Publications BPE group

Max Planck Institute for Dynamics of Complex Technical Systems

Journal Article (354)

2020

Journal Article

Kupke, S. Y.; Ly, L.-H.; Börno, S. T.; Ruff, A.; Timmermann, B.; Vingron, M.; Haas , S.; Reichl, U.: Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication. Viruses 12 (1), 71 (2020)

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Leoz, D.; A., M. L.; Duewer, D. L.; Fung, A.; Liu, L.; Yau, H. K.; Potter, O.; Staples, G. O.; Furuki, K.; Frenkel, R. et al.; Hu, Y.; Sosic, Z.; Zhang, P.; Altmann, F.; Gruber, C.; Shao, C.; Zaia, J.; Evers, W.; Pangelley, S.; Suckau, D.; Wiechmann, A.; Resemann, A.; Jabs, W.; Beck, A.; Froehlich, J. W.; Huang, C.; Li, Y.; Liu, Y.; Sun, S.; Wang, Y.; Seo, Y.; An, H. J.; Reichardt, N.-C.; Ruiz, J. E.; Archer‑Hartmann, S.; Azadi, P.; Bell, L.; Lakos, Z.; An, Y.; Cipollo, J. F.; Pučić-Baković, M.; Štambuk, J.; Lauc, G.; Li, X.; Wang, P. G.; Bock, A.; Hennig, R.; Rapp, E.; Creskey, M.; Cyr, T.; Nakano, M.; Sugiyama, T.; Leung, P. A.; Link‑Lenczowski, P.; Jaworek, J.; Yang, S. J.; Zhang, H.; Kelly, T.; Klapoetke, S.; Cao, R.; Kim, J. Y.; Lee, H. K.; Lee, J.; Yoo, J. S.; Kim, S.; Suh, S.; de Haan, N.; Falck, D.; Lageveen-Kammeijer, G. S.M.; Wuhrer, M.; Emery, R. J.; Kozak, R. P.; Liew, L. P.; Royle, L.; Urbanowicz, P. A.; Packer, N.; Song, X.; Everest-Dass, A.; Lattová, E.; Cajic, S.; Alagesan, K.; Kolarich, D.; Kasali, T.; Lindo, V.; Chen, Y.; Goswami, K.; Gau, B.; Amunugama, R.; Jones, R.; Stroop, C. J. M.; Kato, K.; Yagi, H.; Kondo, S.; Yuen, C.; Harazono, A.; Shi, X.; Magnelli, P.; Kasper, B. T.; Mahal, L. K.; Harvey, D. J.; O'Flaherty, R.; Rudd, P. M.; Saldova, R.; Hecht, E. S.; Muddiman, D. C.; Kang, J.; Bhoskar, P.; Menard, D.; Saati, A.; Merle, C.; Mast, S.; Tep, S.; Truong, J.; Nishikaze, T.; Sekiya, S.; Shafer, A.; Funaoka, S.; Toyoda, M.; de Vreugd, P.; Caron, C.; Pradhan, P.; Tan, N. C.; Mechref, Y.; Patil, S.; Rohrer, J. S.; Chakrabarti, R.; Dadke, D.; Lahori, M.; Zou, C.; Cairo, C. W.; Reiz, B.; Whittal, R. M.; Lebrilla, C.; Wu, L. D.; Guttman, A.; Szigeti, M.; Kremkow, B. G.; Lee, K.; Sihlbom, C.; Adamczyk, B.; Jin, C.; Karlsson, N. G.; Örnros, J.; Larson, G.; Nilsson, J.; Meyer, B.; Wiegandt, A.; Komatsu, E.; Perreault, H.; Bodnar, E. D.; Said, N.; Francois, Y.; Leize-Wagner, E.; Maier, S.; Zeck, A.; Heck, A. J. R.; Yang, Y.; Haselberg, R.; Yu, Y. Q.; Alley, W.; Leone, J. W.; Yuan, H.; Stein, S. E.: NIST interlaboratory study on glycosylation analysis of monoclonal antibodies: comparison of results from diverse analytical methods. Molecular and Cellular Proteomics 19 (1), pp. 11 - 30 (2020)

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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)

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Nikolay, A.; de Grooth, J.; Genzel, Y.; Wood, J. A.; Reichl, U.: Virus harvesting in perfusion culture: Choosing the right typeof hollow fiber membrane. Biotechnology and Bioengineering 117 (10), pp. 3040 - 3052 (2020)

