Publications

 

2013

  • Eisenreich W, Huber C, Kutzner E, Knispel N, Schramek N. Isotopologue Profiling – Towards a better understanding of metabolic pathways. In The Handbook of Plant Metabolomics, Wiley VCH, in press.
  • Heuner K, Eisenreich W. The intracellular metabolism of legionella by isotopologue profiling.  Methods Mol Biol. 954, 163-181.
  • Lechner, S., Patra, P., Klumpp, S. und Bertram, R. “Interplay between population dynamics and drug tolerance of Staphylococcus aureus persister cells“ J Mol Microbiol Biotechnol [AKZEPTIERT].
  • Schuster, C. F., Park J. H., Prax, M., Herbig, A., Nieselt, K., Rosenstein, R., Inouye M. und Bertram R. (2013). “Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum” J Bacteriol 195(1): 115-125.  

2012

  • Gamez, G., and S. Hammerschmidt (2012) Combat pneumococcal infections: adhesins as candidates for protein-based vaccine development. Curr Drug Targets 13(3):323-337. PMID: 22206255
  • Hartel, T., E. Eylert, C. Schulz, L. Petruschka, P. Gierok, S. Grubmueller, M. Lalk, W. Eisenreich, and S. Hammerschmidt (2012) Characterization of the central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling. J Biol Chem 287(6):4260-4274.
  • Eylert E, Bacher A, Eisenreich W. NMR-based isotopologue profiling of microbial carotenoids. Methods Mol Biol. 892, 315-333.
  • Härtel T, Eylert E, Schulz C, Petruschka L, Gierok P, Grubmüller S, Lalk M, Eisenreich W, Hammerschmidt S. Characterization of central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling. J Biol Chem. 287, 4260-4274.
  • Willenborg J, Koczula A, Huber C, Keil B, Eisenreich W, Valentin-Weigand P, Goethe R.  Analysis of the carbon metabolism and amino acid biosynthesis of Streptococcus suis.  Int. J. Med. Microbiol., 302, 75.
  • Kriegeskorte A, Grubmüller S, Kahl B, von Eiff C, Proctor RA, Peters G, Eisenreich W, Becker K.  Comprehensive investigation of the metabolism of Staphylococcus aureus comparing normal and small colony-variant (SCV) phenotypes. Int. J. Med. Microbiol., 302, 135.
  • Schunder E, Gillmaier N, Herrmann V, Eisenreich W, Lautner M, Heuner K. Investigation of Legionella pneumophila metabolism via C-13-isotopologue profiling. Int. J. Med. Microbiol., 302, 85.
  • Leiba J, Hartmann T, Cluzel ME, Cohen-Gonsaud, Delolme F, Bischoff M, Molle V. A novel mode of regulation of the Staphylococcus aureus catabolite control protein A (CcpA) mediated by Stk1 phosphorylation. J. Biol. Chem. 287:43607-19.
  • Hofreuter,D.,  Mohr,J., Wensel,O., Rademacher,S., Schreiber,K., Schomburg,D., Gao,B., Galán,J.E., Contribution of Amino Acid Catabolism to the Tissue Specific Persistence of Campylobacter jejuni in a Murine Colonization Model PLoS One. 2012; 7(11): e50699.
  • Lechner, S., Lewis K. und Bertram R. (2012). “Staphylococcus aureus Persisters Tolerant to Bactericidal Antibiotics” J Mol Microbiol Biotechnol 22(4): 235-44.
  • Gauger, T., Weihs, F., Mayer, S., Krismer, B., Liese, J., Kull, M. und Bertram, R. (2012). ”In vivo monitoring of protein expression in Staphylococcus aureus by peptide tag-induced reporter fluorescence“ Microb Biotechnol 5(1): 129-134.
  • Dandekar T, Fieselmann A, Majeed S, and Ahmed Z. 2012. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform. 2012 Nov 9. [Epub ahead of print] PMID: 23142828
