Publikacje

Wybrane publikacje naukowe pracowników Katedry Bioinformatyki PJATK:

2024

• Ociepa T., Genome sequencing as a tool for understanding microorganisms. W: Microbial genetics Boca Raton/Abingdon 2024, CRC Press, s. 61-71, 978-1-032-35841-3. DOI: 10.1201/9781003328933
• Ociepa T., Metagenomics: a road to novel microbial genes and genomes. W: Microbial genetics Boca Raton/Abingdon 2024, CRC Press, s. 52-60, 978-1-032-35841-3. DOI: 10.1201/9781003328933
• Sendecki A, Ledwoń D, Tuszy A, Nycz J, Wąsowska A, Boguszewska-Chachulska A, Mitas AW, Wylęgała E, Teper S. Fundus Image Deep Learning Study to Explore the Association of Retinal Morphology with Age-Related Macular Degeneration Polygenic Risk Score. 2024. Biomedicines. 12(9):2092.
• Sendecki A, Ledwoń D, Nycz J, Wąsowska A, Boguszewska-Chachulska A, Mitas AW, Wylęgała E, Teper S. A deep learning approach to explore the association of age-related macular degeneration polygenic risk score with retinal optical coherence tomography: A preliminary study. 2024. Acta Ophthalmol. 102(7):e1029-e1039
• Sendecki, A.; Ledwoń, D.; Tuszy, A.; Nycz, J.; Wąsowska, A.; Boguszewska-Chachulska, A.; Wylęgała, A.; Mitas, A.W.; Wylęgała, E.; Teper, S. Association of Genetic Risk for Age-Related Macular Degeneration with Morphological Features of the Retinal Microvascular Network. Diagnostics. 2024. 14(7):770.
• Jakowiecki J, Orzeł U, Miszta P, Młynarczyk K, Filipek S “Conformational Changes and Unfolding of β-Amyloid Substrates in the Active Site of γ-Secretase” Int. J. Mol. Sci. 2024, 25, Doi: 10.3390/ijms25052564

2023

• Kuzdraliński, A., Miśkiewicz, M., Szczerba, H., Mazurczyk, W., Nivala, J., & Księżopolski, B. (2023). Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons. Nature Communications, 14(1), 6052.
• Anna Wąsowska, Adam Sendecki, Anna Boguszewska-Chachulska, Sławomir Teper. Polygenic Risk Score and Rare Variant Burden Identified by Targeted Sequencing in a Group of Patients with Pigment Epithelial Detachment in Age-Related Macular Degeneration. Genes. 2023. 14(9), 1707.
• Elżbieta Krytkowska, Zofia Ulańczyk, Aleksandra Grabowicz, Krzysztof Safranow, Miłosz Piotr Kawa, Andrzej Pałucha, Anna Wąsowska, Ewa Matczyńska, Anna Boguszewska-Chachulska, Anna Machalińska. Influence of Clinical and Genetic Factors on the Progression of Age-Related Macular Degeneration: A 3-Year Follow-Up. J Clin Med. 2023. 12(5), 1963.
• Anna Wąsowska, Sławomir Teper, Ewa Matczyńska, Przemysław Łyszkiewicz, Adam Sendecki, Anna Machalińska, Edward Wylęgała, Anna Boguszewska-Chachulska. Polygenic Risk Score impact on susceptibility to age-related macular degeneration in Polish patients. J Clin Med. 2023, 12(1), 295.
• Orzeł U, Pasznik P, Miszta P, Lorkowski M, Niewieczerzał S, Jakowiecki J, Filipek S “GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex” Nucleic Acids Res. 2023 May 19; doi:10.1093/nar/gkad409
• Jakowiecki J, Orzeł U, Gliździnska A, Możajew M, Filipek S. “Specificities of Protein Homology Modeling for Allosteric Drug Design” Methods Mol. Biol. 2023; 2627:339-348. doi:10.1007/978-1-0716-2974-1_19.

