Publications & preprints

Preprints

• Pysz K.G., Bartczak A., Kwiecień J., Krajewski P., Dyrka W. (2026). Distribution-based deep multiple instance learning for tumor proportion scoring in NSCLC. arXiv, arXiv:2606.27579.

Journal Articles & Book Chapters

• Pysz K.G., Gałązka J., Dyrka W. (2025). Harnessing deep learning for proteome-scale detection of amyloid signaling motifs. Bioinformatics, 41(Supplement_1), i420–i428.
• Pietluch F., Mackiewicz P., Sidorczuk K., Gagat P. (2025). Dating the origin and spread of plastids and chromatophores. International Journal of Molecular Sciences, 26(12), 5569.
• Polańska O., Szulc N., Dyrka W., Wojciechowska A.W., Kotulska M., Żak A.M., Gąsior-Głogowska M.E., Szefczyk M.E. (2025). Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: molecular and structural insights into amyloid assembly. International Journal of Biological Macromolecules, 304(Pt 1), 140773.
• Szulc N., Gąsior-Głogowska M.E., Żyłka P., Szefczyk M.E., Wojciechowski J., Żak A.M., Dyrka W., Kaczorowska A.M., Burdukiewicz M., Tarek M., Kotulska M. (2024). Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 313, 124094.
• Wojciechowski J., Tekoglu E., Gąsior-Głogowska M.E., Coustou V., Szulc N., Szefczyk M.E., Kopaczyńska M., Saupe S.J., Dyrka W. (2022). Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. PLOS Computational Biology, 18(12), e1010787.
• Clave C., Dyrka W., Turcotte E.A., Granger-Farbos A., Ibarlosa L., Pinson B., Vance R.E., Saupe S.J., Daskalov A. (2022). Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proceedings of the National Academy of Sciences, 119(7), e2109418119.
• Dyrka W., Gąsior-Głogowska M.E., Szefczyk M.E., Szulc N. (2021). Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. BMC Bioinformatics, 22(1), 222.
• Dyrka W., Coustou V., Daskalov A., Lends A., Bardin T., Berbon M., Kauffmann B., Blancard C., Salin B., Loquet A., Saupe S.J. (2020). Identification of NLR-associated amyloid signaling motifs in bacterial genomes. Journal of Molecular Biology, 432(23), 6005–6027.
• Daskalov A., Dyrka W., Saupe S.J. (2020). NLR function in fungi as revealed by the study of self/non-self recognition systems. In: Genetics and Biotechnology, The Mycota, Vol. 2 (3rd ed.), 123–141. Springer, Cham.
• Dyrka W., Pyzik M., Coste F., Talibart H. (2019). Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ, 7, e6559.
• 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. (2018). The first MICCAI challenge on PET tumor segmentation. Medical Image Analysis, 44, 177–195.
• Konopka B.M., Marciniak M., Dyrka W. (2017). Quantiprot - a Python package for quantitative analysis of protein sequences. BMC Bioinformatics, 18(1), 339.