  • Dandekar T, Astrid F, Jasmin P, Hensel M. 2012. Salmonella enterica: a surprisingly   well-adapted intracellular lifestyle. Front Microbiol. 2012;3:164. Epub 2012 May 3. PubMed PMID: 22563326; PubMed Central PMCID: PMC3342586.
  • Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, and Dandekar T. 2012. Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin. Plant Cell 24, 1793-814.
  • Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. 2012. Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights. 6, 97-128.
  • Papenfort K, Podkaminski D, Hinton JC, Vogel J. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):E757-64. doi: 10.1073/pnas.1119414109. Epub 2012 Mar 1. PubMed PMID: 22383560; PubMed Central PMCID: PMC3323961.
  • Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T. 2012. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics. 2012 May 11. [Epub ahead of print] PubMed PMID: 22581175.
  • Fuchs TM, Eisenreich W, Kern T, Dandekar T. 2012. Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol. 2012;3:23. Epub 2012 Feb 3. PubMed PMID: 22347216; PubMed Central PMCID: PMC3271275.
  • Madeo, M., O’Riordan, N., Fuchs, T. M., Utratna, M., Karatzas, K.-A., and O’Byrne, C (2012). Thiamine plays a critical role in the acid tolerance of Listeria monocytogenes. FEMS Microbiology Letters 326: 137-143.
  • Fuchs, T. M., Eisenreich, W., Heesemann, J., and W. Goebel (2012). Metabolic adaptation of human pathogenic and related non-pathogenic bacteria to extra- and intracellular habitats. FEMS Reviews Microbiology 36, 435-462.
  • Ratzka C, Förster F, Liang C, Kupper M, Dandekar T, Feldhaar H, Gross R. 2012. Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus. PLoS One 7(8):e43036.
  • Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T. 2012. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst Biol. 6(1):72. 
  • Zirkel J, Cecil A, Schäfer F, Rahlfs S, Ouedraogo A, Xiao K, Sawadogo S, Coulibaly B, Becker K, Dandekar T. 2012. Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling. Bioinform Biol Insights. 2012;6:287-302. doi: 10.4137/BBI.S10193.
  • Ahmed Z., Saman M, Dandekar T. 2012. Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications towards Metabolic Flux Analysis. (2012) Recent Patents on Computer Science, Vol.5, No.3, December 2012
  • Ahmed Z., Saman M., Dandekar T. 2012. Formal UML Modelling of Isotopo, Bioinformatical Software for Mass Isotopomers Distribution Analysis. Software Engineering Journal, SAP Publishing, 2(4): 147-159.
  • Ahmed Z., Dandekar T., Majeed S. 2012. Semantic Web; Ontology Specific Languages for Web Application Development. International Journal of Web applications 4 (1), pp. 42-50.
  • Ahmed Z., Saman M., Dandekar T. 2012. Unified Modeling and HCI Mockup Designing towards MIDA. International Journal of Emerging Sciences, Vol. 2, No. 3, Pages: 361-382.
  • Naseem M and Dandekar T. 2012. The role of auxin-cytokinin antagonism in plant-pathogen interactions. PLoS Pathog. 2012 Nov;8(11):e1003026.
  • Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Voelker U, Dandekar T (2012) Metabolic Adaptation and Protein Complexes in Prokaryotes Metabolites 2(4), 940-958; doi:10.3390/metabo2040940

