ARBEITSGRUPPE

DATENBANKEN UND

SOFTWARE ENGINEERING

Abgeschlossene Projekte

• Integrated Cycles for Urban Biomass (ICU): Optimierung von Biomasseströmen und -verwertungswegen in urbanen Wohngebäuden mit dem Ziel einer CO2-neutralen Stadt
  Laufzeit: 01.12.2019 - 28.02.2021
  
  
• InflammatorySystems-Microbiome: Systemdiagnostik des menschlichen Darmmikrobioms bei entzündungsbedingten Erkrankungen mittels Metaproteomeanalyse
  Laufzeit: 01.10.2017 - 31.10.2018
  
  
• Prozesskontrolle und Optimierung der Biogasproduktion mittels Metaproteomanalyse
  Laufzeit: 01.08.2011 - 30.07.2014
  
  

• Roman Zoun, Kay Schallert, David Broneske, Ivayla Trifonova, Xiao Chen, Robert Heyer, Dirk Benndorf, and Gunter Saake. An Investigation of Alternatives to Transform Protein Sequence Databases to a Columnar Index Schema. Algorithms, 14(2), 2021. accepted for publication.
   
• Alberto Scoma, Way Cern Khor, Marta Coma, Robert Heyer, Ruben Props, Jonas Schoelynck, Tim Bouts, Dirk Benndorf, Desheng Li, Hemin Zhang, et al. Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate. Frontiers in microbiology, Volume 11, page 530, 2020.
   
• Robert Heyer, Johanna Klang, Patrick Hellwig, Kay Schallert, Philipp Kress, Benedikt Huelsemann, Susanne Theuerl, Udo Reichl, and Dirk Benndorf. Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants. Bioresource Technology, 2020.
   
• Irena Maus, Tom Tubbesing, Daniel Wibberg, Robert Heyer, Julia Hassa, Geizecler Tomazetto, Liren Huang, Boyke Bunk, Cathrin Spröer, Dirk Benndorf, Vladimir Zverlov, Alfred Pühler, Michael Klocke, and Sczyrba. The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms, 8(12, ARTICLE-NUMBER = 2024), 2020.
   
• Roman Zoun, Kay Schallert, David Broneske, Ivayla Trifonova, Xiao Chen, Robert Heyer, Dirk Benndorf, and Gunter Saake. Efficient Transformation of Protein Sequence Databases to Columnar Index Schema. In International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD-DEXA), volume 1062 of CCIS, pages 67–72. IEEE, August 2019.
   
• Robert Heyer, Kay Schallert, Corina Siewert, Fabian Kohrs, J. Greve, I. Maus, J. Klang, M. Klocke, M. Heiermann, M. Hoffmann, S. Puettker, M. Calusinska, Roman Zoun, Gunter Saake, Dirk Benndorf, and Udo Reichl. Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. Microbiome, 7(1):69, April 2019.
   
• Roman Zoun, Kay Schallert, David Broneske, Wolfram Fenske, Marcus Pinnecke, Robert Heyer, Sven Brehmer, Dirk Benndorf, and Gunter Saake. MSDataStream - Connecting a Bruker Mass Spectrometer to the Internet. In Datenbanksysteme für Business, Technologie und Web, pages 507 – 510. Gesellschaft für Informatik, March 2019.
   
• Robert heyer, Kay Schallert, Anja Buedel, Roman Zoun, Sebastian Dorl, Alexander Behne, Fabian Kohrs, Sebastian Puettker, Corina Siewert, Thilo Muth, Gunter Saake, Udo Reichl, and Dirk Benndorf. A robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 hours using phenol extraction, FASP digest and the MetaProteomeAnalyzer. Frontiers in Microbiology, Volume 10 1883, 2019.
   
• Roman Zoun, Kay Schallert, David Broneske, Sören Falkenberg, Robert Heyer, Sabine Wehnert, Sven Brehmer, Dirk Benndorf, and Gunter Saake. MStream: Proof of Concept of an Analytic Cloud Platform for Near-Real-Time Diagnostics using Mass Spectrometry Data. 002-2019, Otto-von-Guericke-University Magdeburg, 2019.
   
• R. Heyer, K. Schallert, C. Siewert, F. Kohrs, J. Greve, I. Maus, J. Klang, M. Klocke, M. Heiermann, M. Hoffmann, S. Puttker, M. Calusinska, R. Zoun, G. Saake, D. Benndorf, and U. Reichl. Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. Microbiome, Volume 7, 2019. Hv5rv Times Cited:1 Cited References Count:70.
   
