Publications

  1. Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S: Flexible docking of peptides to proteins using CABS‐dock. Protein Science 2019.
  2. Kmiecik S, Wabik J, Kolinski M, Kouza M, Kolinski A. Protein Dynamics Simulations Using Coarse-Grained Models. In: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: Springer, Cham; 2019. pp. 61-87.
  3. Dec R, Koliński M, Dzwolak W. Beyond amino acid sequence: disulfide bonds and the origins of the extreme amyloidogenic properties of insulin’s H‐fragment. The FEBS journal 2019.
  4. Blaszczyk M, Gront D, Kmiecik S, Kurcinski M, Kolinski M, Ciemny MP, Ziolkowska K, Panek M, Kolinski A. Protein Structure Prediction Using Coarse-Grained Models. In: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: Springer, Cham; 2019. pp. 27-59.
  5. Szulczyk D, Dobrowolski MA, Roszkowski P, Bielenica A, Stefańska J, Koliński M, Kmiecik S, Jóźwiak M, Wrzosek M, et al. 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 2018,156:631-640.
  6. Sokołowska B, Sadura-Sieklucka T, Czerwosz L, Hallay-Suszek M, Lesyng B, Księżopolska-Orłowska K. Estimation of Posturographic Trajectory Using k-Nearest Neighbors Classifier in Patients with Rheumatoid Arthritis and Osteoarthritis. Progress in Medical Research 2018:85-95.
  7. Sadura-Sieklucka T, Sokołowska B, Prusinowska A, Trzaska A, Księżopolska-Orłowska K. Benefits of wrist splinting in patients with rheumatoid arthritis. Reumatologia 2018,56:362.
  8. Klemba A, Purzycka-Olewiecka JK, Wcisło G, Czarnecka AM, Lewicki S, Lesyng B, Szczylik C, Kieda C. Surface markers of cancer stem-like cells of ovarian cancer and their clinical relevance. Contemporary Oncology 2018,22:48.
  9. Daniluk P, Firlik G, Lesyng B. Implementation of a maximum clique search procedure on CUDA. Journal of Heuristics 2018:1-25.
  10. Bielenica A, Drzewiecka-Antonik A, Rejmak P, Stefańska J, Koliński M, Kmiecik S, Lesyng B, Włodarczyk M, Pietrzyk P, et al. Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper (II) complexes of 1, 3-disubstituted thiourea ligands. Journal of inorganic biochemistry 2018,182:61-70.
  11. Niebroj-Dobosz I, Sokołowska B, Madej-Pilarczyk A, Marchel M, Hausmanowa-Petrusewicz I. Dysfunctional lamins as mediators of oxidative stress in Emery-Dreifuss muscular dystrophy. Folia neuropathologica 2017,55:193-198.
  12. Gogolewski K, Wronowska W, Lech A, Lesyng B, Gambin A. Inferring molecular processes heterogeneity from transcriptional data. BioMed research international 2017,2017.
  13. Czerwosz L, Szczepek E, Nowiński K, Sokołowska B, Jurkiewicz J, Czernicki Z, Koszewski W. Discriminant analysis of intracranial volumetric variables in patients with normal pressure hydrocephalus and brain atrophy. In: Current Concepts in Medical Research and Practice: Springer; 2017. pp. 83-94.
  14. Troć A, Zimnicka M, Koliński M, Danikiewicz W. Structural Elucidation of β‐Lactam Diastereoisomers through Ion Mobility Mass Spectrometry Studies and Theoretical Calculations. Journal of Mass Spectrometry 2016,51:282-290.
  15. Pulawski W, Jamroz M, Kolinski M, Kolinski A, Kmiecik S. Coarse-grained simulations of membrane insertion and folding of small helical proteins using the CABS model. Journal of chemical information and modeling 2016,56:2207-2215.
  16. Mielecki M, Lesyng B. Cinnamic acid derivatives as inhibitors of oncogenic protein kinases–structure, mechanisms and biomedical effects. Current medicinal chemistry 2016,23:954-982.
  17. Księżopolska-Orłowska K, Sadura-Sieklucka T, Kasprzak K, Gaszewska E, Rodkiewicz-Bogusławska A, Sokołowska B. The beneficial effects of rehabilitation on hand function in patients with rheumatoid arthritis. Reumatologia 2016,54:285.