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Rexer, T.; Wenzel, L.; Hoffmann, M.; Tischlik, S.; Bergmann, C.; Grote, V.; Boecker, S.; Bettenbrock, K.; Schildbach, A.; Kottler, R. et al.; Mahour, R.; Rapp, E.; Pietzsch, M.; Reichl, U.: Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. Journal of Biotechnology 322 (10), pp. 54 - 65 (2020)

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Rodrigues, A. F.; Fernandes, P.; Laske, T.; Castro, R.; Marques Alves, P.; Genzel, Y.; Coroadinha, A. S.: Cell Bank Origin of MDCK Parental Cells Shapes Adaptation to Serum-Free Suspension Culture and Canine Adenoviral Vector Production. International Journal of Molecular Sciences 21 (17), 6111 (2020)

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Rodrigues Correia Ramos, J.; Rath, A.; Genzel, Y.; Sandig, V.; Reichl, U.: A dynamic model linking cell growth to intracellular metabolism and extracellular by‐product accumulation. Biotechnology and Bioengineering 117 (5), pp. 1533 - 1553 (2020)

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Schaffert, A.; Hanić, M.; Novokmet, M.; Zaytseva, O.; Krištić, J.; Lux, A.; Nitschke, L.; Peipp, M.; Pezer, M.; Hennig, R. et al.; Rapp, E.; Lauc, G.; Nimmerjahn, F.: Minimal B Cell Extrinsic IgG Glycan Modifications of Pro- and Anti-Inflammatory IgG Preparations in vivo. Frontiers in Immunology 10, 3024 (2020)

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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)

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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)

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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)

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Vogel , S. K.; Wölfer, C.; Ramirez-Diaz, D. A.; Flassig, R.; Sundmacher, K.; Schwille, P.: Symmetry breaking and emergence of directional flows in minimal actomyosin cortices. Cells 9 (6), 1432 (2020)

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2019

Journal Article

Bdeir, N.; Arora, P.; Gärtner, S.; Hoffmann, M.; Reichl, U.; Pöhlmann, S.; Winkler, M.: A system for production of defective interfering particles in the absence of infectious influenza A virus. PLoS One 14 (3), e0212757 (2019)

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Bissinger, T.; Fritsch, J.; Mihut, A. N.; Wu, Y.; Liu, X.; Genzel, Y.; Tan, W.-S.; Reichl, U.: Semi-perfusion cultures of suspension MDCK cells enable high cell concentrations and efficient influenza A virus production. Vaccine 37 (47), pp. 7003 - 7010 (2019)

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Bule, P.; Chuzel, L.; Blagova, E.; Wu, L.; Gray, M. A.; Henrissat, B.; Rapp, E.; Bertozzi, C. R.; Taron, C. H.; Davies, G. J.: Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Nature Communications 10, 4816 (2019)

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Campbell, M.P.; Abrahams, J.L.; Rapp, E.; Struwe, W.B.; Costello, C.E.; Novotny, M.; Ranzinger, R.; York, W.S.; Kolarich, D.; Rudd, P.M. et al.; Kettner, C.: The minimum information required for a glycomics experiment (MIRAGE) project: LC guidelines. Glycobiology 29 (5), pp. 349 - 354 (2019)

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Coronel, J.; Behrendt, I.; Bürgin, T.; Anderlei, T.; Sandig, V.; Reichl, U.; Genzel, Y.: Influenza A virus production in a single-use orbital shaken bioreactor with ATF or TFF perfusion systems. Vaccine 37 (47), pp. 7011 - 7018 (2019)

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Fischöder, T.; Cajic, S.; Grote, V.; Heinzler, R.; Reichl, U.; Franzreb, M.; Rapp, E.; Elling, L.: Enzymatic Cascades for Tailored 13C6 and 15N Enriched Human Milk Oligosaccharides. Molecules 24 (19), 3482 (2019)

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Fischöder, T.; Cajic, S.; Reichl, U.; Rapp, E.; Elling , L.: Enzymatic cascade synthesis provides novel linear human milk oligosaccharides as reference standards for xCGE-LIF based high-throughput analysis. Biotechnology Journal 14 (3), 1800305 (2019)

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Fortuna, A. R.; Van Teeffelen, S.; Ley, A.; Fischer, L. M.; Taft, F.; Genzel, Y.; Villain, L.; Wolff, M.; Reichl, U.: Use of sulfated cellulose membrane adsorbers for chromatographic purification of cell cultured-derived influenza A and B viruses. Separation and Purification Technology (226), pp. 350 - 358 (2019)

