@misc{KolendaBurdukiewiczWimonćetal., author = {Kolenda, Rafał and Burdukiewicz, Michał and Wimonć, Marcjanna and Aleksandrowicz, Adrianna and Ali, Aamir and Szabo, Istvan and Tedin, Karsten and Bartholdson, Scott J. and Pickhard, Derek and Schierack, Peter}, title = {Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens}, series = {Applied and Environmental Microbiology}, volume = {87}, journal = {Applied and Environmental Microbiology}, number = {2}, issn = {1098-5336}, doi = {10.1128/AEM.02177-20}, language = {en} } @misc{ChilimoniukGosiewskaSłowiketal., author = {Chilimoniuk, Jarosław and Gosiewska, Alicja and Słowik, Jadwiga and Weiss, Romano and Deckert, P. Markus and R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {coutfitteR: efficient selection of count distributions to assess DNA damage}, series = {Annals of Translational Medicine}, volume = {9}, journal = {Annals of Translational Medicine}, number = {7}, issn = {2305-5847}, doi = {10.21037/atm-20-6363}, language = {en} } @misc{SidorczukBurdukiewiczCerketal., author = {Sidorczuk, Katarzyna and Burdukiewicz, Michał and Cerk, Klara and Fritscher, Joachim and Kingsley, Robert A. and Schierack, Peter and Hildebrand, Falk and Kolenda, Rafał}, title = {AdhesiomeR: a tool for Escherichia coli adhesin classification and analysis}, series = {BMC Genomics}, volume = {25}, journal = {BMC Genomics}, number = {1}, publisher = {Springer Science and Business Media LLC}, issn = {1471-2164}, doi = {10.1186/s12864-024-10525-6}, pages = {1 -- 10}, abstract = {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.}, language = {en} } @misc{ChilimoniukErolRoedigeretal., author = {Chilimoniuk, Jarosław and Erol, Anna and R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {Challenges and opportunities in processing NanoString nCounter data}, series = {Computational and Structural Biotechnology Journal}, volume = {23}, journal = {Computational and Structural Biotechnology Journal}, publisher = {Elsevier BV}, issn = {2001-0370}, doi = {10.1016/j.csbj.2024.04.061}, pages = {1951 -- 1958}, language = {en} }