogs. Journal of computational chemistry, 2016. 37(9): p. 848-860.
  24. Bielenica, A., E. Kędzierska, M. Koliński, S. Kmiecik, A. Koliński, F. Fiorino, B. Severino, E. Magli, A. Corvino, and I. Rossi, 5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1, 3-disubstituted thiourea derivatives. European journal of medicinal chemistry, 2016. 116: p. 173-186.
  25. Yuan, S., K. Palczewski, Q. Peng, M. Kolinski, H. Vogel, and S. Filipek, The Mechanism of Ligand‐Induced Activation or Inhibition of μ‐and κ‐Opioid Receptors. Angewandte Chemie International Edition, 2015. 54(26): p. 7560-7563.
  26. Wronowska, W., A. Charzyńska, K. Nienałtowski, and A. Gambin, Computational modeling of sphingolipid metabolism. BMC systems biology, 2015. 9(1): p. 47.
  27. Wilczynski, P.D. and B. Lesyng, WeBIAS: a web server for publishing bioinformatics applications. BMC Research Notes, 2015. 8.
  28. Stawujak, K., M. Startek, A. Gambin, and D. Grzebelus, MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula. Genetica, 2015. 143(4): p. 433-440.
  29. Startek, M., P. Szafranski, T. Gambin, I.M. Campbell, P. Hixson, C.A. Shaw, P. Stankiewicz, and A. Gambin, Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination. Nucleic acids research, 2015. 43(4): p. 2188-2198.
  30. Sobieraj, M., K. Krzyśko, A. Jarmuła, M. Kalinowski, B. Lesyng, M. Prokopowicz, J. Cieśla, A. Gojdź, and B. Kierdaszuk, A QM-MD simulation approach to the analysis of FRET processes in (bio) molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A. Journal of molecular modeling, 2015. 21(4): p. 75.
  31. Sinkiewicz-Darol, E., A.F. Lacerda, A. Kostera-Pruszczyk, A. Potulska-Chromik, B. Sokołowska, D. Kabzińska, C.R. Brunetti, I. Hausmanowa-Petrusewicz, and A. Kochański, The LITAF/SIMPLE I92V sequence variant results in an earlier age of onset of CMT1A/HNPP diseases. neurogenetics, 2015. 16(1): p. 27-32.
  32. Niebroj-Dobosz, I.M., B. Sokołowska, A. Madej-Pilarczyk, M. Marchel, and I. Hausmanowa-Petrusewicz, Tissue inhibitors of matrix metalloproteinases in serum are cardiac biomarkers in Emery-Dreifuss muscular dystrophy. Kardiologia Polska (Polish Heart Journal), 2015. 73(5): p. 360-365.
  33. Horwacik, I., P. Golik, P. Grudnik, M. Kolinski, M. Zdzalik, H. Rokita, and G. Dubin, Structural basis of GD2 ganglioside and mimetic peptide recognition by 14G2a antibody. Molecular & Cellular Proteomics, 2015. 14(10): p. 2577-2590.
  34. Dziubiński, M., P. Daniluk, and B. Lesyng, ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins. Bioinformatics, 2015. 32(1): p. 25-34.
  35. Zimnicka, M., A. Troć, M. Ceborska, M. Jakubczak, M. Koliński, and W. Danikiewicz, Structural elucidation of specific noncovalent association of folic acid with native cyclodextrins using an ion mobility mass spectrometry and theoretical approach. Analytical chemistry, 2014. 86(9): p. 4249-4255.
  36. Sokołowska, B., A. Jóźwik, I. Niebroj-Dobosz, and I. Hausmanowa-Petrusewicz, A pattern recognition approach to Emery-Dreifuss muscular dystrophy (EDMD) study. Journal of Medical Informatics & Technologies, 2014. 23: p. 165–172.
  37. Sokołowska, B., L. Czerwosz, M. Hallay-Suszek, T. Sadura-Sieklucka, and K. Księżopolska-Orłowska, Posturography in patients with rheumatoid arthritis and osteoarthritis, in Lung Cancer and Autoimmune Disorders. 2014, Springer. p. 63-70.
  38. Sen, P., A.V. Dharmadhikari, T. Majewski, M.A. Mohammad, T.V. Kalin, J. Zabielska, X. Ren, M. Bray, H.M. Brown, and S. Welty, Comparative analyses of lung transcriptomes in patients with alveolar capillary dysplasia with misalignment of pulmonary veins and in foxf1 heterozygous knockout mice. PLoS One, 2014. 9(4): p. e94390.
  39. Niebroj-Dobosz, I., B. Sokołowska, A. Madej-Pilarczyk, M. Marchel, and I. Hausmanowa-Petrusewicz, Cardiovascular risk markers in dilated cardiomyopathy in Emery–Dreifuss muscular dystrophy (EDMD). International journal of cardiology, 2014. 173(2): p. 324-325.