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Gränicher, G.; Coronel, J.; Pralow, A.; Marichal-Gallardo, P.; Wolff, M. W.; Rapp, E.; Karlas, A.; Sandig, V.; Genzel, Y.; Reichl, U.: Efficient influenza A virus production in high cell density using the novel porcine suspension cell line PBG.PK2.1. Vaccine 37 (47), pp. 7019 - 7028 (2019)

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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)

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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)

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Hinneburg, H.; Chatterjee, S.; Schirmeister, F.; Nguyen-Khoung, T.; Packer, N.; Rapp, E.; Thaysen-Andersen, M.: Post-Column Make-Up Flow (PCMF) Enhances the Performance of Capillary-Flow PGC-LC-MS/MS-Based Glycomics. Analytical Chemistry 91 (7), pp. 4559 - 4567 (2019)

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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)

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Kupke, S. Y.; Riedel, D.; Frensing, T.; Zmora, P.; Reichl, U.: A Novel Type of Influenza A Virus-Derived Defective Interfering Particle with Nucleotide Substitutions in Its Genome. Journal of Virology 93 (4), 01786-18 (2019)

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Laske, T.; Bachmann, M.; Dostert, M.; Karlas, A.; Wirth, D.; Frensing, T.; Meyer, T. F.; Hauser, H.; Reichl, U.: Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth. PLoS Computational Biology 15 (4), e1006944 (2019)

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Lehmann, T.; Schallert, K.; Vilchez-Vargas, R.; Benndorf, D.; Püttker, S.; Sydor, S.; Schulz, C. U.; Bechmann, L. P.; Canbay, A. E.; Heidrich, B. et al.; Reichl, U.; Link, A.; Heyer, R.: Metaproteomics of fecal samples of Crohn's disease and Ulcerative Colitis. Journal of Proteomics 201, pp. 93 - 103 (2019)

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Munoz, R.I.; Kaehne, T.; Herrera, H.; Rodriguez, S.; Guerra, M.M.; Vio , K.; Hennig, R.; Rapp, E.; Rodriguez, E.: The subcommissural organ and the Reissner fiber: old friends revisited. Cell and Tissue Research 375 (2), pp. 507 - 529 (2019)

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Reiding, K.R.; Bondt, A.; Hennig, R.; Gardner, R.A.; O'Flaherty, R.; Trbojević-Akmačić, I.; Shubhakar, A.; Hazes, J.; Reichl, U.; Fernandes, D.L. et al.; Pucic-Bakovic, M.; Rapp, E.; Spencer, D.I.R.; Dolhain, R.; Rudd, P.; Lauc, G.; Wuhrer, M.: High-throughput serum N-glycomics: method comparison and application to study rheumatoid arthritis and pregnancy-associated changes. Molecular and Cellular Proteomics 18 (1), pp. 3 - 15 (2019)

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Rossdam, C.; Konze, S.; Oberbeck, A.; Rapp, E.; Gerardy-Schahn, R.; von Itzstein, M.; Buettner, F.: Approach for Profiling of Glycosphingolipid Glycosylation by Multiplexed Capillary Gel Electrophoresis Coupled to Laser-Induced Fluorescence Detection to Identify Cell-Surface Markers of Human Pluripotent Stem Cells and Derived Cardiomyocytes. Analytical Chemistry 91 (10), pp. 6413 - 6418 (2019)

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Rüdiger, D.; Kupke, S. Y.; Laske, T.; Zmora, P.; Reichl, U.: Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions. PLoS Computational Biology 15 (2), e1006819 (2019)

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Scoma, A.; Heyer, R.; Rifai, R.; Dandyk, C.; Marshall, I.; Kerckhof, F.-M.; Marietou, A.; Boshker, H. T. S.; Meysman, F. J. R.; Malmos, K. G. et al.; Vosegaard, T.; Vermeir, P.; Banat, I. M.; Benndorf, D.; Boon, N.: Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities. The ISME Journal 13 (4), pp. 1004 - 1018 (2019)

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Tapia, F.; Laske, T.; Wasik, M.; Rammhold, M.; Genzel, Y.; Reichl, U.: Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling. Frontiers in Bioengineering and Biotechnology 7, 275 (2019)

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Tapia, F.; Wohlfahrt, D.; Sandig, V.; Jordan, I.; Genzel, Y.; Reichl, U.: Continuous influenza virus production in a tubular bioreactor system provides stable titers and avoids the “von Magnus effect”. PLoS One 14 (11), e0224317 (2019)