• T. Lehmann, K. Schallert, R. Vilchez-Vargas, D. Benndorf, S. Puttker, S. Sydor, C. Schulz, L. Bechmann, A. Canbay, B. Heidrich, U. Reichl, A. Link, and R. Heyer. Metaproteomics of fecal samples of Crohn's disease and Ulcerative Colitis. J Proteomics, Volume 201, pages 93–103, 2019. Lehmann, T Schallert, K Vilchez-Vargas, R Benndorf, D Puttker, S Sydor, S Schulz, C Bechmann, L Canbay, A Heidrich, B Reichl, U Link, A Heyer, R eng Netherlands 2019/04/23 06:00 J Proteomics. 2019 Jun 15;201:93-103. doi: 10.1016/j.jprot.2019.04.009. Epub.
   
• A. Scoma, R. Heyer, R. Rifai, C. Dandyk, I. Marshall, F. M. Kerckhof, A. Marietou, H. T. S. Boshker, F. J. R. Meysman, K. G. Malmos, T. Vosegaard, P. Vermeir, I. M. Banat, D. Benndorf, and N. Boon. Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities. ISME J, 13(4):1004–1018, 2019. Scoma, Alberto Heyer, Robert Rifai, Ridwan Dandyk, Christian Marshall, Ian Kerckhof, Frederiek-Maarten Marietou, Angeliki Boshker, Henricus T S Meysman, Filip J R Malmos, Kirsten G Vosegaard, Thomas Vermeir, Pieter Banat, Ibrahim M Benndorf, Dirk Boon, Ni.
   
• C. E. Thorn, C. Bergesch, A. Joyce, G. Sambrano, K. McDonnell, F. Brennan, R. Heyer, D. Benndorf, and F. Abram. A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures. Mol Ecol Resour, 19(2):439–455, 2019. Thorn, Camilla E Bergesch, Christian Joyce, Aoife Sambrano, Gustavo McDonnell, Kevin Brennan, Fiona Heyer, Robert Benndorf, Dirk Abram, Florence eng NUI Galway England 2018/12/20 06:00 Mol Ecol Resour. 2019 Mar;19(2):439-455. doi: 10.1111/1755-0998.12979.
   
• Roman Zoun, Gabriel Campero Durand, Kay Schallert, Apoorva Patrikar, David Broneske, Wolfram Fenske, Robert Heyer, Dirk Benndorf, and Gunter Saake. Protein Identification as a Suitable Application for Fast Data Architecture. In International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD-DEXA), pages 168 – 178. IEEE, September 2018.
   
• Roman Zoun, Kay Schallert, Atin Janki, Rohith Ravindran, Gabriel Campero Durand, Wolfram Fenske, David Broneske, Robert Heyer, Dirk Benndorf, and Gunter Saake. Streaming FDR Calculation for Protein Identication. In Advances in Databases and Information Systems, pages 80 – 87, September 2018.
   
• Atin Janki, Roman Zoun, Kay Schallert, Rohith Ravindran, David Broneske, Wolfram Fenske, Robert Heyer, Dirk Benndorf, and Gunter Saake. Connecting X! Tandem to a Database Management System. In GI-Workshop Grundlagen von Datenbanken, GvDB, pages 77–82, May 2018.
   
• T. Muth, F. Kohrs, R. Heyer, D. Benndorf, E. Rapp, U. Reichl, L. Martens, and B. Y. Renard. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. Anal Chem, 90(1):685–689, 2018. Muth, Thilo Kohrs, Fabian Heyer, Robert Benndorf, Dirk Rapp, Erdmann Reichl, Udo Martens, Lennart Renard, Bernhard Y eng U24 CA199347/CA/NCI NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2017/12/08 06:00 Anal Chem. 2018 Ja.
   
• Lisa Wenzel, Robert Heyer, Kay Schallert, Lucy Löser, Röbbe Wünschiers, Udo Reichl, and Dirk Benndorf. SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples. Engineering in Life Sciences, Volume 18, 2018.
   
• R. Zoun, G. C. Durand, K. Schallert, A. Patrikar, D. Broneske, W. Fenske, R. Heyer, D. Benndorf, and G. Saake. Protein Identification as a Suitable Application for Fast Data Architecture. Database and Expert Systems Applications: Dexa 2018 International Workshops, Volume 903, pages 168–178, 2018. Bm1ts Times Cited:1 Cited References Count:30 Communications in Computer and Information Science.
   