2011

  • Schatschneider S, Vorhölter FJ, Rückert C, Becker A, Eisenreich W, Pühler A, Niehaus K. Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling.Mol Genet Genomics. 286, 247-259.
  • Härtel T, Schulz C, Eylert E, Grubmüller S, Eisenreich W, Hammerschmidt S.Amino acid metabolism in Streptococcus pneumoniae as analyzed by C-13-isotopologue profiling. Int J Med Microbiol. 301, 90.
  • Polzin S, Elsenhans I, Eisenreich W, Schmidt H. Differential proteomic expression of enterohemorrhagic E. coli O157:H7 EDL933 in vitro. Int J Med Microbiol. 301, 60.
  • Popp J, Dandekar T, Eisenreich W. Metabolism of intracellular Salmonella enterica: One lifestyle in intracellular infections. Int J Med Microbiol. 301, 76.
  • Sadykov MR, Hartmann T, Mattes TA, Hiatt M, Jann NJ, Zhu Y, Ledala N, Landmann R, Herrmann M, Rohde H, Bischoff M, Somerville GA. CcpA coordinates central metabolism and biofilm formation in Staphylococcus epidermidis. Microbiology 157:3458-68.
  • Ratzka C, Liang C, Dandekar T, Gross R, Feldhaar H. 2011. Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect Biochem Mol Biol. 2011 Aug;41(8):529-36. doi: 10.1016/j.ibmb.2011.03.002.
  • Cecil A, Rikanovic C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder  T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. 2011. Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol. 2011 Mar 21;12(3):R24. [Epub ahead of print] PubMed PMID: 21418624.
  • Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. 2011. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst. 2011 Apr 1;7(4):1241-53. Epub 2011 Feb 16. PubMed PMID: 21327190.
  • Helle, L., Kull, M., Mayer, S., Marincola, G., Zelder, M.-E., Goerke, C., Wolz, C. und Bertram, R. (2011).”Vectors for improved Tet repressor dependent gradual gene induction or silencing in Staphylococcus aureus” Microbiology 157(12): 3314-3323
  • Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G.2011. Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor. J Cell Biochem. 2011 Feb 10. doi: 10.1002/jcb.23034. [Epub ahead of print] PubMed PMID: 21312235.
  • Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. 2011. Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35.
  • Kröger, C, Srikumar S, Ellwart J, Fuchs TM.  2011.  Bistability in myo-Inositol Utilization by Salmonella enterica Serovar Typhimurium.. Journal of bacteriology. 193(6):1427-35.
  • Chatterjee, I, Maisonneuve E, Ezraty B, Herrmann M, Dukan S.  2011.  Staphylococcus aureus ClpC is involved in protection of carbon-metabolizing enzymes from carbonylation during stationary growth phase.. International journal of medical microbiology : IJMM.
  • Scheer, M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D.  2011.  BRENDA, the enzyme information system in 2011.. Nucleic acids research. 39(Database issue):D670-6. 
  • Srikumar, S, Fuchs TM.  2011.  Ethanolamine utilization contributes to proliferation of Salmonella enterica serovar Typhimurium in food and in nematodes.. Applied and environmental microbiology. 77(1):281-90. 
  • Härtel, T, Klein M, Koedel U, Rohde M, Petruschka L, Hammerschmidt S.  2011.  Impact of glutamine transporters on pneumococcal fitness under infection-related conditions.. Infection and immunity. 79(1):44-58.
  • Bordes, P, Lavatine L, Phok K, Barriot R, Boulanger A, Castanié-Cornet M-P, Déjean G, Lauber E, Becker A, Arlat M et al..  2011.  Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of {sigma}E-dependent activity.. Journal of bacteriology. 193(1):246-64.
  • Herrmann, V, Eidner A, Rydzewski K, Blädel I, Jules M, Buchrieser C, Eisenreich W, Heuner K.  2011.  GamA is a eukaryotic-like glucoamylase responsible for glycogen- and starch-degrading activity of Legionella pneumophila.. International journal of medical microbiology : IJMM. 301(2):133-9.
  • Kriegeskorte A, König S, Sander G, Pirkl A, Mahabir E, Proctor RA, von Eiff C,
    Peters G, Becker K. Small colony variants of Staphylococcus aureus reveal
    distinct protein profiles. Proteomics. 2011 Jun;11(12):2476-90. doi:
    10.1002/pmic.201000796. Epub 2011 May 18. PubMed PMID: 21595038.
  • Thiele, I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA et al..  2011.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC systems biology. 5:8.