  18. Kowalczyk P, Jaworek J, Kot M, Sokolowska B, Bielen A, Janowska B, Ciesla J, Szparecki G, Sados B, et al. Inflammation increases oxidative DNA Damage repair and stimulates preneoplastic changes in colons of newborn rats. Journal of Physiology and Pharmacology 2016,67:277-286.
  19. Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-grained protein models and their applications. Chemical Reviews 2016,116:7898-7936.
  20. Dziubiński M, Lesyng B. Toward the identification of molecular cogs. Journal of computational chemistry 2016,37:848-860.
  21. Bielenica A, Kędzierska E, Koliński M, Kmiecik S, Koliński A, Fiorino F, Severino B, Magli E, Corvino A, et al. 5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1, 3-disubstituted thiourea derivatives. European journal of medicinal chemistry 2016,116:173-186.
  22. Yuan S, Palczewski K, Peng Q, Kolinski M, Vogel H, Filipek S. The Mechanism of Ligand‐Induced Activation or Inhibition of μ‐and κ‐Opioid Receptors. Angewandte Chemie International Edition 2015,54:7560-7563.
  23. Wronowska W, Charzyńska A, Nienałtowski K, Gambin A. Computational modeling of sphingolipid metabolism. BMC systems biology 2015,9:47.
  24. Wilczynski PD, Lesyng B. WeBIAS: a web server for publishing bioinformatics applications. BMC Research Notes 2015,8.
  25. Stawujak K, Startek M, Gambin A, Grzebelus D. MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula. Genetica 2015,143:433-440.
  26. Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination. Nucleic acids research 2015,43:2188-2198.
  27. Sobieraj M, Krzyśko K, Jarmuła A, Kalinowski M, Lesyng B, Prokopowicz M, Cieśla J, Gojdź A, Kierdaszuk B. 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 2015,21:75.
  28. Sinkiewicz-Darol E, Lacerda AF, Kostera-Pruszczyk A, Potulska-Chromik A, Sokołowska B, Kabzińska D, Brunetti CR, Hausmanowa-Petrusewicz I, Kochański A. The LITAF/SIMPLE I92V sequence variant results in an earlier age of onset of CMT1A/HNPP diseases. neurogenetics 2015,16:27-32.
  29. Niebroj-Dobosz IM, Sokołowska B, Madej-Pilarczyk A, Marchel M, Hausmanowa-Petrusewicz I. Tissue inhibitors of matrix metalloproteinases in serum are cardiac biomarkers in Emery-Dreifuss muscular dystrophy. Kardiologia Polska (Polish Heart Journal) 2015,73:360-365.
  30. Lesyng B. Short history of conference” Inhibitors of Protein Kinases”. Postepy biochemii 2015,61:241.
  31. Horwacik I, Golik P, Grudnik P, Kolinski M, Zdzalik M, Rokita H, Dubin G. Structural basis of GD2 ganglioside and mimetic peptide recognition by 14G2a antibody. Molecular & Cellular Proteomics 2015,14:2577-2590.
  32. Dziubiński M, Daniluk P, Lesyng B. ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins. Bioinformatics 2015,32:25-34.
  33. Zimnicka M, Troć A, Ceborska M, Jakubczak M, Koliński M, Danikiewicz W. Structural elucidation of specific noncovalent association of folic acid with native cyclodextrins using an ion mobility mass spectrometry and theoretical approach. Analytical chemistry 2014,86:4249-4255.
  34. Sokołowska B, Jóźwik A, Niebroj-Dobosz I, Hausmanowa-Petrusewicz I. A pattern recognition approach to Emery-Dreifuss muscular dystrophy (EDMD) study. Journal of Medical Informatics & Technologies 2014,23:165–172.
  35. Sokołowska B, Czerwosz L, Hallay-Suszek M, Sadura-Sieklucka T, Księżopolska-Orłowska K. Posturography in patients with rheumatoid arthritis and osteoarthritis. In: Lung Cancer and Autoimmune Disorders: Springer; 2014. pp. 63-70.
  36. Sen P, Dharmadhikari AV, Majewski T, Mohammad MA, Kalin TV, Zabielska J, Ren X, Bray M, Brown HM, et al. 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:e94390.
