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List of IBVT related publications


  1. 2018

    1. Lange,J., Mueller,F., Takors,R. and Blombach,B. (2018) Harnessing Novel Chromosomal Integration Loci to Utilize an    Organosolv-Derived Hemicellulose Fraction Forisobutanol Production with    Engineered Corynebacterium Glutamicum. MICROBIAL BIOTECHNOLOGY, 11, 257–263.
    2. Lott,S.C., Schäfer,R.A., Mann,M., Backofen,R., Hess,W.R., Voß,B. and Georg,J. (2018) GLASSgo - Automated and Reliable Detection of sRNA Homologs from a Single Input Sequence. Frontiers in Genetics, 9.
    3. Failmezger,J., Scholz,S., Blombach,B. and Siemann-Herzberg,M. (2018) Cell-Free Protein Synthesis From Fast-Growing Vibrio Natriegens. Frontiers in Microbiology, 9.
  2. 2017

    1. Hellmers,F., Takors,R. and Thum,O. (2017) Robust Enzyme Immobilizates for Industrial Isomalt Production. accepted.
    2. Wolf,S., Barbosa,S., Bücher,J. and Takors,R. (2017) Automatic Network Generation Describes Differential Gene Data in User Friendly and Expeditiously Analyzable Network Views. 2, 1–14.
    3. Lange,J., Mueller,F., Bernecker,K., Dahmen,N., Takors,R. and Blombach,B. (2017) Valorization of Pyrolysis Water: A Biorefinery Side Stream, for    1,2-Propanediol Production with Engineered Corynebacterium Glutamicum. BIOTECHNOLOGY FOR BIOFUELS, 10.
    4. Niess,A., Loeffler,M., Simen,J.D. and Takors,R. (2017) Repetitive Short-Term Stimuli Imposed in Poor Mixing Zones Induce    Long-Term Adaptation of E-Coli Cultures in Large-Scale Bioreactors:    Experimental Evidence and Mathematical Model. FRONTIERS IN MICROBIOLOGY, 8.
    5. Hoffart,E., Grenz,S., Lange,J., Nitschel,R., Mueller,F., Schwentner,A., Feith,A., Lenfers-Luecker,M., Takors,R. and Blombach,B. (2017) High Substrate Uptake Rates Empower Vibrio Natriegens as Production Host    for Industrial Biotechnology. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 83.
    6. Michalowski,A., Siemann-Herzberg,M. and Takors,R. (2017) Escherichia Coli HGT: Engineered for High Glucose Throughput Even under    Slowly Growing or Resting Conditions. METABOLIC ENGINEERING, 40, 93–103.
    7. Delvigne,F., Takors,R., Mudde,R., van Gulik,W. and Noorman,H. (2017) Bioprocess Scale-Up/Down as Integrative Enabling Technology: From Fluid    Mechanics to Systems Biology and beyond. MICROBIAL BIOTECHNOLOGY, 10, 1267–1274.
    8. Simen,J.D., Loeffler,M., Jaeger,G., Schaeferhoff,K., Freund,A., Matthes,J., Mueller,J., Takors,R. and RecogNice-Team (2017) Transcriptional Response of Escherichia Coli to Ammonia and Glucose    Fluctuations. MICROBIAL BIOTECHNOLOGY, 10, 858–872.
    9. Failmezger,J., Ludwig,J., Niess,A. and Siemann-Herzberg,M. (2017) Quantifying Ribosome Dynamics in Escherichia Coli Using Fluorescence. FEMS MICROBIOLOGY LETTERS, 364.
    10. Kuschel,M., Siebler,F. and Takors,R. (2017) Lagrangian Trajectories to Predict the Formation of Population Heterogeneity in Large-Scale Bioreactors. Bioengineering, 4, 27.
    11. Loeffler,M., Simen,J.D., Mueller,J., Jaeger,G., Laghrami,S., Schaeferhoff,K., Freund,A., Takors,R. and RecogNice-Team (2017) Switching between Nitrogen and Glucose Limitation: Unraveling    Transcriptional Dynamics in Escherichia Coli. JOURNAL OF BIOTECHNOLOGY, 258, 2–12.
    12. Pfreundt,U., Spungin,D., Hou,S., Voß,B., Berman-Frank,I. and Hess,W.R. (2017) Genome of a Giant Bacteriophage from a Decaying Trichodesmium Bloom. Marine Genomics, 33, 21–25.
    13. Lange,J., Takors,R. and Blombach,B. (2017) Zero-Growth Bioprocesses: A Challenge for Microbial Production Strains    and Bioprocess Engineering. ENGINEERING IN LIFE SCIENCES, 17, 27–35.
    14. Teleki,A., Rahnert,M., Bungart,O., Gann,B., Ochrombel,I. and Takors,R. (2017) Robust Identification of Metabolic Control for Microbial L-Methionine    Production Following an Easy-to-Use Puristic Approach. METABOLIC ENGINEERING, 41, 159–172.
    15. Eigenstetter,G. and Takors,R. (2017) Dynamic Modeling Reveals a Three-Step Response of Saccharomyces    Cerevisiae to High CO2 Levels Accompanied by Increasing ATP Demands. FEMS YEAST RESEARCH, 17.
    16. Niess,A., Failmezger,J., Kuschel,M., Siemann-Herzberg,M. and Takors,R. (2017) Experimentally Validated Model Enables Debottlenecking of in Vitro    Protein Synthesis and Identifies a Control Shift under in Vivo    Conditions. ACS SYNTHETIC BIOLOGY, 6, 1913–1921.
    17. Failmezger,J., Rauter,M., Nitschel,R., Kraml,M. and Siemann-Herzberg,M. (2017) Cell-Free Protein Synthesis from Non-Growing, Stressed Escherichia Coli. SCIENTIFIC REPORTS, 7.
  3. 2016