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Thorn, C.E.; Bergesch , C.; Joyce, A.; Sambrano, G.; McDonnell, K.; Brennan, F.; Heyer, R.; Benndorf, D.; Abram, F.: A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures. Molecular Ecology Resources 19 (2), pp. 439 - 455 (2019)

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Vazquez-Ramirez, D.; Jordan, I.; Sandig, V.; Genzel, Y.; Reichl, U.: High titer MVA and influenza A virus production using a hybrid fed-batch/perfusion strategy with an ATF system. Applied Microbiology and Biotechnology 103 (7), pp. 3025 - 3035 (2019)

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Weigel, T.; Soliman, R.; Wolff, M. W.; Reichl, U.: Hydrophobic-interaction chromatography for purification of influenza A and B virus. Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences 1117, pp. 103 - 117 (2019)

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Weinrich, S.; Koch, S.; Bonk, F.; Popp, D.; Benndorf, D.; Klamt, S.; Centler, F.: Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. Frontiers in Microbiology 10, 1095 (2019)

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2018

Journal Article

Carvalho, S. B.; Fortuna, A. R.; Wolff, M. W.; Peixoto, C.; Alves, P. M.; Reichl, U.; Carrondo, M. J. T.: Purification of influenza virus-like particles using sulfated cellulose membrane adsorbers. Journal of Chemical Technology and Biotechnology 93 (7), pp. 1988 - 1996 (2018)

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Chuzel, L.; Ganatra, M. B.; Rapp, E.; Henrissat, B.; Taron, C. H.: Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156). The Journal of Biological Chemistry 293, pp. 18138 - 18150 (2018)

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Clerc, F.; Novokmet, M.; Dotz, V.; Reiding, K. R.; de Haan , N.; Kammeijer, G. S.M.; Dalebout, H.; Bladergroen, M. R.; Vukovic, F.; Rapp, E. et al.; Targan, S. R.; Barron, G.; Manetti , N.; Latiano, A.; McGovern, D. P.B.; Annese, V.; Lauc, G.; Wuhrer, M.: Plasma N-Glycan Signatures Are Associated With Features of Inflammatory Bowel Diseases. Gastroenterology 155 (3), pp. 829 - 843 (2018)

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Fischer, L. M.; Wolff, M. W.; Reichl, U.: Purification of cell culture-derived influenza A virus via continuous anion exchange chromatography on monoliths. Vaccine 36 (22), pp. 3153 - 3160 (2018)

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Journal Article

Fortuna, A. R.; Taft, F.; Villain, L.; Wolff, M. W.; Reichl, U.: Optimization of cell culture-derived inﬂuenza A virus particles puriﬁcation using sulfated cellulose membrane adsorbers. Engineering in Life Sciences 18 (1), pp. 29 - 39 (2018)

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Hoffmann, M.; Pioch, M.; Pralow, A.; Hennig, R.; Kottler, R.; Reichl, U.; Rapp, E.: The Fine Art of Destruction: A Guide to In-Depth Glycoproteomic Analyses – Exploiting the Diagnostic Potential of Fragment Ions. Proteomics 18 (24), e1800282 (2018)

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supplementary-material

Journal Article

Mahour, R.; Klapproth, J.; Rexer, T.; Schildbach, A.; Klamt, S.; Pietzsch, M.; Rapp, E.; Reichl, U.: Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. Journal of Biotechnology 283, pp. 120 - 129 (2018)

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Journal Article

Möginger, U.; Grunewald, S.; Hennig, R.; Kuo, C.-W.; Schirmeister, F.; Voth, H.; Rapp, E.; Khoo, K.-H.; Seeberger, P. H.; Simon, J. C. et al.; Kolarich, D.: Alterations of the Human Skin N- and O-Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma. Frontiers in Oncology 8, 70 (2018)

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Muth, T.; Kohrs, F.; Heyer, R.; Benndorf, D.; Rapp, E.; Reichl, U.; Martens, L.; Renard, B. Y.: MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. Analytical Chemistry 90, pp. 685 - 689 (2018)

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Journal Article

Nguyen-Khuong, T.; Pralow, A.; Reichl, U.; Rapp, E.: Improvement of electrospray stability in negative ion mode for nano-PGC-LC-MS glycoanalysis via post-column make-up flow. Glycoconjugate Journal 35 (6), pp. 499 - 509 (2018)

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Journal Article

Nikolay, A.; Casthilho, L. R.; Reichl, U.; Genzel, Y.: Propagation of Brazilian Zika virus strains in static and suspension cultures using Vero and BHK cells. Vaccine 36 (22), pp. 3140 - 3145 (2018)

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