2010

  • Kreikemeyer, B., G. Gamez, I. Margarit, J.C. Giard, S. Hammerschmidt, A. Hartke, and A. Podbielski. 2010. Genomic organization, structure, regulation and pathogenic role of pilus constituents in major pathogenic Streptococci and Enterococci. Int J Med Microbiol 301(3):240-51.
  • Dandekar,T. and Xiao,K. 2010. New bioinformaic strategies against apicomplexan parasites pp. 21-33. In: Katja Becker (Ed.), Apicomplexan Parasites: Molecular Approaches toward Targeted Drug Development. Wiley-VCH, Weinheim.
  • Vainshtein, Y.*, Sanchez,M., Brazma,A., Hentze,M.W., Dandekar T* and Martina U. Muckenthaler*. 2010. The IronChip Evaluation Package: A package of Perl modules for robust analysis of custom microarrays. BMC Bioinformatics 11:112.
  • Friedrich T, Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Hacker J, Müller T, Dobrindt U. 2010. High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC Genomics. 2010 Oct 21;11:591. PubMed PMID: 20964857;
  • Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. 2010. Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics. 2010 Aug;10(16):2982-3000. PubMed PMID: 20662099.
  • Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. 2010. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2011 Jan;5(1):61-70. Epub 2010 Jul 8. PubMed PMID: 20613790.
  • Trcek, J, Fuchs TM, Trülzsch K.  2010.  Analysis of Yersinia enterocolitica invasin expression in vitro and in vivo using a novel luxCDABE reporter system.. Microbiology (Reading, England). 156(Pt 9):2734-45.
  • Dandekar, T, Dandekar G.  2010.  Pharmacogenomic strategies against microbial resistance: from bright to bleak to innovative.. Pharmacogenomics. 11(9):1193-6.
  • Spanier, B, Starke M, Higel F, Scherer S, Fuchs TM.  2010.  Yersinia enterocolitica infection and tcaA-dependent killing of Caenorhabditis elegans.. Applied and environmental microbiology. 76(18):6277-85.
  • Bumann, D.  2010.  Pathogen proteomes during infection: A basis for infection research and novel control strategies.. Journal of proteomics. 73(11):2267-76.
  • Tuchscherr, L, Heitmann V, Hussain M, Viemann D, Roth J, von Eiff C, Peters G, Becker K, Löffler B.  2010.  Staphylococcus aureus small-colony variants are adapted phenotypes for intracellular persistence.. The Journal of infectious diseases. 202(7):1031-40.
  • Krol, E, Blom J, Winnebald J, Berhörster A, Barnett MJ, Goesmann A, Baumbach J, Becker A.  2010.  RhizoRegNet-A database of rhizobial transcription factors and regulatory networks.. Journal of biotechnology.
  • Grundmeier, M, Tuchscherr L, Brück M, Viemann D, Roth J, Willscher E, Becker K, Peters G, Löffler B.  2010.  Staphylococcal strains vary greatly in their ability to induce an inflammatory response in endothelial cells.. The Journal of infectious diseases. 201(6):871-80.
  • Trunk, K, Benkert B, Quäck N, Münch R, Scheer M, Garbe J, Jänsch L, Trost M, Wehland J, Buer J et al..  2010.  Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons.. Environmental microbiology. 12(6):1719-33.
  • Eisenreich, W, Dandekar T, Heesemann J, Goebel W.  2010.  Carbon metabolism of intracellular bacterial pathogens and possible links to virulence.. Nature reviews. Microbiology. 8(6):401-12.
  • Frimmersdorf, E, Horatzek S, Pelnikevich A, Wiehlmann L, Schomburg D.  2010.  How Pseudomonas aeruginosa adapts to various environments: a metabolomic approach.. Environmental microbiology. 12(6):1734-47.