    1. Sanchez-Kopper,A., Becker,M., Pfizenmaier,J., Kessler,C., Karau,A. and Takors,R. (2016) Tracking Dipeptides at Work-Uptake and Intracellular Fate in CHO Culture. AMB EXPRESS, 6.
    2. Schäfer,R.A. and Voß,B. (2016) VisualGraphX: Interactive Graph Visualization within Galaxy. Bioinformatics, 10.1093/bioinformatics/btw414.
    3. Pfizenmaier,J., Junghans,L., Teleki,A. and Takors,R. (2016) Hyperosmotic Stimulus Study Discloses Benefits in ATP Supply and Reveals    miRNA/mRNA Targets to Improve Recombinant Protein Production of CHO    Cells. BIOTECHNOLOGY JOURNAL, 11, 1037–1047.
    4. Wutz,J., Lapin,A., Siebler,F., Schaefer,J.E., Wucherpfennig,T., Berger,M. and Takors,R. (2016) Predictability of k(L)a in Stirred Tank Reactors under Multiple    Operating Conditions Using an Euler-Lagrange Approach. ENGINEERING IN LIFE SCIENCES, 16, 633–642.
    5. Failmezger,J., Nitschel,R., Sanchez-Kopper,A., Kraml,M. and Siemann-Herzberg,M. (2016) Site-Specific Cleavage of Ribosomal RNA in Escherichia Coli-Based    Cell-Free Protein Synthesis Systems. PLoS One, 11.
    6. Lieder,S., Jahn,M., Koepff,J., Mueller,S. and Takors,R. (2016) Environmental Stress Speeds up DNA Replication in Pseudomonas Putida in    Chemostat Cultivations. BIOTECHNOLOGY JOURNAL, 11, 155–163.
    7. Álvarez,D., Voß,B., Maass,D., Wüst,F., Schaub,P., Beyer,P. and Welsch,R. (2016) 5’UTR-Mediated Translational Control of Splice Variants of Phytoene Synthase. Plant Physiol.
    8. Stazic,D. and Voß,B. (2016) The Complexity of Bacterial Transcriptomes. Journal of Biotechnology, 232, 69--78.
    9. Takors,R. and de Lorenzo,V. (2016) Editorial Overview: Microbial Systems Biology: Systems Biology Prepares    the Ground for Successful Synthetic Biology. CURRENT OPINION IN MICROBIOLOGY, 33, VIII–X.
    10. Junghans,L., Teleki,A., Becker,M. and Takors,R. (2016) LC-MS-Based Compartment-Specific Metabolome Analysis in CHO. NEW BIOTECHNOLOGY, 33, S33–S34.
    11. Takors,R. (2016) Editorial: How Can We Ensure the Successful Transfer from Lab- to    Large-Scale Production? ENGINEERING IN LIFE SCIENCES, 16, 587.
    12. Loeffler,M., Simen,J.D., Jaeger,G., Schaeferhoff,K., Freund,A. and Takors,R. (2016) Engineering E-Coli for Large-Scale Production - Strategies Considering    ATP Expenses and Transcriptional Responses. METABOLIC ENGINEERING, 38, 73–85.
  4. 2015

    1. Pfizenmaier,J., Matuszczyk,J.-C. and Takors,R. (2015) Changes in Intracellular ATP-Content of CHO Cells as Response to    Hyperosmolality. BIOTECHNOLOGY PROGRESS, 31, 1212–1216.
    2. Teleki,A., Sanchez-Kopper,A. and Takors,R. (2015) Alkaline Conditions in Hydrophilic Interaction Liquid Chromatography for    Intracellular Metabolite Quantification Using Tandem Mass Spectrometry. ANALYTICAL BIOCHEMISTRY, 475, 4–13.
    3. Vallon,T., Simon,O., Rendgen-Heugle,B., Frana,S., Mueckschel,B., Broicher,A., Siemann-Herzberg,M., Pfannenstiel,J., Hauer,B., Huber,A., et al. (2015) Applying Systems Biology Tools to Study N-Butanol Degradation in    Pseudomonas Putida KT2440. ENGINEERING IN LIFE SCIENCES, 15, 760–771.
    4. Rimbon,J., Sanchez-Kopper,A., Wahl,A. and Takors,R. (2015) Monitoring Intracellular Protein Degradation in Antibody-Producing    Chinese Hamster Ovary Cells. ENGINEERING IN LIFE SCIENCES, 15, 499–508.
    5. Matuszczyk,J.-C., Teleki,A., Pfizenmaier,J. and Takors,R. (2015) Compartment-Specific Metabolomics for CHO Reveals That ATP Pools in    Mitochondria Are Much Lower than in Cytosol. BIOTECHNOLOGY JOURNAL, 10, 1639–1650.
    6. Henkel,M., Zwick,M., Beuker,J., Willenbacher,J., Baumann,S., Oswald,F., Neumann,A., Siemann-Herzberg,M., Syldatk,C. and Hausmann,R. (2015) Teaching Bioprocess Engineering to Undergraduates: Multidisciplinary    Hands-on Training in a One-Week Practical Course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 43, 189–202.
    7. Kopf,M., Klähn,S., Scholz,I., Hess,W.R. and Voß,B. (2015) Variations in the Non-Coding Transcriptome as a Driver of Inter-Strain Divergence and Physiological Adaptation in Bacteria. Scientific Reports, 5.
    8. Lieder,S., Nikel,P.I., de Lorenzo,V. and Takors,R. (2015) Genome Reduction Boosts Heterologous Gene Expression in Pseudomonas    Putida. MICROBIAL CELL FACTORIES, 14.
    9. Lott,S.C., Voß,B., Hess,W.R. and Steglich,C. (2015) CoVennTree: A New Method for the Comparative Analysis of Large Datasets. Bioinformatics and Computational Biology, 6, 43.
  5. 2014