  37. Niebroj-Dobosz I, Sokołowska B, Madej-Pilarczyk A, Marchel M, Hausmanowa-Petrusewicz I. Cardiovascular risk markers in dilated cardiomyopathy in Emery–Dreifuss muscular dystrophy (EDMD). International journal of cardiology 2014,173:324-325.
  38. Mielecki M, Milner-Krawczyk M, Grzelak K, Mielecki D, A Krzysko K, Lesyng B, Priebe W. Analogs of cinnamic acid benzyl amide as nonclassical inhibitors of activated JAK2 kinase. Current cancer drug targets 2014,14:638-651.
  39. Lazarova T, Mlynarczyk K, Filipek S, Kolinski M, Wassenaar TA, Querol E, Renugopalakrishnan V, Viswanathan S, Padrós E. The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin. The FEBS journal 2014,281:1181-1195.
  40. Kmiecik S, Wabik J, Kolinski M, Kouza M, Kolinski A. Coarse-grained modeling of protein dynamics. In: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: Springer, Berlin, Heidelberg; 2014. pp. 55-79.
  41. Kmiecik S, Jamroz M, Kolinski M. Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors. Biophysical journal 2014:2408–2416.
  42. Dharmadhikari AV, Gambin T, Szafranski P, Cao W, Probst FJ, Jin W, Fang P, Gogolewski K, Gambin A, et al. Molecular and clinical analyses of 16q24. 1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite. BMC medical genetics 2014,15:128.
  43. Daniluk P, Lesyng B. Theoretical and computational aspects of protein structural alignment. In: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: Springer; 2014. pp. 557-598.
  44. Bartnik M, Nowakowska B, Derwińska K, Wiśniowiecka-Kowalnik B, Kędzior M, Bernaciak J, Ziemkiewicz K, Gambin T, Sykulski M, et al. Application of array comparative genomic hybridization in 256 patients with developmental delay or intellectual disability. Journal of applied genetics 2014,55:125-144.
  45. Wiśniowiecka-Kowalnik B, Kastory-Bronowska M, Bartnik M, Derwińska K, Dymczak-Domini W, Szumbarska D, Ziemka E, Szczałuba K, Sykulski M, et al. Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders. European Journal of Human Genetics 2013,21:620.
  46. Startek M, Le Rouzic A, Capy P, Grzebelus D, Gambin A. Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations. Theoretical population biology 2013,90:145-151.
  47. Smyk M, Szafranski P, Startek M, Gambin A, Stankiewicz P. Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Chromosome research 2013,21:781-788.
  48. Rybiński M, Szymańska Z, Lasota S, Gambin A. Modelling the efficacy of hyperthermia treatment. Journal of The Royal Society Interface 2013,10:20130527.
  49. Plazinska A, Kolinski M, Wainer IW, Jozwiak K. 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 2013,19:4919-4930.
  50. Mielecki M, Krawiec K, Kiburu I, Grzelak K, Zagórski W, Kierdaszuk B, Kowa K, Fokt I, Szymanski S, et al. Development of novel molecular probes of the Rio1 atypical protein kinase. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2013,1834:1292-1301.
  51. Gambin A, Charzyńska A, Ellert-Miklaszewska A, Rybiński M. Computational models of the JAK1/2-STAT1 signaling. Jak-stat 2013,2:e24672.
  52. Dittwald P, Claesen Jr, Burzykowski T, Valkenborg D, Gambin A. BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry. Analytical chemistry 2013,85:1991-1994.
  53. Czerwosz L, Szczepek E, Sokolowska B, Jurkiewicz J, Czernicki Z. Posturography in differential diagnosis of normal pressure hydrocephalus and brain atrophy. In: Respiratory Regulation-Clinical Advances: Springer; 2013. pp. 311-324.
  54. Swiatek-Machado K, Mieczkowski J, Ellert-Miklaszewska A, Swierk P, Fokt I, Szymanski S, Skora S, Szeja W, Grynkiewicz G, et al. Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells. Cancer biology & therapy 2012,13:657-670.
  55. Sokołowska B, Jóźwik A, Niebroj-Dobosz I, Janik P. The pair-wise linear classifier and the k-NN rule in application to ALS progression differentiation. Journal of Medical Informatics & Technologies 2012,20.