  • Abu-Qatouseh, LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J, Rozhdestvensky TS, Peters G, von Eiff C, Becker K.  2010.  Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype.. Journal of molecular medicine (Berlin, Germany). 88(6):565-75.
  • Eylert, E, Herrmann V, Jules M, Gillmaier N, Lautner M, Buchrieser C, Eisenreich W, Heuner K.  2010.  Isotopologue profiling of Legionella pneumophila: role of serine and glucose as carbon substrates.. The Journal of biological chemistry. 285(29):22232-43.
  • Jensch, I, Gámez G, Rothe M, Ebert S, Fulde M, Somplatzki D, Bergmann S, Petruschka L, Rohde M, Nau R et al..  2010.  PavB is a surface-exposed adhesin of Streptococcus pneumoniae contributing to nasopharyngeal colonization and airways infections.. Molecular microbiology. 77(1):22-43.
  • Albert-Weissenberger, C, Sahr T, Sismeiro O, Hacker J, Heuner K, Buchrieser C.  2010.  Control of flagellar gene regulation in Legionella pneumophila and its relation to growth phase.. Journal of bacteriology. 192(2):446-55.
  • Kröger, C, Stolz J, Fuchs TM.  2010.  myo-Inositol transport by Salmonella enterica serovar Typhimurium.. Microbiology (Reading, England). 156(Pt 1):128-38.
  • Stary, E, Gaupp R, Lechner S, Leibig M, Tichy E, Kolb M, Bertram R.  2010.  New architectures for Tet-on and Tet-off regulation in Staphylococcus aureus.. Applied and environmental microbiology. 76(3):680-7.
  • Kadioglu, A, Brewin H, Härtel T, Brittan JL, Klein M, Hammerschmidt S, Jenkinson HF.  2010.  Pneumococcal protein PavA is important for nasopharyngeal carriage and development of sepsis.. Molecular oral microbiology. 25(1):50-60.
  • Wurm, M, Schöpke B, Lutz D, Müller J, Zeng A-P.  2010.  Microtechnology meets systems biology: the small molecules of metabolome as next big targets.. Journal of biotechnology. 149(1-2):33-51.
  • Teufel, R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G.  2010.  Bacterial phenylalanine and phenylacetate catabolic pathway revealed.. Proceedings of the National Academy of Sciences of the United States of America. 107(32):14390-5.
  • Beisser, D, Klau GW, Dandekar T, Müller T, Dittrich MT.  2010.  BioNet: an R-Package for the functional analysis of biological networks.. Bioinformatics (Oxford, England). 26(8):1129-30.
  • Schär, J, Stoll R, Schauer K, Loeffler DIM, Eylert E, Joseph B, Eisenreich W, Fuchs TM, Goebel W.  2010.  Pyruvate carboxylase plays a crucial role in carbon metabolism of extra- and intracellularly replicating Listeria monocytogenes.. Journal of bacteriology. 192(7):1774-84.
  • Werth, N, Beerlage C, Rosenberger C, Yazdi AS, Edelmann M, Amr A, Bernhardt W, von Eiff C, Becker K, Schäfer A et al..  2010.  Activation of hypoxia inducible factor 1 is a general phenomenon in infections with human pathogens.. PloS one. 5(7):e11576.
    Bannert, C, Welfle A, Aus dem Spring C, Schomburg D.  2010.  BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.. BMC bioinformatics. 11:589.
  • Götz, A, Eylert E, Eisenreich W, Goebel W.  2010.  Carbon metabolism of enterobacterial human pathogens growing in epithelial colorectal adenocarcinoma (Caco-2) cells.. PloS one. 5(5):e10586.
  • Schneider, J, Vorhölter F-J, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A.  2010.  CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.. Genetics and molecular research : GMR. 9(3):1660-72.
  • Schauer, K, Geginat G, Liang C, Goebel W, Dandekar T, Fuchs TM.  2010.  Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling.. BMC genomics. 11:573.
  • Heinen, S, Thielen B, Schomburg D.  2010.  KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes.. BMC bioinformatics. 11:375.

2009

  • Bumann, D.  2009.  System-level analysis of Salmonella metabolism during infection.. Current opinion in microbiology. 12(5):559-67.
  • Spura, J, Reimer L C, Wieloch P, Schreiber K, Buchinger S, Schomburg D.  2009.  A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast.. Analytical biochemistry. 394(2):192-201.
  • Biswas, L, Biswas R, Schlag M, Bertram R, Götz F.  2009.  Small-colony variant selection as a survival strategy for Staphylococcus aureus in the presence of Pseudomonas aeruginosa.. Applied and environmental microbiology. 75(21):6910-2.
  • Schmid, A, Neumayer W, Trülzsch K, Israel L, Imhof A, Roessle M, Sauer G, Richter S, Lauw S, Eylert E et al..  2009.  Cross-talk between type three secretion system and metabolism in Yersinia.. The Journal of biological chemistry. 284(18):12165-77.
  • Hiller, K, Hangebrauk J, Jäger C, Spura J, Schreiber K, Schomburg D.  2009.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis.. Analytical chemistry. 81(9):3429-39.
  • Herbst, K, Bujara M, Heroven A K, Opitz W, Weichert M, Zimmermann A, Dersch P.  2009.  Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA.. PLoS pathogens. 5(5):e1000435.
  • Watt, T F, Vucur M, Baumgarth B, Watt S A, Niehaus K.  2009.  Low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-III secretion system in Xanthomonas campestris pv. campestris.. Journal of biotechnology. 140(1-2):59-67.
  • Gerlach, RG, Jäckel D, Hölzer SU, Hensel M.  2009.  Rapid oligonucleotide-based recombineering of the chromosome of Salmonella enterica.. Applied and environmental microbiology. 75(6):1575-80.
  • Chatterjee, I, Schmitt S, Batzilla CF, Engelmann S, Keller A, Ring MW, Kautenburger R, Ziebuhr W, Hecker M, Preissner KT et al..  2009.  Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence.. Proteomics. 9(5):1152-76.
  • Zech, H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R.  2009.  Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade.. Proteomics. 9(14):3677-97.
  • Kröger, C, Fuchs TM.  2009.  Characterization of the myo-inositol utilization island of Salmonella enterica serovar Typhimurium.. Journal of bacteriology. 191(2):545-54.
    Grote, A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D,
  • Münch R.  2009.  PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes.. Nucleic acids research. 37(Database issue):D61-5.
  • Leber, M, Egelhofer V, Schomburg I, Schomburg D.  2009.  Automatic assignment of reaction operators to enzymatic reactions.. Bioinformatics (Oxford, England). 25(23):3135-42.
  • Rudack, C, Sachse F, Albert N, Becker K, von Eiff C.  2009.  Immunomodulation of nasal epithelial cells by Staphylococcus aureus-derived serine proteases.. Journal of immunology (Baltimore, Md. : 1950). 183(11):7592-601.
  • Uliczka, F, Kornprobst T, Eitel J, Schneider D, Dersch P.  2009.  Cell invasion of Yersinia pseudotuberculosis by invasin and YadA requires protein kinase C, phospholipase C-gamma1 and Akt kinase.. Cellular microbiology. 11(12):1782-801.
  • Noske, N, Kämmerer U, Rohde M, Hammerschmidt S.  2009.  Pneumococcal interaction with human dendritic cells: phagocytosis, survival, and induced adaptive immune response are manipulated by PavA.. Journal of immunology (Baltimore, Md. : 1950). 183(3):1952-63.
  • Schauer, K, Stolz J, Scherer S, Fuchs TM.  2009.  Both thiamine uptake and biosynthesis of thiamine precursors are required for intracellular replication of Listeria monocytogenes.. Journal of bacteriology. 191(7):2218-27.
  • Seidl, K, Müller S, François P, Kriebitzsch C, Schrenzel J, Engelmann S, Bischoff M, Berger-Bächi B.  2009.  Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus.. BMC microbiology. 9:95.
  • Haddad, I, Hiller K, Frimmersdorf E, Benkert B, Schomburg D, Jahn D.  2009.  An emergent self-organizing map based analysis pipeline for comparative metabolome studies.. In silico biology. 9(4):163-78.
  • Melzer, G, Esfandabadi M E, Franco-Lara E, Wittmann C.  2009.  Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties.. BMC systems biology. 3:120.
  • Spanier, B, Lasch K, Marsch S, Benner J, Liao W, Hu H, Kienberger H, Eisenreich W, Daniel H.  2009.  How the intestinal peptide transporter PEPT-1 contributes to an obesity phenotype in Caenorhabditits elegans.. PloS one. 4(7):e6279.
  • Liang, C, Schmid A, López-Sánchez M J, Moya A, Gross R, Bernhardt J, Dandekar T.  2009.  JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.. BMC bioinformatics. 10:391. 

2008

  • Seidl, K, Bischoff M, Berger-Bächi B.  2008.  CcpA mediates the catabolite repression of tst in Staphylococcus aureus.. Infection and immunity. 76(11):5093-9.
  • Lannergård, J, von Eiff C, Sander G, Cordes T, Seggewiss J, Peters G, Proctor RA, Becker K, Hughes D.  2008.  Identification of the genetic basis for clinical menadione-auxotrophic small-colony variant isolates of Staphylococcus aureus.. Antimicrobial agents and chemotherapy. 52(11):4017-22.
    Ohlsen, K, Dandekar G, Schwarz R, Dandekar T.  2008.  New trends in
  • pharmacogenomic strategies against resistance development in microbial infections.. Pharmacogenomics. 9(11):1711-23.
  • Seidl, K, Goerke C, Wolz C, Mack D, Berger-Bächi B, Bischoff M.  2008.  Staphylococcus aureus CcpA affects biofilm formation.. Infection and immunity. 76(5):2044-50.
  • Vorhölter, F-J, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J et al..  2008.  The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.. Journal of biotechnology. 134(1-2):33-45.
  • Leibig, M, Krismer B, Kolb M, Friede A, Götz F, Bertram R.  2008.  Marker removal in staphylococci via Cre recombinase and different lox sites.. Applied and environmental microbiology. 74(5):1316-23.
  • Serrania, J, Vorhölter F-J, Niehaus K, Pühler A, Becker A.  2008.  Identification of Xanthomonas campestris pv. campestris galactose utilization genes from transcriptome data.. Journal of biotechnology. 135(3):309-17.
  • Heroven, A K, Böhme K, Rohde M, Dersch P.  2008.  A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM.. Molecular microbiology. 68(5):1179-95.
  • Klein, J, Leupold S, Münch R, Pommerenke C, Johl T, Kärst U, Jänsch L, Jahn D, Retter I.  2008.  ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.. Nucleic acids research. 36(Web Server issue):W460-4.
  • Glöckner, G, Albert-Weissenberger C, Weinmann E, Jacobi S, Schunder E, Steinert M, Hacker J, Heuner K.  2008.  Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands.. International journal of medical microbiology : IJMM. 298(5-6):411-28.
  • Bertram, R, Hillen W.  2008.  The application of Tet repressor in prokaryotic gene regulation and expression.. Microbial biotechnology. 1(1):2-16.
  • Pobigaylo, N, Szymczak S, Nattkemper TW, Becker A.  2008.  Identification of genes relevant to symbiosis and competitiveness in Sinorhizobium meliloti using signature-tagged mutants.. Molecular plant-microbe interactions : MPMI. 21(2):219-31.
  • Neuweger, H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A.  2008.  MeltDB: a software platform for the analysis and integration of metabolomics experiment data.. Bioinformatics (Oxford, England). 24(23):2726-32.
  • Rajashekar, R, Liebl D, Seitz A, Hensel M.  2008.  Dynamic remodeling of the endosomal system during formation of Salmonella-induced filaments by intracellular Salmonella enterica.. Traffic (Copenhagen, Denmark). 9(12):2100-16.
  • Krömer, JO, Bolten CJ, Heinzle E, Schröder H, Wittmann C.  2008.  Physiological response of Corynebacterium glutamicum to oxidative stress induced by deletion of the transcriptional repressor McbR.. Microbiology (Reading, England). 154(Pt 12):3917-30.
  • Eylert, E, Schär J, Mertins S, Stoll R, Bacher A, Goebel W, Eisenreich W.  2008.  Carbon metabolism of Listeria monocytogenes growing inside macrophages.. Molecular microbiology. 69(4):1008-17.

2007

  • Bolten, CJ, Kiefer P, Letisse F, Portais J-C, Wittmann C.  2007.  Sampling for metabolome analysis of microorganisms.. Analytical chemistry. 79(10):3843-9.
  • Thöne, F, Schwanhäusser B, Becker D, Ballmaier M, Bumann D.  2007.  FACS-isolation of Salmonella-infected cells with defined bacterial load from mouse spleen.. Journal of microbiological methods. 71(3):220-4.
  • Pfeiffer, V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J.  2007.  A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome.. Molecular microbiology. 66(5):1174-91.
  • Herebian, D, Küpper U, Schomburg D, Marner F-J.  2007.  In vivo labeling with stable isotopes as a tool for the identification of unidentified peaks in the metabolome analysis of Corynebacterium glutamicum by GC/MS.. Biological chemistry. 388(8):865-71.
  • Bumann, D, Valdivia RH.  2007.  Identification of host-induced pathogen genes by differential fluorescence induction reporter systems.. Nature protocols. 2(4):770-7.
  • Schwarz, R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T.  2007.  Integrated network reconstruction, visualization and analysis using YANAsquare.. BMC bioinformatics. 8:313.