    1. Giegerich,R. and Voß,B. (2014) RNA Secondary Structure Analysis Using Abstract Shapes. In Handbook of RNA Biochemistry, Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 579--594.
    2. Kopf,M., Klähn,S., Pade,N., Weingärtner,C., Hagemann,M., Voß,B. and Hess,W.R. (2014) Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803. DNA Research, 21, 255--266.
    3. Kopf,M., Klähn,S., Voß,B., Stüber,K., Huettel,B., Reinhardt,R. and Hess,W.R. (2014) Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis Sp. Strain PCC 6714. Genome Announcements, 2, e00757--14.
    4. Buchholz,J., Graf,M., Blombach,B. and Takors,R. (2014) Improving the Carbon Balance of Fermentations by Total Carbon Analyses. BIOCHEMICAL ENGINEERING JOURNAL, 90, 162–169.
    5. Schuhmacher,T., Loeffler,M., Hurler,T. and Takors,R. (2014) Phosphate Limited Fed-Batch Processes: Impact on Carbon Usage and Energy    Metabolism in Escherichia Coli. JOURNAL OF BIOTECHNOLOGY, 190, 96–104.
    6. Voigt,K., Sharma,C.M., Mitschke,J., Joke Lambrecht,S., Voß,B., Hess,W.R. and Steglich,C. (2014) Comparative Transcriptomics of Two Environmentally Relevant Cyanobacteria Reveals Unexpected Transcriptome Diversity. The ISME Journal, 10.1038/ismej.2014.57.
    7. Lieder,S., Jahn,M., Seifert,J., von Bergen,M., Mueller,S. and Takors,R. (2014) Subpopulation-Proteomics Reveal Growth Rate, but Not Cell Cycling, as a    Major Impact on Protein Composition in Pseudomonas Putida KT2440. AMB EXPRESS, 4.
    8. Buchholz,J., Graf,M., Freund,A., Busche,T., Kalinowski,J., Blombach,B. and Takors,R. (2014) CO2/HCO3 (-) Perturbations of Simulated Large Scale Gradients in a    Scale-down Device Cause Fast Transcriptional Responses in    Corynebacterium Glutamicum (Vol 98, Pg 8563, 2014). APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 98, 8775.
    9. Sudarsan,S., Dethlefsen,S., Blank,L.M., Siemann-Herzberg,M. and Schmid,A. (2014) The Functional Structure of Central Carbon Metabolism in Pseudomonas    Putida KT2440. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80, 5292–5303.
    10. Buchholz,J., Graf,M., Freund,A., Busche,T., Kalinowski,J., Blombach,B. and Takors,R. (2014) CO2/HCO3 (-) Perturbations of Simulated Large Scale Gradients in a    Scale-down Device Cause Fast Transcriptional Responses in    Corynebacterium Glutamicum. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 98, 8563–8572.
    11. Gelves,R., Dietrich,A. and Takors,R. (2014) Modeling of Gas-Liquid Mass Transfer in a Stirred Tank Bioreactor    Agitated by a Rushton Turbine or a New Pitched Blade Impeller. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 37, 365–375.
    12. Rogato,A., Richard,H., Sarazin,A., Voß,B., Navarro,S.C., Champeimont,R., Navarro,L., Carbone,A., Hess,W.R. and Falciatore,A. (2014) The Diversity of Small Non-Coding RNAs in the Diatom Phaeodactylum Tricornutum. BMC Genomics, 15, 698.
    13. Bischler,T., Kopf,M. and Voß,B. (2014) Transcript Mapping Based on dRNA-Seq Data. BMC Bioinformatics, 15, 122.
    14. Huang,J. and Voß,B. (2014) Analysing RNA-Kinetics Based on Folding Space Abstraction. BMC Bioinformatics, 15, 60.
    15. Kopf,M., Klähn,S., Scholz,I., Matthiessen,J.K.F., Hess,W.R. and Voß,B. (2014) Comparative Analysis of the Primary Transcriptome of Synechocystis Sp. PCC 6803. DNA Research, 21, 527--539.
    16. Lindner,R., Moosmann,A., Dietrich,A., Boettinger,H., Kontermann,R. and Siemann-Herzberg,M. (2014) Process Development of Periplasmatically Produced Single Chain Fragment    Variable against Epidermal Growth Factor Receptor in Escherichia Coli. JOURNAL OF BIOTECHNOLOGY, 192, 136–145.
    17. Voß,B. and Hess,W.R. (2014) The Identification of Bacterial Non-Coding RNAs through Complementary Approaches. In Handbook of RNA Biochemistry, Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787--800.
  6. 2013

    1. Buchholz,J., Schwentner,A., Brunnenkan,B., Gabris,C., Grimm,S., Gerstmeir,R., Takors,R., Eikmanns,B.J. and Blombach,B. (2013) Platform Engineering of Corynebacterium Glutamicum with Reduced Pyruvate    Dehydrogenase Complex Activity for Improved Production of L-Lysine,    L-Valine, and 2-Ketoisovalerate. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79, 5566–5575.
    2. Blombach,B., Buchholz,J., Busche,T., Kalinowski,J. and Takors,R. (2013) Impact of Different CO2/HCO3- Levels on Metabolism and Regulation in    Corynebacterium Glutamicum. JOURNAL OF BIOTECHNOLOGY, 168, 331–340.
    3. Vallon,T., Glemser,M., Malca,S.H., Scheps,D., Schmid,J., Siemann-Herzberg,M., Hauer,B. and Takors,R. (2013) Production of 1-Octanol from N-Octane by Pseudomonas Putida KT2440. CHEMIE INGENIEUR TECHNIK, 85, 841–848.
    4. Voß,B., Bolhuis,H., Fewer,D.P., Kopf,M., Möke,F., Haas,F., El-Shehawy,R., Hayes,P., Bergman,B., Sivonen,K., et al. (2013) Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia Spumigena CCY9414 Based on a Genome-Transcriptome Analysis. PLoS ONE, 8, e60224.
    5. Soellner,S., Rahnert,M., Siemann-Herzberg,M., Takors,R. and Altenbuchner,J. (2013) Evolution of Pyruvate Kinase-Deficient Escherichia Coli Mutants Enables    Glycerol-Based Cell Growth and Succinate Production. JOURNAL OF APPLIED MICROBIOLOGY, 115, 1368–1378.
    6. Hein,S., Scholz,I., Voß,B. and Hess,W.R. (2013) Adaptation and Modification of Three CRISPR Loci in Two Closely Related Cyanobacteria. RNA Biology, 10, 93--92.
  7. 2012

