Novo Nordisk Foundation Center for Biosustainability

  1. 2014
  2. Published
  3. Published

    A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.. / Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van; O'Shea, Charlotte; Heyndrickx, Ken S.; Workman, Christopher; Vandepoele, Klaas; Skriver, Karen; De Masi, Federico.

    In: Nucleic Acids Research, Vol. 42, No. 12, 2014, p. 7681-7693.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  4. Published

    Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. / Borodina, