TY - GEN A1 - Kolenda, Rafał A1 - Burdukiewicz, Michał A1 - Schiebel, Juliane A1 - Rödiger, Stefan A1 - Sauer, Lysann A1 - Szabo, Istvan A1 - Orlowska, Aleksandra A1 - Weinreich, Jörg A1 - Nitschke, Jörg A1 - Böhm, Alexander A1 - Gerber, Ulrike A1 - Roggenbuck, Dirk A1 - Schierack, Peter T1 - Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation T2 - Frontiers in Microbiology Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.01905 SN - 1664-302X VL - 9 IS - 1905 ER - TY - GEN A1 - Burdukiewicz, Michał A1 - Rödiger, Stefan A1 - Sobczyk, Piotr A1 - Menschikowski, Mario A1 - Schierack, Peter A1 - Mackiewicz, Pawel T1 - Methods for comparing multiple digital PCR experiments T2 - Biomolecular Detection and Quantification Y1 - 2016 U6 - https://doi.org/10.1016/j.bdq.2016.06.004 SN - 2214-7535 VL - 9 SP - 14 EP - 19 ER - TY - GEN A1 - Kolenda, Rafał A1 - Burdukiewicz, Michał A1 - Schierack, Peter T1 - 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 T2 - Frontiers in Cellular and Infection Microbiology Y1 - 2015 U6 - https://doi.org/10.3389/fcimb.2015.00023 SN - 2235-2988 VL - 5 ER - TY - GEN A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał A1 - Blagodatskikh, Konstantin A. A1 - Jahn, Michael A1 - Schierack, Peter T1 - R as an Environment for the Reproducible Analysis of DNA Amplification Experiments T2 - The R journal Y1 - 2015 UR - https://journal.r-project.org/archive/2015/RJ-2015-011/index.html SN - 2073-4859 VL - 7 IS - 1 SP - 127 EP - 150 ER - TY - GEN A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał A1 - Schierack, Peter T1 - chipPCR: an R package to pre-process raw data of amplification curves. Bioinformatics T2 - Bioinformatics Y1 - 2015 U6 - https://doi.org/10.1093/bioinformatics/btv205 SN - 1367-4803 SN - 1460-2059 VL - 31 IS - 17 SP - 2900 EP - 2902 ER - TY - GEN A1 - Rödiger, Stefan A1 - Lehmann, Werner A1 - Frömmel, Ulrike A1 - Böhm, Alexander A1 - Nitschke, Jörg A1 - Burdukiewicz, Michał A1 - Schröder, Christian A1 - Dangla, Rémi A1 - Droniou, Magali A1 - Schierack, Peter T1 - 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 Universität Berlin, 24.10.2013 Y1 - 2013 UR - https://leibniz-institut.de/Konferenzen/lsd2013/roediger_the_modi_operandi_of_the_videoscan_platform.pdf ER - TY - CHAP A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał T1 - Reproducible Analysis of DNA Amplification Experiments with an Open Source Software Environment T2 - Abstractbook, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, Münster Y1 - 2015 UR - https://www.dghm.org/wp-content/uploads/2018/07/783_dghm2015_abstractbook_update.pdf ER - TY - CHAP A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał A1 - Heiserich, Lisa A1 - Schierack, Peter A1 - Roggenbuck, Dirk T1 - Digital Enumeration of Double Strand Breaks via γH2AX and Aassociated biomarkers in a Computing Environment for Reproducible Research T2 - 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 Y1 - 2015 SN - 978-3-95853-104-8 SP - S. 413 PB - Pabst Science Publishers CY - Lengerich ER - TY - CHAP A1 - Kolenda, Rafał A1 - Burdukiewicz, Michał A1 - Szabo, M. A1 - Orlowska, Aleksandra A1 - Nitschke, Jörg A1 - Böhm, Alexander A1 - Schierack, Peter T1 - Influence of Salmonella FimH sequence variation on binding to pancreatic secretory granule membrane major glycoprotein GP2 of human and porcine origin T2 - 5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016 Y1 - 2016 UR - https://www.asm.org/images/1903%20asm%20salmonella%20program%20web3.pdf SP - S. 125 PB - American Society for Microbiology CY - Washington, DC ER - TY - CHAP A1 - Burdukiewicz, Michał A1 - Mikolajczyk, A. A1 - Szabo, Istvan A1 - Nitschke, Jörg A1 - Böhm, Alexander A1 - Schierack, Peter A1 - Kolenda, Rafał T1 - Automated enumeration of Salmonella spp. in cell line infection assays and screening of cell line infectivity among various Salmonella isolates T2 - 5th ASM Conference on Salmonella, Potsdam, 29.08-01.09.2016 Y1 - 2016 UR - https://www.asm.org/images/1903%20asm%20salmonella%20program%20web3.pdf SP - S. 127 PB - American Society for Microbiology CY - Washington, DC ER - TY - CHAP A1 - Kolenda, Rafał A1 - Burdukiewicz, Michał A1 - Schiebel, Juliane A1 - Szabo, Istvan A1 - Orlowska, Aleksandra A1 - Nitschke, Jörg A1 - Böhm, Alexander A1 - Schierack, Peter T1 - Adhesion of Salmonella to pancreatic secretory granule membrane major glycoprotein GP2 depends on FimH sequence variation T2 - Abstractbook, Microbiology and Infection, 5th Joint Conference of the DGHM & VAAM, VAAM Annual Meeting 2017, 69th Annual Meeting of the DGHM Y1 - 2017 PB - Spektrumverlag CY - Heidelberg ER - TY - GEN A1 - Spiess, Andrej-Nikolai A1 - Rödiger, Stefan A1 - Burdukiewicz, Michał A1 - Volksdorf, Thomas A1 - Tellinghuisen, Joel T1 - System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation T2 - Scientific Reports Y1 - 2016 U6 - https://doi.org/10.1038/srep38951 SN - 2045-2322 VL - 6 ER - TY - GEN A1 - Burdukiewicz, Michał A1 - Sobczyk, Piotr A1 - Rödiger, Stefan A1 - Duda-Madej, Anna A1 - Mackiewicz, Pawel A1 - Kotulska, Malgorzata T1 - Amyloidogenic motifs revealed by n-gram analysis T2 - Scientific Reports Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-13210-9 SN - 2045-2322 VL - 7 ER - TY - GEN A1 - Schiebel, Juliane A1 - Böhm, Alexander A1 - Nitschke, Jörg A1 - Burdukiewicz, Michał A1 - Weinreich, Jörg A1 - Ali, Aamir A1 - Roggenbuck, Dirk A1 - Rödiger, Stefan A1 - Schierack, Peter T1 - Genotypic and phenotypic characteristics in association with biofilm formation in different pathotypes of human clinical Escherichia coli isolates T2 - Applied and Environmental Microbiology Y1 - 2017 U6 - https://doi.org/10.1128/AEM.01660-17 SN - 1098-5336 SN - 0099-2240 VL - 83 IS - 24 ER - TY - GEN A1 - Burdukiewicz, Michał A1 - Spiess, Andrej-Nikolai A1 - Blagodatskikh, Konstantin A. A1 - Lehmann, Werner A1 - Schierack, Peter A1 - Rödiger, Stefan T1 - Algorithms for automated detection of hook effect-bearing amplification curves T2 - Biomolecular Detection and Quantification Y1 - 2018 U6 - https://doi.org/10.1016/j.bdq.2018.08.001 SN - 2214-7535 VL - 16 SP - 1 EP - 4 ER - TY - GEN A1 - Olowe, Olugbenga Adekunle A1 - Adefioye, Olusolabomi J. A1 - Ajayeoba, T. A. A1 - Schiebel, Juliane A1 - Weinreich, Jörg A1 - Ali, Aamir A1 - Burdukiewicz, Michał A1 - Rödiger, Stefan A1 - Schierack, Peter T1 - Phylogenetic grouping and biofilm formation of Multidrug Resistant Escherichia coli Isolates from Humans, Animals and Food products in South-west Nigeria T2 - Scientific African Y1 - 2019 U6 - https://doi.org/10.1016/j.sciaf.2019.e00158 SN - 2468-2276 VL - 6 ER - TY - GEN A1 - Dinter, Franziska A1 - Burdukiewicz, Michał A1 - Schierack, Peter A1 - Lehmann, Werner A1 - Nestler, Jörg A1 - Dame, Gregory A1 - Rödiger, Stefan T1 - Simultaneous detection and quantification of DNA and protein biomarkers in spectrum of cardiovascular diseases in a microfluidic microbead chip T2 - Analytical and Bioanalytical Chemistry Y1 - 2019 U6 - https://doi.org/10.1007/s00216-019-02199-x SN - 1618-2650 SN - 1618-2642 VL - 411 IS - 29 SP - 7725 EP - 7735 ER - TY - GEN A1 - Burdukiewicz, Michał A1 - Sidorczuk, Katarzyna A1 - Rafacz, Dominik A1 - Pietluch, Filip A1 - Chilimoniuk, Jarosław A1 - Rödiger, Stefan A1 - Przemysław, Gagat T1 - Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram T2 - International Journal of Molecular Sciences Y1 - 2020 U6 - https://doi.org/10.3390/ijms21124310 SN - 1422-0067 SN - 1661-6596 VL - 21 IS - 12 ER - TY - GEN A1 - Reimann, Ronny A1 - Zeng, Bo A1 - Jakopec, Martin A1 - Burdukiewicz, Michał A1 - Petrick, Ingolf A1 - Schierack, Peter A1 - Rödiger, Stefan T1 - Classification of dead and living microalgae Chlorella vulgaris by bioimage informatics an machine learning T2 - Algal Research Y1 - 2020 U6 - https://doi.org/10.1016/j.algal.2020.101908 SN - 2211-9264 VL - 48 ER - TY - GEN A1 - Burdukiewicz, Michał A1 - Sidorczuk, Katarzyna A1 - Rafacz, Dominik A1 - Pietluch, Filip A1 - Bakała, Mateusz A1 - Słowik, Jadwiga A1 - Gagat, Przemysław T1 - CancerGram: An Effective Classifier for Differentiating Anticancer from Antimicrobial Peptides T2 - Pharmaceutics Y1 - 2020 U6 - https://doi.org/10.3390/pharmaceutics1211145 SN - 1999-4923 VL - 12 IS - 11 ER - 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 -