2006

  • Boes, N, Schreiber K, Härtig E, Jaensch L, Schobert M.  2006.  The Pseudomonas aeruginosa universal stress protein PA4352 is essential for surviving anaerobic energy stress.. Journal of bacteriology. 188(18):6529-38.
  • Thompson, A, Rolfe MD, Lucchini S, Schwerk P, Hinton JCD, Tedin K.  2006.  The bacterial signal molecule, ppGpp, mediates the environmental regulation of both the invasion and intracellular virulence gene programs of Salmonella.. The Journal of biological chemistry. 281(40):30112-21.
  • Becker, D, Selbach M, Rollenhagen C, Ballmaier M, Meyer TF, Mann M, Bumann D.  2006.  Robust Salmonella metabolism limits possibilities for new antimicrobials.. Nature. 440(7082):303-7.
  • Pobigaylo, N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A.  2006.  Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti.. Applied and environmental microbiology. 72(6):4329-37.
  • Heise, T, Dersch P.  2006.  Identification of a domain in Yersinia virulence factor YadA that is crucial for extracellular matrix-specific cell adhesion and uptake.. Proceedings of the National Academy of Sciences of the United States of America. 103(9):3375-80.
  • Eisenreich, W, Slaghuis J, Laupitz R, Bussemer J, Stritzker J, Schwarz C, Schwarz R, Dandekar T, Goebel W, Bacher A.  2006.  13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA.. Proceedings of the National Academy of Sciences of the United States of America. 103(7):2040-5.
  • Heroven, A K, Dersch P.  2006.  RovM, a novel LysR-type regulator of the virulence activator gene rovA, controls cell invasion, virulence and motility of Yersinia pseudotuberculosis.. Molecular microbiology. 62(5):1469-83.
  • Brüggemann, H, Hagman A, Jules M, Sismeiro O, Dillies M-A, Gouyette C, Kunst F, Steinert M, Heuner K, Coppée J-Y et al..  2006.  Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila.. Cellular microbiology. 8(8):1228-40.
  • Seidl, K, Stucki M, Ruegg M, Goerke C, Wolz C, Harris L, Berger-Bächi B, Bischoff M.  2006.  Staphylococcus aureus CcpA affects virulence determinant production and antibiotic resistance.. Antimicrobial agents and chemotherapy. 50(4):1183-94.

2005

  • Pracht, D, Elm C, Gerber J, Bergmann S, Rohde M, Seiler M, Kim KS, Jenkinson HF, Nau R, Hammerschmidt S.  2005.  PavA of Streptococcus pneumoniae modulates adherence, invasion, and meningeal inflammation.. Infection and immunity. 73(5):2680-9.
  • Chakravortty, D, Rohde M, Jäger L, Deiwick J, Hensel M.  2005.  Formation of a novel surface structure encoded by Salmonella Pathogenicity Island 2.. The EMBO journal. 24(11):2043-52.
  • Chatterjee, I, Becker P, Grundmeier M, Bischoff M, Somerville GA, Peters G, Sinha B, Harraghy N, Proctor RA, Herrmann M.  2005.  Staphylococcus aureus ClpC is required for stress resistance, aconitase activity, growth recovery, and death.. Journal of bacteriology. 187(13):4488-96.
  • Kim, E-J, Wang W, Deckwer W-D, Zeng A-P.  2005.  Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density.. Microbiology (Reading, England). 151(Pt 4):1127-38.
  • Dandekar, T, Schmidt S.  2005.  Metabolites and pathway flexibility.. In silico biology. 5(2):103-10.

2004

  • Krömer, J O, Sorgenfrei O, Klopprogge K, Heinzle E, Wittmann C.  2004.  In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome.. Journal of bacteriology. 186(6):1769-84.
  • Pizarro-Cerdá, J, Tedin K.  2004.  The bacterial signal molecule, ppGpp, regulates Salmonella virulence gene expression.. Molecular microbiology. 52(6):1827-44.

2003

  • Kim, E-J, Sabra W, Zeng A-P.  2003.  Iron deficiency leads to inhibition of oxygen transfer and enhanced formation of virulence factors in cultures of Pseudomonas aeruginosa PAO1.. Microbiology (Reading, England). 149(Pt 9):2627-34.

2002

  • Sabra, W, Kim E-J, Zeng A-P.  2002.  Physiological responses of Pseudomonas aeruginosa PAO1 to oxidative stress in controlled microaerobic and aerobic cultures.. Microbiology (Reading, England). 148(Pt 10):3195-202.
  • Dandekar, T, Sauerborn R.  2002.  Comparative genome analysis and pathway reconstruction.. Pharmacogenomics. 3(2):245-56.

2001

  • Tedin, K, Norel F.  2001.  Comparison of DeltarelA strains of Escherichia coli and Salmonella enterica serovar Typhimurium suggests a role for ppGpp in attenuation regulation of branched-chain amino acid biosynthesis.. Journal of bacteriology. 183(21):6184-96.
  • Becker, P, Hufnagle W, Peters G, Herrmann M.  2001.  Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using micro-representational-difference analysis.. Applied and environmental microbiology. 67(7):2958-65.

2000

  • Eisenreich, W, Bacher A.  2000.  Elucidation of biosynthetic pathways by retrodictive/predictive comparison of isotopomer patterns determined by NMR spectroscopy.. Genetic engineering. 22:121-53.