2022

• Iłowiecka, K., Maślej, M., Czajka, M., Pawłowski, A., Więckowski, P., Styk, T., Gołkiewicz, M., Kuzdraliński, A., & Koch, W. (2022). Lifestyle, Eating Habits, and Health Behaviors Among Dietary Supplement Users in Three European Countries. Frontiers in public health, 10, 892233. https://doi.org/10.3389/fpubh.2022.892233
• Ociepa T., Okoń S., Chromosomal location of Pm12—a novel powdery mildew resistance gene from Avena sterilis. Genes 2022 Vol. 13 Issue 12 Article number 2409, il., bibliogr., sum. DOI: 10.3390/genes13122409
• Masternak K., Okoń S., Kamola M., Ociepa T., Nucia A., Kowalczyk K., Morphological and genetic variation of Melolontha spp. from pine stands with different composition and proportion of admixed tree species. European Journal of Forest Research 2022 Vol. 141 s. 617-628, il., bibliogr., sum. DOI: 10.1007/s10342-022-01464-6
• Cieplak M., Nucia A., Ociepa T., Okoń S., Virulence structure and genetic diversity of Blumeria graminis f. sp. avenae from different regions of Europe. Plants 2022 Vol. 11 Iss. 10 Article number 1358, il., bibliogr., sum. DOI: 10.3390/plants11101358

2021

• Kuzdraliński, A., Leśniowska-Nowak, J., Nowak, M., Kawęcka, M., Kot, A., et. al. (2021). Novel Primer Sets for Rapid Detection of Zymoseptoria tritici in Wheat. Plant Disease, 105(2), 251-254.
• Okoń, S., Cieplak, M., Kuzdraliński, A., & Ociepa, T. (2021). New Pathotype Nomenclature for Better Characterisation the Virulence and Diversity of Blumeria graminis f. sp. avenae Populations. Agronomy, 11(9), 1852.
• Okoń S., Ociepa T., Nucia A., Cieplak M., Kowalczyk K., Is every wild species a rich source of disease resistance? Avena fatua L. – potential donor of resistance to powdery mildew. Plants 2021 Vol. 10 Iss. 3 Article number 560, il., bibliogr., sum. DOI: 10.3390/plants10030560
• Cieplak M., Terlecka K., Ociepa T., Zimowska B., Okoń S., Virulence structure of Blumeria graminis f. sp. avenae populations in Poland across 2014-2015. Plant pathol. j. 2021 Vol.37 No.2 s. 115-123, il., bibliogr., sum. DOI: 10.5423/PPJ.OA.10.2020.0193
• Miszta, P; Pasznik, P; Niewieczerzal, S; Jakowiecki, J; Filipek, S; “GPCRsignal: webserver for analysis of the interface between G protein-coupled receptors and their effector proteins by dynamics and mutations” Nucleic Acids Res. 2021, 49, W247-W256, doi:10.1093/nar/gkab434
• Jakowiecki, J.; Abel, R.; Orzel, U.; Pasznik, P.; Preissner, R.; Filipek, S. Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol-A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling. Molecules 2021, 26, doi:10.3390/molecules26092456.
• Orzeł, U.; Jakowiecki, J; Młynarczyk, K.; Filipek, S.; The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex. Biomolecules 2021, 11(7):935. doi: 10.3390/biom11070935

2020

• Jakowiecki, J.; Orzel, U.; Chawananon, S.; Miszta, P.; Filipek, S. The Hydrophobic Ligands Entry and Exit from the GPCR Binding Site-SMD and SuMD Simulations. Molecules 2020, 25, doi:10.3390/molecules25081930.
• Jakowiecki J, Miszta P, Niewieczerzał S, Filipek S “Structural diversity in ligand recognition by GPCRs” (a chapter in a book: GPCR’s) 2020 doi:10.1016/B978-0-12-816228-6.00003-9
• Cieplak M., Terlecka K., Ociepa T., Zimowska B., Okoń S., Virulence structure of Blumeria graminis f. sp. avenae populations in Poland across 2014-2015. Plant pathol. j. 2021 Vol.37 No.2 s. 115-123, il., bibliogr., sum. DOI: 10.5423/PPJ.OA.10.2020.0193
• Ociepa T., Okoń S., Nucia A., Leśniowska-Nowak J., Paczos-Grzęda E., Bisaga M., Molecular identification and chromosomal localization of new powdery mildew resistance gene Pm11 in oat. Theor. appl. genet. 2020 Vol. 133 Issue 1 s. 179-185, il., bibliogr.,sum. DOI: 10.1007/s00122-019-03449-3
• Dudziak, K., Sozoniuk, M., Szczerba, H., Kuzdraliński, A., Kowalczyk, K., Börner, A., & Nowak, M. (2020). Identification of stable reference genes for qPCR studies in common wheat (Triticum aestivum L.) seedlings under short-term drought stress. Plant Methods, 16, 1-8.
• Szczerba, H., Komoń-Janczara, E., Krawczyk, M., Dudziak, K., Nowak, A., Kuzdraliński, A., et. al. (2020). Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2-a novel bio-based succinic acid producer. Scientific Reports, 10(1), 1-13.