  40. Mielecki, M., M. Milner-Krawczyk, K. Grzelak, D. Mielecki, K. A Krzysko, B. Lesyng, and W. Priebe, Analogs of cinnamic acid benzyl amide as nonclassical inhibitors of activated JAK2 kinase. Current cancer drug targets, 2014. 14(7): p. 638-651.
  41. Lazarova, T., K. Mlynarczyk, S. Filipek, M. Kolinski, T.A. Wassenaar, E. Querol, V. Renugopalakrishnan, S. Viswanathan, and E. Padrós, The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin. The FEBS journal, 2014. 281(4): p. 1181-1195.
  42. Kmiecik, S., J. Wabik, M. Kolinski, M. Kouza, and A. Kolinski, Coarse-grained modeling of protein dynamics, in Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. 2014, Springer, Berlin, Heidelberg. p. 55-79.
  43. Kmiecik, S., M. Jamroz, and M. Kolinski, Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors. Biophysical journal, 2014: p. 2408–2416.
  44. Dharmadhikari, A.V., T. Gambin, P. Szafranski, W. Cao, F.J. Probst, W. Jin, P. Fang, K. Gogolewski, A. Gambin, and J.K. George-Abraham, Molecular and clinical analyses of 16q24. 1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite. BMC medical genetics, 2014. 15(1): p. 128.
  45. Daniluk, P. and B. Lesyng, Theoretical and computational aspects of protein structural alignment, in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. 2014, Springer. p. 557-598.
  46. Bartnik, M., B. Nowakowska, K. Derwińska, B. Wiśniowiecka-Kowalnik, M. Kędzior, J. Bernaciak, K. Ziemkiewicz, T. Gambin, M. Sykulski, and N. Bezniakow, Application of array comparative genomic hybridization in 256 patients with developmental delay or intellectual disability. Journal of applied genetics, 2014. 55(1): p. 125-144.
  47. Wiśniowiecka-Kowalnik, B., M. Kastory-Bronowska, M. Bartnik, K. Derwińska, W. Dymczak-Domini, D. Szumbarska, E. Ziemka, K. Szczałuba, M. Sykulski, and T. Gambin, Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders. European Journal of Human Genetics, 2013. 21(6): p. 620.
  48. Startek, M., A. Le Rouzic, P. Capy, D. Grzebelus, and A. Gambin, Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations. Theoretical population biology, 2013. 90: p. 145-151.
  49. Smyk, M., P. Szafranski, M. Startek, A. Gambin, and P. Stankiewicz, Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Chromosome research, 2013. 21(8): p. 781-788.
  50. Rybiński, M., Z. Szymańska, S. Lasota, and A. Gambin, Modelling the efficacy of hyperthermia treatment. Journal of The Royal Society Interface, 2013. 10(88): p. 20130527.
  51. Plazinska, A., M. Kolinski, I.W. Wainer, and K. Jozwiak, Molecular interactions between fenoterol stereoisomers and derivatives and the β 2-adrenergic receptor binding site studied by docking and molecular dynamics simulations. Journal of molecular modeling, 2013. 19(11): p. 4919-4930.
  52. Mielecki, M., K. Krawiec, I. Kiburu, K. Grzelak, W. Zagórski, B. Kierdaszuk, K. Kowa, I. Fokt, S. Szymanski, and P. Świerk, Development of novel molecular probes of the Rio1 atypical protein kinase. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2013. 1834(7): p. 1292-1301.
  53. Dittwald, P., J.r. Claesen, T. Burzykowski, D. Valkenborg, and A. Gambin, BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry. Analytical chemistry, 2013. 85(4): p. 1991-1994.
  54. Czerwosz, L., E. Szczepek, B. Sokolowska, J. Jurkiewicz, and Z. Czernicki, Posturography in differential diagnosis of normal pressure hydrocephalus and brain atrophy, in Respiratory Regulation-Clinical Advances. 2013, Springer. p. 311-324.
  55. Swiatek-Machado, K., J. Mieczkowski, A. Ellert-Miklaszewska, P. Swierk, I. Fokt, S. Szymanski, S. Skora, W. Szeja, G. Grynkiewicz, and B. Lesyng, Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells. Cancer biology & therapy, 2012. 13(8): p. 657-670.
  56. Sokołowska, B., A. Jóźwik, I. Niebroj-Dobosz, and P. Janik, The pair-wise linear classifier and the k-NN rule in application to ALS progression differentiation. Journal of Medical Informatics & Technologies, 2012. 20.
  57. Niebroj-Dobosz, I., B. Sokołowska, and A. Madej-Pilarczyk, Natriuretic peptides assessment in dilated cardiomyopathy in patients with Emery–Dreifuss muscular dystrophy. J Clin Exp Cardiol, 2012. 3: p. 2-7.
  58. Kolinski, M., A. Plazinska, and K. Jozwiak, Recent progress in understanding of structure, ligand interactions and the mechanism of activation of the β 2-adrenergic receptor. Current medicinal chemistry, 2012. 19(8): p. 1155-1163.
  59. Ishikawa, T., K.A. Krzysko, B. Kowalska-Loth, A.M. Skrajna, A. Czubaty, A. Girstun, M.K. Cieplak, B. Lesyng, and K. Staron, Activities of topoisomerase I in its complex with SRSF1. Biochemistry, 2012. 51(8): p. 1803-1816.
  60. Gawinkowski, S., Ł. Walewski, A. Vdovin, A. Slenczka, S. Rols, M.R. Johnson, B. Lesyng, and J. Waluk, Vibrations and hydrogen bonding in porphycene. Physical Chemistry Chemical Physics, 2012. 14(16): p. 5489-5503.
  61. Dawid, A., M. Kolinski, A. Koliński, and S. Kmiecik, Modelowanie Molekularne Białek Błonowych (Molecular Modeling of Membrane Proteins). Na pograniczu chemii i biologii (At the Treshold of Chemistry and Biology) vol. XXVIII, H. Koroniak, J. Barciszewski eds, Wydawnictwo Naukowe UAM, Poznań, 2012.
  62. Czerwosz, L., E. Szczepek, B. Sokołowska, J. Jurkiewicz, and Z. Czernicki, Recognition of posture and gait disturbances in patients with normal pressure hydrocephalus using a posturography and computer dynography systems, in Hydrocephalus. 2012, InTech.
  63. Sokołowska, B., A.M. Maciejewska, A. Jóźwik, and J.T. Kuśmierek, Estimation of significance of AlkB and AlkA proteins in DNA repair in Escherichia coli model. Journal of Medical Informatics & Technologies, 2011. 17.
  64. Niebroj-Dobosz, I., A. Madej-Pilarczyk, M. Marchel, B. Sokołowska, and I. Hausmanowa-Petrusewicz, Circulating tenascin-C levels in patients with dilated cardiomyopathy in the course of Emery-Dreifuss muscular dystrophy. Clinica Chimica Acta, 2011. 412(17-18): p. 1533-1538.
  65. Niebroj-Dobosz, I., A. Madej-Pilarczyk, M. Marchel, B. Sokołowska, and I. Hausmanowa-Petrusewicz, Osteopontin–a fibrosis-related marker–in dilated cardiomyopathy in patients with Emery-Dreifuss muscular dystrophy. Scandinavian journal of clinical and laboratory investigation, 2011. 71(8): p. 658-662.
  66. Jozwik, A., B. Sokolowska, I. Niebroj-Dobosz, P. Janik, and H. Kwiecinski, Extraction of biomedical traits for patients with amyotrophic lateral sclerosis using parallel and hierarchical classifiers. International Journal of Biometrics, 2011. 3(1): p. 85-94.
  67. Daniluk, P. and B. Lesyng, A novel method to compare protein structures using local descriptors. BMC Bioinformatics, 2011. 12(1): p. 344.
  68. Ahmed, A.A., J. Goldsmith, I. Fokt, X.-F. Le, K.A. Krzysko, B. Lesyng, R.C. Bast, and W. Priebe, A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer. Cancer chemotherapy and pharmacology, 2011. 68(4): p. 1033-1044.
  69. Sokołowska, B. and A. Jóźwik, Pattern recognition approach for analysis of metabolic response to intermittent hypoxia. Journal of Medical Informatics & Technologies, 2010. 15.
  70. Niebroj‐Dobosz, I., P. Janik, B. Sokołowska, and H. Kwiecinski, Matrix metalloproteinases and their tissue inhibitors in serum and cerebrospinal fluid of patients with amyotrophic lateral sclerosis. European journal of neurology, 2010. 17(2): p. 226-231.
  71. Maciejewska, A.M., B. Sokołowska, A. Nowicki, and J.T. Kuśmierek, The role of AlkB protein in repair of 1, N 6-ethenoadenine in Escherichia coli cells. Mutagenesis, 2010. 26(3): p. 401-406.
  72. Maciejewska, A.M., K.P. Ruszel, J. Nieminuszczy, J. Lewicka, B. Sokołowska, E. Grzesiuk, and J.T. Kuśmierek, Chloroacetaldehyde-induced mutagenesis in Escherichia coli: the role of AlkB protein in repair of 3, N4-ethenocytosine and 3, N4-α-hydroxyethanocytosine. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2010. 684(1-2): p. 24-34.