@misc{KolendaBurdukiewiczSchiebeletal., author = {Kolenda, Rafał and Burdukiewicz, Michał and Schiebel, Juliane and R{\"o}diger, Stefan and Sauer, Lysann and Szabo, Istvan and Orlowska, Aleksandra and Weinreich, J{\"o}rg and Nitschke, J{\"o}rg and B{\"o}hm, Alexander and Gerber, Ulrike and Roggenbuck, Dirk and Schierack, Peter}, title = {Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation}, series = {Frontiers in Microbiology}, volume = {9}, journal = {Frontiers in Microbiology}, number = {1905}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.01905}, pages = {15}, language = {en} } @misc{BurdukiewiczRoedigerSobczyketal., author = {Burdukiewicz, Michał and R{\"o}diger, Stefan and Sobczyk, Piotr and Menschikowski, Mario and Schierack, Peter and Mackiewicz, Pawel}, title = {Methods for comparing multiple digital PCR experiments}, series = {Biomolecular Detection and Quantification}, volume = {9}, journal = {Biomolecular Detection and Quantification}, issn = {2214-7535}, doi = {10.1016/j.bdq.2016.06.004}, pages = {14 -- 19}, language = {en} } @misc{KolendaBurdukiewiczSchierack, author = {Kolenda, Rafał and Burdukiewicz, Michał and Schierack, Peter}, title = {A systematic review and meta-analysis of the epidemiology of pathogenic Escherichia coli of calves and the role of calves as reservoirs for human pathogenic E. coli}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {5}, journal = {Frontiers in Cellular and Infection Microbiology}, issn = {2235-2988}, doi = {10.3389/fcimb.2015.00023}, pages = {12}, language = {en} } @misc{RoedigerBurdukiewiczBlagodatskikhetal., author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Blagodatskikh, Konstantin A. and Jahn, Michael and Schierack, Peter}, title = {R as an Environment for the Reproducible Analysis of DNA Amplification Experiments}, series = {The R journal}, volume = {7}, journal = {The R journal}, number = {1}, issn = {2073-4859}, pages = {127 -- 150}, language = {en} } @misc{RoedigerBurdukiewiczSchierack, author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Schierack, Peter}, title = {chipPCR: an R package to pre-process raw data of amplification curves. Bioinformatics}, series = {Bioinformatics}, volume = {31}, journal = {Bioinformatics}, number = {17}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btv205}, pages = {2900 -- 2902}, language = {en} } @misc{RoedigerLehmannFroemmeletal., author = {R{\"o}diger, Stefan and Lehmann, Werner and Fr{\"o}mmel, Ulrike and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Burdukiewicz, Michał and Schr{\"o}der, Christian and Dangla, R{\´e}mi and Droniou, Magali and Schierack, Peter}, title = {The Modi Operandi of the VideoScan Platform for the Detection and Analysis of Nucleic Acids. Life Science Day 2013 \& 17. Leibniz Conference of Advanced Science, Freie Universit{\"a}t Berlin, 24.10.2013}, pages = {1}, language = {en} } @inproceedings{RoedigerBurdukiewicz, author = {R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {Reproducible Analysis of DNA Amplification Experiments with an Open Source Software Environment}, series = {Abstractbook, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, M{\"u}nster}, booktitle = {Abstractbook, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, M{\"u}nster}, language = {en} } @inproceedings{RoedigerBurdukiewiczHeiserichetal., author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Heiserich, Lisa and Schierack, Peter and Roggenbuck, Dirk}, title = {Digital Enumeration of Double Strand Breaks via γH2AX and Aassociated biomarkers in a Computing Environment for Reproducible Research}, series = {From autoantibody research to standardized diagnostic assays in the management of human diseases, report on the 12th Dresden Symposium on Autoantibodies, September 23-26, 2015}, booktitle = {From autoantibody research to standardized diagnostic assays in the management of human diseases, report on the 12th Dresden Symposium on Autoantibodies, September 23-26, 2015}, publisher = {Pabst Science Publishers}, address = {Lengerich}, isbn = {978-3-95853-104-8}, pages = {S. 413}, language = {en} } @inproceedings{KolendaBurdukiewiczSzaboetal., author = {Kolenda, Rafał and Burdukiewicz, Michał and Szabo, M. and Orlowska, Aleksandra and Nitschke, J{\"o}rg and B{\"o}hm, Alexander and Schierack, Peter}, title = {Influence of Salmonella FimH sequence variation on binding to pancreatic secretory granule membrane major glycoprotein GP2 of human and porcine origin}, series = {5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016}, booktitle = {5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016}, publisher = {American Society for Microbiology}, address = {Washington, DC}, pages = {S. 125}, language = {en} } @inproceedings{BurdukiewiczMikolajczykSzaboetal., author = {Burdukiewicz, Michał and Mikolajczyk, A. and Szabo, Istvan and Nitschke, J{\"o}rg and B{\"o}hm, Alexander and Schierack, Peter and Kolenda, Rafał}, title = {Automated enumeration of Salmonella spp. in cell line infection assays and screening of cell line infectivity among various Salmonella isolates}, series = {5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016}, booktitle = {5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016}, publisher = {American Society for Microbiology}, address = {Washington, DC}, pages = {S. 127}, language = {en} } @inproceedings{KolendaBurdukiewiczSchiebeletal., author = {Kolenda, Rafał and Burdukiewicz, Michał and Schiebel, Juliane and Szabo, Istvan and Orlowska, Aleksandra and Nitschke, J{\"o}rg and B{\"o}hm, Alexander and Schierack, Peter}, title = {Adhesion of Salmonella to pancreatic secretory granule membrane major glycoprotein GP2 depends on FimH sequence variation}, series = {Abstractbook, Microbiology and Infection, 5th Joint Conference of the DGHM \& VAAM, VAAM Annual Meeting 2017, 69th Annual Meeting of the DGHM}, booktitle = {Abstractbook, Microbiology and Infection, 5th Joint Conference of the DGHM \& VAAM, VAAM Annual Meeting 2017, 69th Annual Meeting of the DGHM}, publisher = {Spektrumverlag}, address = {Heidelberg}, pages = {S. 118}, language = {en} } @misc{SpiessRoedigerBurdukiewiczetal., author = {Spiess, Andrej-Nikolai and R{\"o}diger, Stefan and Burdukiewicz, Michał and Volksdorf, Thomas and Tellinghuisen, Joel}, title = {System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/srep38951}, pages = {10}, language = {en} } @misc{BurdukiewiczSobczykRoedigeretal., author = {Burdukiewicz, Michał and Sobczyk, Piotr and R{\"o}diger, Stefan and Duda-Madej, Anna and Mackiewicz, Pawel and Kotulska, Malgorzata}, title = {Amyloidogenic motifs revealed by n-gram analysis}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/s41598-017-13210-9}, pages = {12}, language = {en} } @misc{SchiebelBoehmNitschkeetal., author = {Schiebel, Juliane and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Burdukiewicz, Michał and Weinreich, J{\"o}rg and Ali, Aamir and Roggenbuck, Dirk and R{\"o}diger, Stefan and Schierack, Peter}, title = {Genotypic and phenotypic characteristics in association with biofilm formation in different pathotypes of human clinical Escherichia coli isolates}, series = {Applied and Environmental Microbiology}, volume = {83}, journal = {Applied and Environmental Microbiology}, number = {24}, issn = {1098-5336}, doi = {10.1128/AEM.01660-17}, language = {en} } @misc{BurdukiewiczSpiessBlagodatskikhetal., author = {Burdukiewicz, Michał and Spiess, Andrej-Nikolai and Blagodatskikh, Konstantin A. and Lehmann, Werner and Schierack, Peter and R{\"o}diger, Stefan}, title = {Algorithms for automated detection of hook effect-bearing amplification curves}, series = {Biomolecular Detection and Quantification}, volume = {16}, journal = {Biomolecular Detection and Quantification}, issn = {2214-7535}, doi = {10.1016/j.bdq.2018.08.001}, pages = {1 -- 4}, language = {en} } @misc{OloweAdefioyeAjayeobaetal., author = {Olowe, Olugbenga Adekunle and Adefioye, Olusolabomi J. and Ajayeoba, T. A. and Schiebel, Juliane and Weinreich, J{\"o}rg and Ali, Aamir and Burdukiewicz, Michał and R{\"o}diger, Stefan and Schierack, Peter}, title = {Phylogenetic grouping and biofilm formation of Multidrug Resistant Escherichia coli Isolates from Humans, Animals and Food products in South-west Nigeria}, series = {Scientific African}, volume = {6}, journal = {Scientific African}, issn = {2468-2276}, doi = {10.1016/j.sciaf.2019.e00158}, pages = {11}, language = {en} } @misc{DinterBurdukiewiczSchieracketal., author = {Dinter, Franziska and Burdukiewicz, Michał and Schierack, Peter and Lehmann, Werner and Nestler, J{\"o}rg and Dame, Gregory and R{\"o}diger, Stefan}, title = {Simultaneous detection and quantification of DNA and protein biomarkers in spectrum of cardiovascular diseases in a microfluidic microbead chip}, series = {Analytical and Bioanalytical Chemistry}, volume = {411}, journal = {Analytical and Bioanalytical Chemistry}, number = {29}, issn = {1618-2650}, doi = {10.1007/s00216-019-02199-x}, pages = {7725 -- 7735}, language = {en} } @misc{BurdukiewiczSidorczukRafaczetal., author = {Burdukiewicz, Michał and Sidorczuk, Katarzyna and Rafacz, Dominik and Pietluch, Filip and Chilimoniuk, Jarosław and R{\"o}diger, Stefan and Przemysław, Gagat}, title = {Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {12}, issn = {1422-0067}, doi = {10.3390/ijms21124310}, pages = {13}, language = {en} } @misc{ReimannZengJakopecetal., author = {Reimann, Ronny and Zeng, Bo and Jakopec, Martin and Burdukiewicz, Michał and Petrick, Ingolf and Schierack, Peter and R{\"o}diger, Stefan}, title = {Classification of dead and living microalgae Chlorella vulgaris by bioimage informatics an machine learning}, series = {Algal Research}, volume = {48}, journal = {Algal Research}, issn = {2211-9264}, doi = {10.1016/j.algal.2020.101908}, pages = {11}, language = {en} } @misc{BurdukiewiczSidorczukRafaczetal., author = {Burdukiewicz, Michał and Sidorczuk, Katarzyna and Rafacz, Dominik and Pietluch, Filip and Bakała, Mateusz and Słowik, Jadwiga and Gagat, Przemysław}, title = {CancerGram: An Effective Classifier for Differentiating Anticancer from Antimicrobial Peptides}, series = {Pharmaceutics}, volume = {12}, journal = {Pharmaceutics}, number = {11}, issn = {1999-4923}, doi = {10.3390/pharmaceutics1211145}, pages = {14}, language = {en} } @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} }