Publications of Dirk Benndorf

Bartholomäus, A.; Kolte, B.; Mustafayeva, A.; Goebel, I.; Fuchs, S.; Benndorf, D.; Engelmann, S.; Ignatova, Z.: smORFer: a modular algorithm to detect small ORFs in prokaryotes. Nucleic Acids Research (London) 49 (15), e89 (2021)

Bastida, F.; Jehmlich, N.; Starke, R.; Schallert, K.; Benndorf, D.; López-Mondéjar, R.; Plaza, C.; Freixino, Z.; Ramírez-Ortuño, C.; Ruiz-Navarro, A. et al.; Díaz-López, M.; Vera, A.; Moreno, J.L.; Eldridge, D.J.; García, C.; Delgado-Baquerizo, M.: Structure and function of bacterial metaproteomes across biomes. Soil Biology and Biochemistry 160, 108331 (2021)

Biemann, R.; Buß, E.; Benndorf, D.; Lehmann, T.; Schallert, K.; Püttker, S.; Reichl, U.; Isermann, B.; Schneider, J. G.; Saake, G. et al.; Heyer, R.: Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss. Biomolecules 11 (5), 726 (2021)

De Vrieze, J.; Heyer, R.; Props, R.; Van Meulebroek, L.; Gille, K.; Vanhaecke, L.; Benndorf, D.; Boon, N.: Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles. Water Research 202 (1), 117422 (2021)

Hassa, J.; Klang, J.; Benndorf, D.; Pohl, M.; Hülsemann, B.; Mächtig, T.; Effenberger, M.; Pühler, A.; Schlüter, A.; Theuerl, S.: Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants. Microorganisms 9 (7), 1457 (2021)

Hein, M. D.; Kollmus, H.; Marichal-Gallardo, P.; Püttker, S.; Benndorf, D.; Genzel, Y.; Schughart, K.; Kupke, S. Y.; Reichl, U.: OP7, a novel influenza A virus defective interfering particle: production, purification, and animal experiments demonstrating antiviral potential. Applied Microbiology and Biotechnology 105 (1), pp. 129 - 146 (2021)

Meinusch, N.; Kramer, S.; Körner, O.; Wiese, J.; Seick, I.; Beblek, A.; Berges, R.; Illenberger, B.; Illenberger, M.; Uebbing, J. et al.; Wolf, M.; Saake, G.; Benndorf, D.; Reichl, U.; Heyer, R.: Integrated Cycles for Urban Biomass as a Strategy to Promote a CO2-Neutral Society—A Feasibility Study. Sustainability 13 (17), 9505 (2021)

Starke, R.; Siles, J. A.; Fernandes, M. L. P.; Schallert, K.; Benndorf, D.; Plaza, C.; Jehmlich, N.; Delgado-Baquerizo, M.; Bastida, F.: The structure and function of soil archaea across biomes. Journal of Proteomics 237, 104147 (2021)

Van Den Bossche, T.; Arntzen, M. Ø.; Becher, D.; Benndorf, D.; Eijsink, V. G. H.; Henry, C.; Jagtap, P. D.; Jehmlich, N.; Juste, C.; Kunath, B. J. et al.; Mesuere, B.; Muth, T.; Pope, P. B.; Seifert, J.; Tanca, A.; Uzzau, S.; Wilmes, P.; Hettich, R. L.; Armengaud, J.: The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome 9 (1), 243 (2021)

Van Den Bossche, T.; Kunath, B. J.; Schallert, K.; Schäpe, S. S.; Abraham, P. E.; Armengaud, J.; Arntzen, M. Ø.; Bassignani, A.; Benndorf, D.; Fuchs, S. et al.; Giannone, R. J.; Griffin, T. J.; Hagen, L. H.; Halder, R.; Henry, C.; Hettich, R. L.; Heyer, R.; Jagtap, P.; Jehmlich, N.; Jensen, M.; Juste, C.; Kleiner, M.; Langella, O.; Lehmann, T.; Leith, E.; May, P.; Mesuere, B.; Miotello, G.; Peters, S. L.; Pible, O.; Reichl, U.; Renard, B. Y.; Schiebenhoefer, H.; Scryba, A.; Tanca, A.; Trappe, K.; Trezzi, J.-P.; Uzzau, S.; Verschaffelt, P.; von Bergen, M.; Wilmes, P.; Wolf, M.; Martens, L.; Muth, T.: Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. Nature Communications 12 (1), 7305 (2021)

Walke, D.; Schallert, K.; Ramesh, P.; Benndorf, D.; Lange, E.; Reichl, U.; Heyer, R.: MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. International Journal of Molecular Sciences 22 (20), 10992 (2021)

Heyer, R.; Klang, J.; Hellwig, P.; Schallert, K.; Kress, P.; Huelsemann, B.; Theuerl, S.; Reichl, U.; Benndorf, D.: Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants. Bioresource Technology 314, 123679 (2020)

Maus, I.; Tubbesing, T.; Wibberg, D.; Heyer, R.; Hassa, J.; Tomazetto, G.; Huang, L.; Bunk, B.; Spröer, C.; Benndorf, D. et al.; Zverlov, V.; Pühler, A.; Klocke, M.; Sczyrba, A.; Schlüter, A.: The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms 8 (12), 2024 (2020)

Schiebenhoefer, H.; Schallert, K.; Renard, B. Y.; Trappe, K.; Schmid, E.; Benndorf, D.; Riedel, K.; Muth, T.; Fuchs, S.: A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. Nature Protocols 15, pp. 3212 - 3239 (2020)

Schütze, A.; Benndorf, D.; Püttker, S.; Kohrs, F.; Bettenbrock, K.: The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12. Frontiers in Microbiology 11, 233 (2020)

Scoma, A.; Khor, W. C.; Coma, M.; Heyer, R.; Props, R.; Schoelynk, J.; Bouts, T.; Benndorf, D.; Li, D.; Zhang, H. et al.; Rabaey, K.: Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate. Frontiers in Microbiology 11, 530 (2020)

Van Den Bossche, T.; Verschaffelt, P.; Schallert, K.; Barsnes, H.; Dawyndt, P.; Benndorf, D.; Renard, B. Y.; Mesuere, B.; Martens, L.; Muth, T.: Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis. Journal of Proteome Research 19 (8), pp. 3562 - 3566 (2020)

Heyer, R.; Schallert, K.; Büdel, A.; Zoun, R.; Dorl, S.; Behne, A.; Kohrs, F.; Püttker, S.; Siewert, C.; Muth, T. et al.; Saake, G.; Reichl, U.; Benndorf, D.: A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer. Frontiers in Microbiology 10, 1883 (2019)

Heyer, R.; Schallert, K.; Siewert, C.; Kohrs, F.; Greve, J.; Maus, I.; Klang, J.; Klocke, M.; Heiermann, M.; Hoffmann, M. et al.; Püttker, S.; Calusinska, M.; Zoun, R.; Saake, G.; Benndorf, D.; Reichl, U.: Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. Microbiome (7), 69 (2019)

Koch, S.; Kohrs, F.; Lahmann, P.; Bissinger, T.; Wendschuh, S.; Benndorf, D.; Reichl, U.; Klamt, S.: RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PLoS Computational Biology 15 (2), e1006759 (2019)