    1. Madhugiri,R., Pessi,G., Voß,B., Hahn,J., Sharma,C.M., Reinhardt,R., Vogel,J., Hess,W.R., Fischer,H.-M. and Evguenieva-Hackenberg,E. (2012) Small RNAs of the Bradyrhizobium/Rhodopseudomonas Lineage and Their Analysis. RNA Biology, 9, 45--56.
    2. Huang,J., Backofen,R. and Voß,B. (2012) Abstract Folding Space Analysis Based on Helices. RNA, 18, 2135--2147.
    3. Gierga,G., Voß,B. and Hess,W.R. (2012) Non-Coding RNAs in Marine Synechococcus and Their Regulation under Environmentally Relevant Stress Conditions. The ISME Journal, 6, 1544--1557.
    4. Trautmann,D., Voß,B., Wilde,A., Al-Babili,S. and Hess,W.R. (2012) Microevolution in Cyanobacteria: Re-Sequencing a Motile Substrain of Synechocystis Sp. PCC 6803. DNA Research, 10.1093/dnares/dss024.
    5. Pfreundt,U., Stal,L.J., Voß,B. and Hess,W.R. (2012) Dinitrogen Fixation in a Unicellular Chlorophyll D-Containing Cyanobacterium. ISME J.
    6. Takors,R. (2012) Scale-up of Microbial Processes: Impacts, Tools and Open Questions. JOURNAL OF BIOTECHNOLOGY, 160, 3–9.
  8. 2011

    1. Babski,J., Tjaden,B., Voß,B., Jellen-Ritter,A., Marchfelder,A., Hess,W.R. and Soppa,J. (2011) Bioinformatic Prediction and Experimental Verification of sRNAs in the Haloarchaeon Haloferax Volcanii. RNA Biology, 8, 806--816.
    2. Mitschke,J., Georg,J., Scholz,I., Sharma,C.M., Dienst,D., Bantscheff,J., Voß,B., Steglich,C., Wilde,A., Vogel,J., et al. (2011) An Experimentally Anchored Map of Transcriptional Start Sites in the Model Cyanobacterium Synechocystis Sp. PCC6803. Proceedings of the National Academy of Sciences, 108, 2124--2129.
    3. Wenzel,M., Mueller,A., Siemann-Herzberg,M. and Altenbuchner,J. (2011) Self-Inducible Bacillus Subtilis Expression System for Reliable and    Inexpensive Protein Production by High-Cell-Density Fermentation. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 77, 6419–6425.
    4. Bongaerts,J., Esser,S., Lorbach,V., Al-Momani,L., Mueller,M.A., Franke,D., Grondal,C., Kurutsch,A., Bujnicki,R., Takors,R., et al. (2011) Diversity-Oriented Production of Metabolites Derived from Chorismate and    Their Use in Organic Synthesis. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50, 7781–7786.
    5. Vielhauer,O., Zakhartsev,M., Horn,T., Takors,R. and Reuss,M. (2011) Simplified Absolute Metabolite Quantification by Gas    Chromatography-Isotope Dilution Mass Spectrometry on the Basis of    Commercially Available Source Material. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL  AND LIFE SCIENCES, 879, 3859–3870.
    6. Huang,J. and Voß,B. (2011) RNAHeliCes – Folding Space Analysis Based on Position Aware Structure Abstraction. In Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011), Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011).p. RT--31.
  9. 2010

    1. Hardiman,T., Meinhold,H., Hofmann,J., Ewald,J.C., Siemann-Herzberg,M. and Reuss,M. (2010) Prediction of Kinetic Parameters from DNA-Binding Site Sequences for    Modeling Global Transcription Dynamics in Escherichia Coli. METABOLIC ENGINEERING, 12, 196–211.
    2. Canelas,A.B., Harrison,N., Fazio,A., Zhang,J., Pitkanen,J.-P., van den Brink,J., Bakker,B.M., Bogner,L., Bouwman,J., Castrillo,J.I., et al. (2010) Integrated Multilaboratory Systems Biology Reveals Differences in    Protein Metabolism between Two Reference Yeast Strains. NATURE COMMUNICATIONS, 1.
    3. Georg,J., Honsel,A., Voß,B., Rennenberg,H. and Hess,W.R. (2010) A Long Antisense RNA in Plant Chloroplasts. New Phytologist, 186, 615--622.
    4. Mohr,R., Voß,B., Schliep,M., Kurz,T., Maldener,I., Adams,D.G., Larkum,A.D.W., Chen,M. and Hess,W.R. (2010) A New Chlorophyll D-Containing Cyanobacterium: Evidence for Niche Adaptation in the Genus Acaryochloris. ISME J, 4, 1456--1469.
    5. Schuhmacher,T., Lemuth,K., Hardiman,T., Vacun,G., Reuss,M. and Siemann-Herzberg,M. (2010) Quantifying Cytosolic Messenger RNA Concentrations in Escherichia Coli    Using Real-Time Polymerase Chain Reaction for a Systems Biology Approach. ANALYTICAL BIOCHEMISTRY, 398, 212–217.
    6. Voß,B., Meinecke,L., Kurz,T., Al-Babili,S., Beck,C.F. and Hess,W.R. (2010) Hemin and Mg-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas Reinhardtii. Plant Physiol., 10.1104/pp.110.158683.
    7. Bogomolov,S., Mann,M., Voß,B., Podelski,A. and Backofen,R. (2010) Shape-Based Barrier Estimation for RNAs. In In Proceedings of German Conference on Bioinformatics GCB’10, In Proceedings of German Conference on Bioinformatics GCB’10. GI, Vol. 173, pp. 42--51.
    8. Ionescu,D., Voß,B., Oren,A., Hess,W.R. and Muro-Pastor,A.M. (2010) Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria. Journal of Molecular Biology, 398, 177--188.
  10. 2009

    1. Magnus,J.B., Oldiges,M. and Takors,R. (2009) The Identification of Enzyme Targets for the Optimization of a Valine    Producing Corynebacterium Glutamicum Strain Using a Kinetic Model. BIOTECHNOLOGY PROGRESS, 25, 754–762.
    2. Voß,B., Hölscher,M., Baumgarth,B., Kalbfleisch,A., Kaya,C., Hess,W.R., Becker,A. and Elena Evguenieva-Hackenberg (2009) Expression of Small RNAs in Rhizobiales and Protection of a Small RNA and Its Degradation Products by Hfq in Sinorhizobium Meliloti. Biochemical and Biophysical Research Communications, 390, 331--336.
    3. Georg,J., Voß,B., Scholz,I., Mitschke,J., Wilde,A. and Hess,W.R. (2009) Evidence for a Major Role of Antisense RNAs in Cyanobacterial Gene Regulation. Mol Syst Biol, 5.
    4. Voß,B., Georg,J., Schon,V., Ude,S. and Hess,W. (2009) Biocomputational Prediction of Non-Coding RNAs in Model Cyanobacteria. BMC Genomics, 10, 123.
    5. Gierga,G., Voß,B. and Hess,W.R. (2009) The Yfr2 ncRNA Family, a Group of Abundant RNA Molecules Widely Conserved in Cyanobacteria. RNA Biology, 6, 222--227.
    6. Soppa,J., Straub,J., Brenneis,M., Jellen-Ritter,A., Heyer,R., Fischer,S., Granzow,M., Voß,B., Hess,W.R., Tjaden,B., et al. (2009) Small RNAs of the Halophilic Archaeon Haloferax Volcanii. Biochemical Society Transactions, 37, 133--136.
  11. 2008

    1. Hardiman,T., Windeisen,V., Ewald,J.C., Zibek,S., Schlack,P., Rebell,J., Reuss,M. and Siemann-Herzberg,M. (2008) In Vitro Synthesis and Characterization of Guanosine 3 `,5    `-Bis(diphosphate). ANALYTICAL BIOCHEMISTRY, 383, 337–339.
    2. Lemuth,K., Hardiman,T., Winter,S., Pfeiffer,D., Keller,M.A., Lange,S., Reuss,M., Schmid,R.D. and Siemann-Herzberg,M. (2008) Global Transcription and Metabolic Flux Analysis of Escherichia Coli in    Glucose-Limited Fed-Batch Cultivations. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 74, 7002–7015.
    3. Steglich,C., Futschik,M.E., Lindell,D., Voß,B., Chisholm,S.W. and Hess,W.R. (2008) The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus. PLoS Genet, 4, e1000173.
  12. 2007

    1. van der Werf,M.J., Takors,R., Smedsgaard,J., Nielsen,J., Ferenci,T., Portais,J.C., Wittmann,C., Hooks,M., Tomassini,A., Oldiges,M., et al. (2007) Standard Reporting Requirements for Biological Samples in Metabolomics    Experiments: Microbial and in Vitro Biology Experiments. METABOLOMICS, 3, 189–194.
    2. Hardiman,T., Lemuth,K., Keller,M.A., Reuss,M. and Siemann-Herzberg,M. (2007) Topology of the Global Regulatory Network of Carbon Limitation in    Escherichia Coli. JOURNAL OF BIOTECHNOLOGY, 132, 359–374.
    3. Luo,B., Groenke,K., Takors,R., Wandrey,C. and Oldiges,M. (2007) Simultaneous Determination of Multiple Intracellular Metabolites in    Glycolysis, Pentose Phosphate Pathway and Tricarboxylic Acid Cycle by    Liquid Chromatography-Mass Spectrometry. JOURNAL OF CHROMATOGRAPHY A, 1147, 153–164.
    4. Noeh,K., Groenke,K., Luo,B., Takors,R., Oldiges,M. and Wiechert,W. (2007) Metabolic Flux Analysis at Ultra Short Time Scale: Isotopically    Non-Stationary C-13 Labeling Experiments. JOURNAL OF BIOTECHNOLOGY, 129, 249–267.
    5. Chen,X.H., Koumoutsi,A., Scholz,R., Eisenreich,A., Schneider,K., Heinemeyer,I., Morgenstern,B., Voß,B., Hess,W.R., Reva,O., et al. (2007) Comparative Analysis of the Complete Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus Amyloliquefaciens FZB42. Nat Biotech, 25, 1007--1014.
    6. Takors,R., Bathe,B., Rieping,M., Hans,S., Kelle,R. and Huthmacher,K. (2007) Systems Biology for Industrial Strains and Fermentation Processes -    Example: Amino Acids. JOURNAL OF BIOTECHNOLOGY, 129, 181–190.
    7. Axmann,I.M., Holtzendorff,J., Voß,B., Kensche,P. and Hess,W.R. (2007) Two Distinct Types of 6S RNA in Prochlorococcus. Gene, 406, 69--78.
    8. Fattash,I., Voß,B., Reski,R., Hess,W. and Frank,W. (2007) Evidence for the Rapid Expansion of microRNA-Mediated Regulation in Early Land Plant Evolution. BMC Plant Biology, 7, 13.
    9. Voß,B., Gierga,G., Axmann,I. and Hess,W. (2007) A Motif-Based Search in Bacterial Genomes Identifies the Ortholog of the Small RNA Yfr1 in All Lineages of Cyanobacteria. BMC Genomics, 8, 375.
  13. 2006

    1. Voß,B., Giegerich,R. and Rehmsmeier,M. (2006) Complete Probabilistic Analysis of RNA Shapes. BMC Biology, 4, 5.
    2. Reeder,J., Höchsmann,M., Rehmsmeier,M., Voß,B. and Giegerich,R. (2006) Beyond Mfold: Recent Advances in RNA Bioinformatics. Journal of Biotechnology, 124, 41--55.
    3. Backofen,R., Borrmann,H.-G., Deck,W., Dedner,A., Raedt,L.D., Desch,K., Diesmann,M., Geier,M., Greiner,A., Hess,W.R., et al. (2006) A Bottom-up Approach to Grid-Computing at a University: The Black-Forest-Grid Initiative. Praxis der Informationsverarbeitung und Kommunikation, 29, 81--87.
    4. Franzreb,M., Siemann-Herzberg,M., Hobley,T. and Thomas,O. (2006) Protein Purification Using Magnetic Adsorbent Particles. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 70, 505–516.
    5. Magnus,J.B., Hollwedel,D., Oldiges,M. and Takors,R. (2006) Monitoring and Modeling of the Reaction Dynamics in the Valine/Leucine    Synthesis Pathway in Corynebacterium Glutamicum. BIOTECHNOLOGY PROGRESS, 22, 1071–1083.
    6. Voß,B. (2006) Structural Analysis of Aligned RNAs. Nucl. Acids Res., 34, 5471--5481.
    7. Wahl,S., Takors,R. and Wiechert,W. (2006) Interpretation of Metabolic Flux Maps by Limitation Potentials and    Constrained Limitation Sensitivities. BIOTECHNOLOGY AND BIOENGINEERING, 94, 263–272.
    8. Talmor-Neiman,M., Stav,R., Frank,W., Voß,B. and Arazi,T. (2006) Novel Micro-RNAs and Intermediates of Micro-RNA Biogenesis from Moss. The Plant Journal, 47, 25--37.
    9. Steffen,P., Voß,B., Rehmsmeier,M., Reeder,J. and Giegerich,R. (2006) RNAshapes: An Integrated RNA Analysis Package Based on Abstract Shapes. Bioinformatics, 22, 500--503.
  14. 2005

    1. Franke,G., Stoepel,N., Reidegeld,K., Siemann-Herzberg,M., Reuss,M., Meyer,H. and Warscheid,B. (2005) Quantitative Profiling of the Phosphotransferase System in Escherichia    Coli. MOLECULAR & CELLULAR PROTEOMICS, 4, S319.
    2. Voß,B. (2005) Advanced Tools for RNA Secondary Structure Analysis.
    3. Franzreb,M., Ebner,N., Siemann,M., Altenbuchner,J., Fritz,C., Mayer,Z., Schultz,N. and Syldakt,C. (2005) Direct Bioproduct Isolation from Crude Feedstocks Using Magnetic Micro    Adsorbents. JOURNAL OF BIOTECHNOLOGY, 118, S53.
    4. Haunschild,M., Freisleben,B., Takors,R. and Wiechert,W. (2005) Investigating the Dynamic Behavior of Biochemical Networks Using Model    Families. BIOINFORMATICS, 21, 1617–1625.
    5. Oldiges,M. and Takors,R. (2005) Applying Metabolic Profiling Techniques for Stimulus-Response    Experiments: Chances and Pitfalls. In TECHNOLOGY TRANSFER IN BIOTECHNOLOGY: FROM LAB TO INDUSTRY TO PRODUCTION, TECHNOLOGY TRANSFER IN BIOTECHNOLOGY: FROM LAB TO INDUSTRY TO PRODUCTION. SPRINGER-VERLAG BERLIN, HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY, Vol. 92, pp. 173–196.
    6. Ternbach,M., Bollman,C., Wandrey,C. and Takors,R. (2005) Application of Model Discriminating Experimental Design for Modeling and    Development of a Fermentative Fed-Batch L-Valine Production Process. BIOTECHNOLOGY AND BIOENGINEERING, 91, 356–368.
    7. Arnold,S., Siemann-Herzberg,M., Schmid,J. and Reuss,M. (2005) Model-Based Inference of Gene Expression Dynamics from Sequence    Information. In Nielsen, J (ed), BIOTECHNOLOGY FOR THE FUTURE, BIOTECHNOLOGY FOR THE FUTURE. SPRINGER-VERLAG BERLIN, HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY, Vol. 100, pp. 89–179.
  15. 2004

    1. Wahl,A., El Massaoudi,M., Schipper,D., Wiechert,W. and Takors,R. (2004) Serial C-13-Based Flux Analysis of an L-Phenylalanine-Producing E-Coli    Strain Using the Sensor Reactor. BIOTECHNOLOGY PROGRESS, 20, 706–714.
    2. Werner,M., Vazques,F., Fritz,C., Vielhauer,O., Siemann-Herzberg,M., Altenbuchner,J. and Syldatk,C. (2004) Cloning of D-Specific Hydantoin Utilization Genes from Arthrobacter    Crystallopoietes. ENGINEERING IN LIFE SCIENCES, 4, 563–572.
    3. Ruffer,N., Heidersdorf,U., Kretzers,I., Sprenger,G., Raeven,L. and Takors,R. (2004) Fully Integrated L-Phenylalanine Separation and Concentration Using    Reactive-Extraction with Liquid-Liquid Centrifuges in a Fed-Batch    Process with E-Coli. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 26, 239–248.
    4. Oldiges,M., Kunze,M., Degenring,D., Sprenger,G. and Takors,R. (2004) Stimulation, Monitoring, and Analysis of Pathway Dynamics by Metabolic    Profiling in the Aromatic Amino Acid Pathway. BIOTECHNOLOGY PROGRESS, 20, 1623–1633.
    5. Zelic,B., Vasic-Racki,D., Wandrey,C. and Takors,R. (2004) Modeling of the Pyruvate Production with Escherichia Coli in a Fed-Batch    Bioreactor. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 26, 249–258.
    6. Zelic,B., Gostovic,S., Vuorilehto,K., Vasic-Racki,B. and Takors,R. (2004) Process Strategies to Enhance Pyruvate Production with Recombinant    Escherichia Coli: From Repetitive Fed-Batch to in Situ Product Recovery    with Fully Integrated Electrodialysis. BIOTECHNOLOGY AND BIOENGINEERING, 85, 638–646.
    7. Voß,B., Meyer,C. and Giegerich,R. (2004) Evaluating the Predictability of Conformational Switching in RNA. Bioinformatics, 20, 1573--1582.
    8. Drysch,A., El Massaoudi,M., Wiechert,W., de Graaf,A. and Takors,R. (2004) Serial Flux Mapping of Corynebacterium Glutamicum during Fed-Batch    L-Lysine Production Using the Sensor Reactor Approach. BIOTECHNOLOGY AND BIOENGINEERING, 85, 497–505.
    9. Takors,R. (2004) Whole Cell ISPR Process Development: Chances and Pitfalls. CHEMIE INGENIEUR TECHNIK, 76, 1807–1814.
    10. Potter,J. and Siemann,M. (2004) A New Method for Determining Delta C-13 and Delta D Simultaneously for    CH4 by Gas Chromatography Continuous-Flow Isotope-Ratio Mass    Spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 18, 175–180.
    11. Giegerich,R., Voß,B. and Rehmsmeier,M. (2004) Abstract Shapes of RNA. Nucl. Acids Res., 32, 4843--4851.
    12. Takors,R. (2004) Model-Based Analysis and Optimization of an ISPR Approach Using Reactive    Extraction for Pilot-Scale L-Phenylalanine Production. BIOTECHNOLOGY PROGRESS, 20, 57–64.
    13. Höchsmann,M., Voß,B. and Giegerich,R. (2004) Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 53--62.
    14. Takors,R. (2004) Complete Cell ISPR Process Development: Chances and Risks. CHEMIE INGENIEUR TECHNIK, 76, 1857–1864.
    15. Degenring,D., Froemel,C., Dikta,G. and Takors,R. (2004) Sensitivity Analysis for the Reduction of Complex Metabolism Models. JOURNAL OF PROCESS CONTROL, 14, 729–745.
  16. 2003

    1. Oelschlaeger,P., Lange,S., Schmitt,J., Siemann,M., Reuss,M. and Schmid,R. (2003) Identification of Factors Impeding the Production of a Single-Chain    Antibody Fragment in Escherichia Coli by Comparing in Vivo and in Vitro    Expression. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 61, 123–132.
    2. Drysch,A., El Massaoudi,M., Mack,C., Takors,R., de Graaf,A. and Sahm,H. (2003) Production Process Monitoring by Serial Mapping of Microbial Carbon Flux    Distributions Using a Novel Sensor Reactor Approach: II -    C-13-Labeling-Based Metabolic Flux Analysis and L-Lysine Production. METABOLIC ENGINEERING, 5, 96–107.
    3. Zelic,B., Gerharz,T., Bott,M., Vasic-Racki,D., Wandrey,C. and Takors,R. (2003) Fed-Batch Process for Pyruvate Production by Recombinant Escherichia    Coli YYC202 Strain. ENGINEERING IN LIFE SCIENCES, 3, 299–305.
    4. El Massaoudi,M., Spelthahn,J., Drysch,A., de Graaf,A. and Takors,R. (2003) Production Process Monitoring by Serial Mapping of Microbial Carbon Flux    Distributions Using a Novel Sensor Reactor Approach: I - Sensor Reactor    System. METABOLIC ENGINEERING, 5, 86–95.
    5. Franke,D., Lorbach,V., Esser,S., Dose,C., Sprenger,G., Halfar,M., Thommes,J., Muller,R., Takors,R. and Muller,M. (2003) (S,S)-2,3-Dihydroxy-2,3-Dihydrobenzoic Acid: Microbial Access with    Engineered Cells of Escherichia Coli and Application as Starting    Material in Natural-Product Synthesis. CHEMISTRY-A EUROPEAN JOURNAL, 9, 4188–4196.
  17. 2002

    1. Gerigk,M., Maass,D., Kreutzer,A., Sprenger,G., Bongaerts,J., Wubbolts,M. and Takors,R. (2002) Enhanced Pilot-Scale Fed-Batch L-Phenylalanine Production with    Recombinant Escherichia Coli by Fully Integrated Reactive Extraction. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 25, 43–52.
    2. Schmitz,M., Hirsch,E., Bongaerts,J. and Takors,R. (2002) Pulse Experiments as a Prerequisite for the Quantification of in Vivo    Enzyme Kinetics in Aromatic Amino Acid Pathway of Escherichia Coli. BIOTECHNOLOGY PROGRESS, 18, 935–941.
    3. Abendroth,J., Niefind,K., May,O., Siemann,M., Syldatk,C. and Schomburg,D. (2002) The Structure of L-Hydantoinase from Arthobacter Aurescens Leads to an    Understanding of Dihydropyrimidinase Substrate and Enantio Specificity. BIOCHEMISTRY, 41, 8589–8597.
    4. Gerigk,M., Bujnicki,R., Ganpo-Nkwenkwa,E., Bongaerts,J., Sprenger,G. and Takors,R. (2002) Process Control for Enhanced L-Phenylalanine Production Using Different    Recombinant Escherichia Coli Strains. BIOTECHNOLOGY AND BIOENGINEERING, 80, 746–754.
    5. Maass,D., Gerigk,M., Kreutzer,A., Weuster-Botz,D., Wubbolts,M. and Takors,R. (2002) Integrated L-Phenylalanine Separation in an E-Coli Fed-Batch Process:    From Laboratory to Pilot Scale. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 25, 85–96.
  18. 2001

    1. Altenbuchner,J., Siemann-Herzberg,M. and Syldatk,C. (2001) Hydantoinases and Related Enzymes as Biocatalysts for the Synthesis of    Unnatural Chiral Amino Acids. CURRENT OPINION IN BIOTECHNOLOGY, 12, 559–563.
    2. Arnold,S., Siemann,M., Scharnweber,K., Werner,M., Baumann,S. and Reuss,M. (2001) Kinetic Modeling and Simulation of in Vitro Transcription by Phage T7    RNA Polymerase. BIOTECHNOLOGY AND BIOENGINEERING, 72, 548–561.
    3. Buchholz,A., Takors,R. and Wandrey,C. (2001) Quantification of Intracellular Metabolites in Escherichia Coli K12    Using Liquid Chromatographic-Electrospray Ionization Tandem Mass    Spectrometric Techniques. ANALYTICAL BIOCHEMISTRY, 295, 129–137.
    4. Curvers,S., Linneman,J., Klauser,T., Wandrey,C. and Takors,R. (2001) Recombinant Protein Production with Pichia Pastoris in Continuous    Fermentation - Kinetic Analysis of Growth and Product Formation. CHEMIE INGENIEUR TECHNIK, 73, 1615–1621.
    5. Wilms,B., Hauck,A., Reuss,M., Syldatk,C., Mattes,R., Siemann,M. and Altenbuchner,J. (2001) High-Cell-Density Fermentation for Production of L-N-Carbamoylase Using    an Expression System Based on the Escherichia Coli rhaBAD Promoter. BIOTECHNOLOGY AND BIOENGINEERING, 73, 95–103.
    6. Takors,R., Gerigk,M., Paschold,H. and Wandrey,C. (2001) Principal-Component Analysis for Microbial L-Phenylalanine Production. BIOPROCESS AND BIOSYSTEMS ENGINEERING, 24, 93–99.
  19. 2000

    1. Schindler,P., Baumann,S., Reuss,M. and Siemann,M. (2000) In Vitro Coupled Transcription Translation: Effects of Modification in    Lysate Preparation on Protein Composition and Biosynthesis Activity. ELECTROPHORESIS, 21, 2606–2609.
    2. Schmitz,G., Franke,D., Stevens,S., Takors,R., Weuster-Botz,D. and Wandrey,C. (2000) Regioselective Oxidation of Terfenadine with Cunninghamella Blakesleeana. JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 10, 313–324.
  20. 1999

    1. Schindler,P., Macherhammer,F., Arnold,S., Reuss,M. and Siemann,M. (1999) Investigation of Translation Dynamics under Cell-Free Protein    Biosynthesis Conditions Using High-Resolution Two-Dimensional Gel    Electrophoresis. ELECTROPHORESIS, 20, 806–812.
    2. Schaefer,U., Boos,W., Takors,R. and Weuster-Botz,D. (1999) Automated Sampling Device for Monitoring Intracellular Metabolite    Dynamics. ANALYTICAL BIOCHEMISTRY, 270, 88–96.
    3. Siemann,M., Alvarado-Marin,A., Pietzsch,M. and Syldatk,C. (1999) A D-Specific Hydantoin Amidohydrolase: Properties of the Metalloenzyme    Purified from Arthrobacter Crystallopoietes. JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 6, 387–397.
    4. Syldatk,C., May,O., Altenbuchner,J., Mattes,R. and Siemann,M. (1999) Microbial Hydantoinases - Industrial Enzymes from the Origin of Life? APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 51, 293–309.
  21. 1998

    1. May,O., Siemann,M., Siemann,M. and Syldatk,C. (1998) The Hydantoin Amidohydrolase from Arthrobacter Aurescens DSM 3745 Is a    Zinc Metalloenzyme. JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 5, 367–370.
    2. May,O., Siemann,M. and Syldatk,C. (1998) A New Method for the Detection of Hydantoinases with Respect to Their    Enantioselectivity on Acrylamide Gels Based on Enzyme Activity Stain. BIOTECHNOLOGY TECHNIQUES, 12, 309–312.
    3. May,O., Habenicht,A., Mattes,R., Syldatk,C. and Siemann,M. (1998) Molecular Evolution of Hydantoinases. BIOLOGICAL CHEMISTRY, 379, 743–747.
    4. May,O., Siemann,M., Pietzsch,M., Kiess,M., Mattes,R. and Syldatk,C. (1998) Substrate-Dependent Enantioselectivity of a Novel Hydantoinase from    Arthrobacter Aurescens DSM 3745: Purification and Characterization as    New Member of Cyclic Amidases. JOURNAL OF BIOTECHNOLOGY, 61, 1–13.
    5. May,O., Siemann,M., Siemann,M. and Syldatk,C. (1998) Catalytic and Structural Function of Zinc for the Hydantoinase from    Arthrobacter Aurescens DSM 3745. JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 4, 211–218.
  22. 1997

    1. Takors,R., Wiechert,W. and WeusterBotz,D. (1997) Experimental Design for the Identification of Macrokinetic Models and    Model Discrimination. BIOTECHNOLOGY AND BIOENGINEERING, 56, 564–576.
    2. Siemann,M., Andersson,L. and Mosbach,K. (1997) Separation and Detection of Macrolide Antibiotics by HPLC Using    Macrolide-Imprinted Synthetic Polymers as Stationary Phases. JOURNAL OF ANTIBIOTICS, 50, 89–91.
  23. 1996

    1. Siemann,M., Andersson,L. and Mosbach,K. (1996) Selective Recognition of the Herbicide Atrazine by Noncovalent    Molecularly Imprinted Polymers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 44, 141–145.
    2. May,O., Siemann,M., Syldatk,C., Niefind,K. and Schomburg,D. (1996) Crystallization and Preliminary X-Ray Analysis of a Hydantoinase from    Arthrobacter Aurescens DSM 3745. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 52, 1209–1210.
    3. Katanaev,V., Spirin,A., Reuss,M. and Siemann,M. (1996) Formation of Bacteriophage MS2 Infectious Units in a Cell-Free    Translation System. FEBS LETTERS, 397, 143–148.
  24. 1994

  25. 1993