2019

• Miśkiewicz, M., Kuzdraliński, A., Rusinek, D., & Księżopolski, B. (2019) DNA Based Cryptographic Key Storage System With a Simple and Automated Method of Primers Selection. Maria Curie-Skłodowska University Press. Selected Topics in Applied Computer Science.
• Latek D, Trzaskowski B, Niewieczerzał S, Miszta P, Młynarczyk K, Dębiński A, Puławski W, Yuan S, Sztyler A, Orzeł U, Jakowiecki J, Filipek, S. “Modeling of Membrane Proteins: From Bioinformatics to Molecular Quantum Mechanics” (a chapter in a book: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes) 2019

2018

• Miszta, P.; Pasznik, P.; Jakowiecki, J.; Sztyler, A.; Latek, D.; Filipek, S. GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models. Nucleic Acids Res. 2018, 46, W387-W395, doi:10.1093/nar/gky429.
• Jakowiecki J, Sztyler A, Filipek S, Li P, Raman K, Barathiraja N, Ramakrishna S, Eswara JR, Altaee A, Sharif AO, Ajayan PM and Renugopalakrishnan V. „Aquaporin–graphene interface: relevance to point-of-care devices for renal cell carcinoma and desalination”. 2018, Interface Focus 8(3): 20170066. doi:10.1098/rsfs.2017.0066
• Miszta P, Jakowiecki J, Rutkowska E, Turant M, Latek D, Filipek S. „Approaches for Differentiation and Interconverting GPCR Agonists and Antagonists” Methods Mol. Biol. 2018;1705:265-296. doi: 10.1007/978-1-4939-7465-8_12.
• Okoń S., Ociepa T., Effectiveness of new sources of resistance against oat powdery mildew identified in A. sterilis. J Plant Dis Protect ( 2006, Print) 2018 Vol. 125 Iss. 5 s. 505-510, il., bibliogr., sum. DOI: 10.1007/s41348-018-0171-7
• Okoń S., Ociepa T., Paczos-Grzęda E., Ladizinsky G., Evaluation of resistance to Blumeria graminis (DC.) f. sp. avenae, in Avena murphyi and A. magna genotypes. Crop Prot. 2018 Vol. 106 s. 177-181, il., bibliogr., sum. DOI: 10.1016/j.cropro.2017.12.025
• Okoń S., Ociepa T., Nucia A., Molecular identification of Pm4 powdery mildew resistant gene in oat. Not. Bot. Horti Agrobot. Cluj-Napoca (Print) 2018 Vol. 46 Issue 2 s. 350-355, il., bibliogr., sum. DOI: 10.15835/nbha46210904
• Kołodziej B., Okoń S., Nucia A., Ociepa T., Luchowska K., Sugier D., Gevrenova R., Max H., Morphological, chemical, and genetic diversity of Gypsophila L. (Caryophyllaceae) species and their potential use in the pharmaceutical industry. Turkish Journal of Botany 2018 Vol. 42 Issue 3 s. 257-270, il., bibliogr., sum. DOI: 10.3906/bot-1707-13
• Kuzdraliński A., Szczerba H., Kot A., Ostrowska A., Nowak M., Muszyńska M. (2018). Development and application of a new PCR method for detection of Blumeria graminis f. sp. tritici. Journal of Molecular Microbiology and Biotechnology,
• Kowalczyk, S., Komoń-Janczara, E., Glibowska, A., Kuzdraliński, A., Czernecki, T., Targoński, Z. (2018). A co-utilization strategy to consume glycerol and monosaccharides by Rhizopus strains for fumaric acid production. AMB Express, 8(1), 69.

etc.