• R. Zoun, K. Schallert, A. Janki, R. Ravindran, G. C. Durand, W. Fenske, D. Broneske, R. Heyer, D. Benndorf, and G. Saake. Streaming FDR Calculation for Protein Identification. New Trends in Databases and Information Systems, Adbis 2018, Volume 909, pages 80–87, 2018. Bm5sq Times Cited:1 Cited References Count:20 Communications in Computer and Information Science.
   
• Robert Heyer, Kay Schallert, Roman Zoun, Beatrice Becher, Gunter Saake, and Dirk Benndorf. Challenges and perspectives of metaproteomic data analysis. Journal of biotechnology, Number 261, pages 24–36, 11 2017.
   
• Roman Zoun, Kay Schallert, David Broneske, Robert Heyer, Dirk Benndorf, and Gunter Saake. Interactive Chord Visualization for Metaproteomics. In International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD-DEXA). IEEE, 2017. www.dxdoi.org/10.1109/DEXA.2017.32.
   
• R. Heyer, K. Schallert, R. Zoun, B. Becher, G. Saake, and D. Benndorf. Challenges and perspectives of metaproteomic data analysis. J Biotechnol, Volume 261, pages 24–36, 2017. Heyer, Robert Schallert, Kay Zoun, Roman Becher, Beatrice Saake, Gunter Benndorf, Dirk eng Review Netherlands 2017/07/01 06:00 J Biotechnol. 2017 Nov 10;261:24-36. doi: 10.1016/j.jbiotec.2017.06.1201. Epub 2017 Jun 27.
   
• F. Kohrs, R. Heyer, T. Bissinger, R. Kottler, K. Schallert, S. Puttker, A. Behne, E. Rapp, D. Benndorf, and U. Reichl. Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition. Anaerobe, Volume 46, pages 56–68, 2017. Kohrs, F Heyer, R Bissinger, T Kottler, R Schallert, K Puttker, S Behne, A Rapp, E Benndorf, D Reichl, U eng England 2017/02/13 06:00 Anaerobe. 2017 Aug;46:56-68. doi: 10.1016/j.anaerobe.2017.02.005. Epub 2017 Feb 9.
   
• R. Zoun, K. Schallert, D. Broneske, R. Heyer, D. Benndorf, and G. Saake. Interactive Chord Visualization for Metaproteomics. 2017 28th International Workshop on Database and Expert Systems Applications (Dexa), 2017. Bj5nr Times Cited:4 Cited References Count:11 International Workshop on Database and Expert Systems Applications-DEXA.
   
• A. Bensmann, R. Hanke-Rauschenbach, R. Heyer, F. Kohrs, D. Benndorf, R. Kausmann, M. Plochl, M. Heiermann, U. Reichl, and K. Sundmacher. Diagnostic concept for dynamically operated biogas production plants. Renewable Energy, Volume 96, pages 479–489, 2016. A Dq5ux Times Cited:12 Cited References Count:25.
   
• R. Heyer, D. Benndorf, F. Kohrs, J. De Vrieze, N. Boon, M. Hoffmann, E. Rapp, A. Schluter, A. Sczyrba, and U. Reichl. Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnol Biofuels, Volume 9, page 155, 2016. Heyer, R Benndorf, D Kohrs, F De Vrieze, J Boon, N Hoffmann, M Rapp, E Schluter, Andreas Sczyrba, Alexander Reichl, U eng England 2016/07/28 06:00 Biotechnol Biofuels. 2016 Jul 26;9:155. doi: 10.1186/s13068-016-0572-4. eCollection 2016.
   
• R. Heyer, F. Kohrs, U. Reichl, and D. Benndorf. Metaproteomics of complex microbial communities in biogas plants. Microb Biotechnol, 8(5):749–63, 2015. Heyer, Robert Kohrs, Fabian Reichl, Udo Benndorf, Dirk eng Research Support, Non-U.S. Gov't Review 2015/04/16 06:00 Microb Biotechnol. 2015 Sep;8(5):749-63. doi: 10.1111/1751-7915.12276. Epub 2015 Apr 15.
   
• F. Kohrs, S. Wolter, D. Benndorf, R. Heyer, M. Hoffmann, E. Rapp, A. Bremges, A. Sczyrba, A. Schluter, and U. Reichl. Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics, 15(20):3585–9, 2015. Kohrs, Fabian Wolter, Sophie Benndorf, Dirk Heyer, Robert Hoffmann, Marcus Rapp, Erdmann Bremges, Andreas Sczyrba, Alexander Schluter, Andreas Reichl, Udo eng Research Support, Non-U.S. Gov't Germany 2015/07/15 06:00 Proteomics. 2015 Oct;15(20):3585-9. do.
   
