TY - GEN A1 - Kolenda, Rafał A1 - Burdukiewicz, Michał A1 - Wimonć, Marcjanna A1 - Aleksandrowicz, Adrianna A1 - Ali, Aamir A1 - Szabo, Istvan A1 - Tedin, Karsten A1 - Bartholdson, Scott J. A1 - Pickhard, Derek A1 - Schierack, Peter T1 - Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens T2 - Applied and Environmental Microbiology Y1 - 2021 U6 - https://doi.org/10.1128/AEM.02177-20 SN - 1098-5336 VL - 87 IS - 2 ER - TY - GEN A1 - Chilimoniuk, Jarosław A1 - Gosiewska, Alicja A1 - Słowik, Jadwiga A1 - Weiss, Romano A1 - Deckert, P. Markus A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał T1 - coutfitteR: efficient selection of count distributions to assess DNA damage T2 - Annals of Translational Medicine Y1 - 2021 U6 - https://doi.org/10.21037/atm-20-6363 SN - 2305-5847 VL - 9 IS - 7 ER - TY - GEN A1 - Sidorczuk, Katarzyna A1 - Burdukiewicz, Michał A1 - Cerk, Klara A1 - Fritscher, Joachim A1 - Kingsley, Robert A. A1 - Schierack, Peter A1 - Hildebrand, Falk A1 - Kolenda, Rafał T1 - AdhesiomeR: a tool for Escherichia coli adhesin classification and analysis T2 - BMC Genomics N2 - AbstractAdhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of E. coli adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. Based on analysis of 15,000 E. coli genomes, we define novel adhesiome profiles and clusters, providing a nomenclature for a unified comparison of E. coli adhesiomes. Y1 - 2024 U6 - https://doi.org/10.1186/s12864-024-10525-6 SN - 1471-2164 VL - 25 IS - 1 SP - 1 EP - 10 PB - Springer Science and Business Media LLC ER - TY - GEN A1 - Chilimoniuk, Jarosław A1 - Erol, Anna A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał T1 - Challenges and opportunities in processing NanoString nCounter data T2 - Computational and Structural Biotechnology Journal Y1 - 2024 U6 - https://doi.org/10.1016/j.csbj.2024.04.061 SN - 2001-0370 VL - 23 SP - 1951 EP - 1958 PB - Elsevier BV ER -