Center for Systems Microbiology

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  1. 2013
  2. Published

    Aquaculture application and ecophysiology of marine bacteria from the Roseobacter clade. / D'Alvise, Paul; Gram, Lone (Main supervisor).

    Søborg : DTU Food, 2013. 79 p.

    Publication: Research › Ph.d. thesis – Annual report year: 2013

  3. Published

    Engineering strategies aimed at control of acidification rate of lactic acid bacteria. / Martinussen, Jan; Solem, Christian; Holm, Anders Koefoed; Jensen, Peter Ruhdal.

    In: Current Opinion in Biotechnology, Vol. 24, No. 2, 2013, p. 124-129.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  4. Published

    Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts.. / Pedersen, Søren Damkiær; Yang, Lei; Molin, Søren; Jelsbak, Lars.

    In: National Academy of Sciences. Proceedings, Vol. 110, No. 19, 2013.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  5. Published

    Expression and functional studies of genes involved in transport and metabolism of glycerol in Pachysolen tannophilus.. / Liu, Xiaoying; Mortensen, Uffe Hasbro; Workman, Mhairi.

    In: Microbial Cell Factories, Vol. 12, 2013, p. 27.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  6. Published

    Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart. / Holch, Anne; Webb, Kristen; Lukjancenko, Oksana; Ussery, David; Rosenthal, Benjamin M.; Gram, Lone.

    In: Applied and Environmental Microbiology, Vol. 79, No. 9, 2013, p. 2944-2951.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  7. Published

    Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. / Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller.

    In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 4, 2013, p. 771-777.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  8. Published

    High beta-Lactamase Levels Change the Pharmacodynamics of beta-Lactam Antibiotics in Pseudomonas aeruginosa Biofilms. / Wang, Hengzhuang; Ciofu, Oana; Yang, Liang; Wu, Hong; Song, Zhijun; Oliver, Antonio; Hoiby, Niels.

    In: Antimicrobial Agents and Chemotherapy, Vol. 57, No. 1, 2013, p. 196-204.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  9. Published

    High in vitro antimicrobial activity of β-peptoid-peptide hybrid oligomers against planktonic and biofilm cultures of Staphylococcus epidermidis.. / Liu, Yang; Knapp, Kolja Michael; Yang, Liang; Molin, Søren; Franzyk, Henrik; Folkesson, Anders.

    In: International Journal of Antimicrobial Agents, Vol. 41, No. 1, 2013, p. 20-27.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  10. Published

    Identification of the Receptor-Binding Protein in Lytic Leuconostoc pseudomesenteroides Bacteriophages. / Kot, Witold Piotr; Hammer, Karin; Neve, Horst; Vogensen, Finn Kvist.

    In: Applied and Environmental Microbiology, Vol. 79, No. 10, 2013, p. 203311-3314.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  11. Published

    Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.. / Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon Guldberg; Olsson, Lisbeth; Nielsen, Jens.

    In: P L o S One, Vol. 8, No. 1, 2013, p. e54144.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  12. Published

    Protection of cod larvae from vibriosis by Phaeobacter spp.: A comparison of strains and introduction times. / D'Alvise, Paul; Lillebø, Siril; Wergeland, Heidrun I.; Gram, Lone; Bergh, Øivind.

    In: Aquaculture, Vol. 384-387, 2013, p. 82-86.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  13. Published

    Rewiring Lactococcus lactis for Ethanol Production. / Solem, Christian; Dehli, Tore Ibsen; Jensen, Peter Ruhdal.

    In: Applied and Environmental Microbiology, Vol. 79, No. 8, 2013, p. 202512-2518.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  14. Published

    Sodium Dodecyl Sulfate (SDS)-Loaded Nanoporous Polymer as Anti-Biofilm Surface Coating Material. / Li, Li; Molin, Søren; Yang, Liang; Ndoni, Sokol.

    In: International Journal of Molecular Sciences (Online), Vol. 14, No. 2, 2013, p. 3050-3064.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  15. Published

    The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk. / de Jong, Anne; Hansen, Morten Ejby; Kuipers, Oscar P.; Kilstrup, Mogens; Kok, Jan.

    In: P L o S One, Vol. 8, No. 1, 2013, p. -.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  16. Published

    Typing of Pseudomonas aeruginosa from hemorrhagic pneumonia in mink (Neovison vison). / Salomonsen, Charlotte Mark; Themudo, G. E.; Jelsbak, Lars; Molin, Søren; Høiby, N.; Hammer , Anne Sofie .

    In: Veterinary Microbiology, Vol. 163, No. 1-2, 2013, p. 103-109.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  17. 2012
  18. Published

    A complex multilevel attack on Pseudomonas aeruginosa algT/U expression and AlgT/U activity results in the loss of alginate production. / Sautter, Robert; Ramos, Damaris; Schneper, Lisa; Ciofu, Oana; Wassermann, Tina; Koh, Chong-Lek; Heydorn, Arne; Hentzer, Morton; Høiby, Niels; Kharazmi, Arsalan; Molin, Søren; DeVries, Caroline A.; Ohman, Dennis E.; Mathee, Kalai.

    In: Gene, Vol. 498, No. 2, 2012, p. 242-253.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  19. Published

    Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective.. / Folkesson, Anders; Jelsbak, Lars; Yang, Lei; Johansen, Helle Krogh; Ciofu, Oana; Høiby, Niels; Molin, Søren.

    In: Nature Reviews. Microbiology, Vol. 10, No. 12, 2012.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  20. Published

    Aspergillus hydrophobins - Identification, classification and characterization. / Jensen, Britt Guillaume; Nielsen, Kristian Fog (Main supervisor); Søndergaard, Ib (Supervisor); Pedersen, Mona Højgaard (Supervisor); Frisvad, Jens Christian (Supervisor); Jelsbak, Lars (Supervisor); Jacobsen, Susanne (Supervisor).

    Department of Systems Biology, DTU, 2012. 212 p.

    Publication: Research › Ph.d. thesis – Annual report year: 2013

  21. Published

    Bioconversion of crude glycerol feedstocks into ethanol by Pachysolen tannophilus. / Liu, Xiaoying; Jensen, Peter Ruhdal; Workman, Mhairi.

    In: Bioresource Technology, Vol. 104, 2012, p. 559-586.

    Publication: Research - peer-review › Journal article – Annual report year: 2011

  22. Published

    Characterization of the AN6448 cluster in Aspergillus nidulans. / Nielsen, Jakob Blæsbjerg; Klejnstrup, Marie Louise; Khorsand-Jamal, Paiman; Holm, Dorte Koefoed; Nielsen, Michael Lynge; Kabat, Anna Monika; Rank, Christian; Gotfredsen, Charlotte Held; Larsen, T. O.; Mortensen, Uffe Hasbro.

    In: Planta Medica, Vol. 78, No. 11, 2012, p. 1113-1113.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  23. Published

    Chitin elicitation of natural product production in marine bacteria. / Månsson, Maria; Wietz, Matthias; Larsen, Thomas Ostenfeld; Gram, Lone.

    2012. Abstract from Gordon Conference on Marine Natural Products, Venture, CA, United States.

    Publication: Research - peer-review › Conference abstract for conference – Annual report year: 2012

  24. Published

    Combating biofilms. / Yang, Liang; Liu, Yang; Wu, Hong; Song, Zhijun; Hoiby, Niels; Molin, Søren; Givskov, Michael.

    In: F E M S Immunology and Medical Microbiology, Vol. 65, No. 2, Sp. Iss. SI, 2012, p. 146-157.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  25. Published

    Context matters — the complex interplay between resistome genotypes and resistance phenotypes. / Dantas, Gautam; Sommer, Morten.

    In: Current Opinion in Microbiology, Vol. 15, No. 5, 2012, p. 577-582.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  26. Published

    Deletion and acquisition of genomic content during early stage adaptation of Pseudomonas aeruginosa to a human host environment. / Rau, Martin H.; Marvig, Rasmus Lykke; Ehrlich, Garth D.; Molin, Søren; Jelsbak, Lars.

    In: Environmental Microbiology, Vol. 14, No. 8, 2012, p. 2200-2211.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  27. Published

    Draft Genome Sequence of the Yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460. / Liu, Xiaoying ; Kaas, Rolf Sommer; Jensen, Peter Ruhdal; Workman, Mhairi.

    In: Eukaryotic Cell (Online Edition), Vol. 11, No. 6, 2012, p. 827.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  28. Published

    Early genetic adaptation associated with chronic pseudomonas aeruginosa airways infection. / Johansen, H. K.; Aanaes, K.; Pressler, Tacjana; Skov, M.; Nielsen, K. G.; Ciofu, Oana; Buchwald, C.; Hoiby, N.; Molin, Søren.

    In: Pediatric Pulmonology, Vol. 47, No. S35, 2012, p. 328-329.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  29. Published

    Engineering strategies aimed at control of acidification rate and product formation of lactic acid bacteria. / Martinussen, Jan; Solem, Christian; Holm, Anders Koefoed; Jensen, Peter Ruhdal.

    In: Current Opinion in Biotechnology, Vol. 24, 2012, p. 1-3.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  30. Published

    Establishing new microbial cell factories for sustainable bioprocesses. / Workman, Mhairi; Holt, Philippe; Liu, Xiaoying .

    In: New Biotechnology, Vol. 29S, 2012, p. S75.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  31. Published

    Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. / Kaas, Rolf Sommer; Rundsten, Carsten Friis; Ussery, David; Aarestrup, Frank Møller.

    In: B M C Genomics, Vol. 13, No. 1, 2012, p. 577.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  32. Published

    European freshwater VHSV genotype Ia isolates divide into two distinct subpopulations. / Kahns, Søren; Skall, Helle Frank; Kaas, Rolf Sommer; Korsholm, H.; Jensen, Ann Britt Bang; Jonstrup, Søren Peter; Dodge, M. J.; Einer-Jensen, Katja; Stone, D.; Olesen, Niels Jørgen.

    In: Diseases of Aquatic Organisms, Vol. 99, No. 1, 2012, p. 23-35.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  33. Published

    Evaluation of cell factory performance through determination of intracellular metabolites using LC-MS/MS. / Magdenoska, Olivera; Martinussen, Jan; Nielsen, Kristian Fog; Thykær, Jette.

    In: New Biotechnology, Vol. 29S, 2012.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  34. Published

    Evolution and diversification of Pseudomonas aeruginosa in the paranasal sinuses of cystic fibrosis children have implications for chronic lung infection. / Hansen, Susse Kirkelund; Rau, Martin Holm; Johansen, Helle Krogh; Ciofu, Oana; Jelsbak, Lars; Yang, Lei; Folkesson, Anders; Jarmer, Hanne Østergaard; Aanæs, Kasper; von Buchwald, Christian; Høiby, Niels; Molin, Søren.

    In: I S M E Journal, Vol. 6, No. 1, 2012, p. 31.

    Publication: Research - peer-review › Journal article – Annual report year: 2011

  35. Published

    Evolutionary dynamics of pseudomonas aeruginosa in CF. / Molin, Soren; Jelsbak, Lars; Johansen, Helle; Hoiby, Niels.

    In: Pediatric Pulmonology, Vol. 47, 2012, p. 152-153.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  36. Published

    Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa. / Gómez Lozano, María; Marvig, Rasmus Lykke; Molin, Søren; Long, Katherine.

    In: Environmental Microbiology, Vol. 14, No. 8, 2012, p. 2006-2016.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  37. Published

    Hemorrhagic pneumonia in mink caused by Pseudomonas aeruginosa. / Salomonsen, Charlotte Mark; Boye, Mette (Main supervisor); Høiby, Niels (Supervisor); Molin, Søren (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 105 p.

    Publication: Research › Ph.d. thesis – Annual report year: 2013

  38. Published

    Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine. / Vejborg, Rebecca Munk; de Evgrafov, Mari Cristina Rodriguez; Phan, Minh Duy; Totsika, Makrina; Schembri, Mark; Hancock, Viktoria .

    In: Infection and Immunity, Vol. 80, No. 9, 2012, p. 3179-3188.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  39. Published

    Initial Pseudomonas aeruginosa infection in patients with cystic fibrosis: characteristics of eradicated and persistent isolates. / Tramper-Stranders, G. A.; van der Ent, C. K.; Molin, Søren; Yang, Liang; Hansen, Susse Kirkelund; Rau, Martin Holm; Ciofu, Oana; Johansen, H. K.; Wolfs, T. F. W.

    In: Clinical Microbiology and Infection, Vol. 18, No. 6, 2012, p. 567-574.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  40. Published

    Modular microfluidic system as a model of cystic fibrosis airways. / Skolimowski, Maciej; Weiss Nielsen , Martin ; Abeille, Fabien; Skafte-Pedersen, Peder; Sabourin, David; Fercher, A.; Papkovsky, D.; Molin, Søren; Taboryski, Rafael J.; Sternberg, Claus; Dufva, Martin; Geschke, Oliver; Emnéus, Jenny.

    In: Biomicrofluidics, Vol. 6, No. 3, 2012, p. 034109.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  41. Published

    Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria. / Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon; Rundsten, Carsten Friis; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W.; Aarestrup, Frank M.; Lund, Ole.

    In: Journal of Clinical Microbiology, Vol. 50, No. 4, 2012, p. 1355-1361.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  42. Published

    Mutations in 23S rRNA Confer Resistance against Azithromycin in Pseudomonas aeruginosa. / Marvig, Rasmus Lykke; Søndergaard, Mette S. R.; Pedersen, Søren Damkiær; Høiby, Niels; Johansen, Helle Krogh; Molin, Søren; Jelsbak, Lars.

    In: Antimicrobial Agents and Chemotherapy, Vol. 56, No. 8, 2012, p. 4519-4521.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  43. Published

    Overnight Control of Blood Glucose in People with Type 1 Diabetes. / Boiroux, Dimitri; Duun-Henriksen, Anne Katrine; Schmidt, Signe; Nørgaard, Kirsten; Madsbad, Sten; Skyggebjerg, Ole; Jensen, Peter Ruhdal; Poulsen, Niels Kjølstad; Madsen, Henrik; Jørgensen, John Bagterp.

    In: Proceedings of the 8th IFAC Symposium on Biological and Medical Systems. 2012.

    Publication: Research - peer-review › Article in proceedings – Annual report year: 2012

  44. Published

    Physiological characterisation of Yarrowia lipolytica yields new features of the strain. / Holt, Philippe; Thykær, Jette; Workman, Mhairi.

    In: New Biotechnology, Vol. 29S, 2012, p. S212.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  45. Published

    Physiological heterogeneities in microbial populations and implications for physical stress tolerance. / Carlquist, Magnus; Fernandes, Rita Lencastre; Helmark, Søren; Heins, Anna-Lena; Lundin, Luisa; Sorensen, Søren J.; Gernaey, Krist ; Eliasson Lantz, Anna.

    In: Microbial Cell Factories, Vol. 11, No. 94, 2012.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  46. Published

    Polyamines Are Required for Virulence in Salmonella enterica Serovar Typhimurium. / Jelsbak, Lotte; Thomsen, Line Elnif; Wallrodt, Inke; Jensen, Peter Ruhdal; Olsen, John Elmerdahl.

    In: P L o S One, Vol. 7, No. 4, 2012.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  47. Published

    Polysaccharides serve as scaffold of biofilms formed by mucoid Pseudomonas aeruginosa.. / Yang, Liang; Hengzhuang, Wang; Wu, Hong; Pedersen, Søren Damkiær; Jochumsen, Nicholas; Song, Zhijun; Givskov, Michael Christian; Høiby, Niels; Molin, Søren.

    In: F E M S Immunology and Medical Microbiology, Vol. 65, No. 2, 2012, p. 366-376.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  48. Published

    Saccharomyces cerevisiae : a model to uncover molecular mechanisms for yeast biofilm biology.. / Bojsen, Rasmus K; Andersen, Kaj Scherz; Regenberg, Birgitte.

    In: F E M S Immunology and Medical Microbiology, Vol. 65, No. 2, 2012, p. 169-182.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  49. Published

    SarA is a negative regulator of Staphylococcus epidermidis biofilm formation. / Martin, Christer; Heinze, C.; Busch, M.; Franke, G.; Hentschke, M.; Dühring, Sara Bayard; Buettner, H.; Kotasinska, M.; Wischnewski, V.; Buck, F.; Molin, Søren; Otto, Michael; Rohde, Henning.

    In: International Journal of Medical Microbiology, Vol. 302, 2012.

    Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2012

  50. Published

    sarA negatively regulates Staphylococcus epidermidis biofilm formation by modulating expression of 1 MDa extracellular matrix binding protein and autolysis‐dependent release of eDNA. / Christner, Martin; Heinze, Constanze; Busch, Michael; Franke, Gefion; Hentschke, Moritz; Dühring, Sara Bayard; Büttner, Henning; Kotasinska, Marta; Wischnewski, Victoria; Kroll, Gesche; Buck, Friedrich; Molin, Søren; Otto, Michael; Rohde, Holger.

    In: Molecular Microbiology, Vol. 86, No. 2, 2012, p. 394-410.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  51. Published

    snpTree - a web-server to identify and construct SNP trees from whole genome sequence data.. / Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund; Rundsten, Carsten Friis; Rasmussen, Simon; Aarestrup, Frank Møller.

    In: B M C Genomics, Vol. 13, No. Suppl 7, 2012, p. S6.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  52. Published

    Staphylococcus epidermidis recovered from indwelling catheters exhibit enhanced biofilm dispersal and "self-renewal" through downregulation of agr. / Dai, Lu; Yang, Liang; Parsons, Chris; Findlay, Victoria J.; Molin, Søren; Qin, Zhiqiang.

    In: B M C Microbiology, Vol. 12, 2012, p. Article No.: 102.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

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