• T. Muth, A. Behne, R. Heyer, F. Kohrs, D. Benndorf, M. Hoffmann, M. Lehteva, U. Reichl, L. Martens, and E. Rapp. The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. J Proteome Res, 14(3):1557–65, 2015. Muth, Thilo Behne, Alexander Heyer, Robert Kohrs, Fabian Benndorf, Dirk Hoffmann, Marcus Lehteva, Miro Reichl, Udo Martens, Lennart Rapp, Erdmann eng Research Support, Non-U.S. Gov't 2015/02/11 06:00 J Proteome Res. 2015 Mar 6;14(3):1557-65. doi: 10.1021/.
   
• S. Puttker, F. Kohrs, D. Benndorf, R. Heyer, E. Rapp, and U. Reichl. Metaproteomics of activated sludge from a wastewater treatment plant - a pilot study. Proteomics, 15(20):3596–601, 2015. Puttker, Sebastian Kohrs, Fabian Benndorf, Dirk Heyer, Robert Rapp, Erdmann Reichl, Udo eng Research Support, Non-U.S. Gov't Germany 2015/07/24 06:00 Proteomics. 2015 Oct;15(20):3596-601. doi: 10.1002/pmic.201400559. Epub 2015 Aug 20.
   
• A. Bensmann, R. Hanke-Rauschenbach, R. Heyer, F. Kohrs, D. Benndorf, U. Reichl, and K. Sundmacher. Biological methanation of hydrogen within biogas plants: A model-based feasibility study. Applied Energy, Volume 134, pages 413–425, 2014. Ar1hp Times Cited:38 Cited References Count:24.
   
• F. Kohrs, R. Heyer, A. Magnussen, D. Benndorf, T. Muth, A. Behne, E. Rapp, R. Kausmann, M. Heiermann, M. Klocke, and U. Reichl. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe, Volume 29, pages 59–67, 2014. Kohrs, F Heyer, R Magnussen, A Benndorf, D Muth, T Behne, A Rapp, E Kausmann, R Heiermann, M Klocke, M Reichl, U eng Research Support, Non-U.S. Gov't England 2013/12/07 06:00 Anaerobe. 2014 Oct;29:59-67. doi: 10.1016/j.anaerobe.2013.11.009. Epub 2013 Dec.
   
• A. Hanreich, U. Schimpf, M. Zakrzewski, A. Schluter, D. Benndorf, R. Heyer, E. Rapp, A. Puhler, U. Reichl, and M. Klocke. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol, 36(5):330–8, 2013. Hanreich, Angelika Schimpf, Ulrike Zakrzewski, Martha Schluter, Andreas Benndorf, Dirk Heyer, Robert Rapp, Erdmann Puhler, Alfred Reichl, Udo Klocke, Michael eng Research Support, Non-U.S. Gov't Germany 2013/05/23 06:00 Syst Appl Microbiol. 2013 Jul;36(5).
   
• R. Heyer, F. Kohrs, D. Benndorf, E. Rapp, R. Kausmann, M. Heiermann, M. Klocke, and U. Reichl. Metaproteome analysis of the microbial communities in agricultural biogas plants. N Biotechnol, 30(6):614–22, 2013. Heyer, R Kohrs, F Benndorf, D Rapp, E Kausmann, R Heiermann, M Klocke, M Reichl, U eng Research Support, Non-U.S. Gov't Netherlands 2013/02/02 06:00 N Biotechnol. 2013 Sep 25;30(6):614-22. doi: 10.1016/j.nbt.2013.01.002. Epub 2013 Jan 29.
   
• A. Hanreich, R. Heyer, D. Benndorf, E. Rapp, M. Pioch, U. Reichl, and M. Klocke. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol, 58(7):917–22, 2012. Hanreich, Angelika Heyer, Robert Benndorf, Dirk Rapp, Erdmann Pioch, Markus Reichl, Udo Klocke, Michael eng Research Support, Non-U.S. Gov't Canada 2012/06/14 06:00 Can J Microbiol. 2012 Jul;58(7):917-22. doi: 10.1139/w2012-058. Epub 2012 Jun 12.
   

• Software and database development for analysis of complex microbial communities
• Metaproteome analysis
• Human gut microbiome