  56. Niebroj-Dobosz I, Sokołowska B, Madej-Pilarczyk A. Natriuretic peptides assessment in dilated cardiomyopathy in patients with Emery–Dreifuss muscular dystrophy. J Clin Exp Cardiol 2012,3:2-7.
  57. Kolinski M, Plazinska A, Jozwiak K. Recent progress in understanding of structure, ligand interactions and the mechanism of activation of the β 2-adrenergic receptor. Current medicinal chemistry 2012,19:1155-1163.
  58. Ishikawa T, Krzysko KA, Kowalska-Loth B, Skrajna AM, Czubaty A, Girstun A, Cieplak MK, Lesyng B, Staron K. Activities of topoisomerase I in its complex with SRSF1. Biochemistry 2012,51:1803-1816.
  59. Gawinkowski S, Walewski Ł, Vdovin A, Slenczka A, Rols S, Johnson MR, Lesyng B, Waluk J. Vibrations and hydrogen bonding in porphycene. Physical Chemistry Chemical Physics 2012,14:5489-5503.
  60. Dawid A, Kolinski M, Koliński A, Kmiecik S. 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.
  61. Czerwosz L, Szczepek E, Sokołowska B, Jurkiewicz J, Czernicki Z. Recognition of posture and gait disturbances in patients with normal pressure hydrocephalus using a posturography and computer dynography systems. In: Hydrocephalus: InTech; 2012.
  62. Sokołowska B, Maciejewska AM, Jóźwik A, Kuśmierek JT. Estimation of significance of AlkB and AlkA proteins in DNA repair in Escherichia coli model. Journal of Medical Informatics & Technologies 2011,17.
  63. Niebroj-Dobosz I, Madej-Pilarczyk A, Marchel M, Sokołowska B, Hausmanowa-Petrusewicz I. Osteopontin–a fibrosis-related marker–in dilated cardiomyopathy in patients with Emery-Dreifuss muscular dystrophy. Scandinavian journal of clinical and laboratory investigation 2011,71:658-662.
  64. Niebroj-Dobosz I, Madej-Pilarczyk A, Marchel M, Sokołowska B, Hausmanowa-Petrusewicz I. Circulating tenascin-C levels in patients with dilated cardiomyopathy in the course of Emery-Dreifuss muscular dystrophy. Clinica Chimica Acta 2011,412:1533-1538.
  65. Jozwik A, Sokolowska B, Niebroj-Dobosz I, Janik P, Kwiecinski H. Extraction of biomedical traits for patients with amyotrophic lateral sclerosis using parallel and hierarchical classifiers. International Journal of Biometrics 2011,3:85-94.
  66. Daniluk P, Lesyng B. A novel method to compare protein structures using local descriptors. BMC Bioinformatics 2011,12:344.
  67. Ahmed AA, Goldsmith J, Fokt I, Le X-F, Krzysko KA, Lesyng B, Bast RC, Priebe W. A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer. Cancer chemotherapy and pharmacology 2011,68:1033-1044.
  68. Sokołowska B, Jóźwik A. Pattern recognition approach for analysis of metabolic response to intermittent hypoxia. Journal of Medical Informatics & Technologies 2010,15.
  69. Niebroj‐Dobosz I, Janik P, Sokołowska B, Kwiecinski H. Matrix metalloproteinases and their tissue inhibitors in serum and cerebrospinal fluid of patients with amyotrophic lateral sclerosis. European journal of neurology 2010,17:226-231.
  70. Maciejewska AM, Sokołowska B, Nowicki A, Kuśmierek JT. The role of AlkB protein in repair of 1, N 6-ethenoadenine in Escherichia coli cells. Mutagenesis 2010,26:401-406.
  71. Maciejewska AM, Ruszel KP, Nieminuszczy J, Lewicka J, Sokołowska B, Grzesiuk E, Kuśmierek JT. 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 2010,684:24-34.
  72. Janik P, Kwiecinski H, Sokolowska B, Niebroj-Dobosz I. Erythropoietin concentration in serum and cerebrospinal fluid of patients with amyotrophic lateral sclerosis. Journal of neural transmission 2010,117:343-347.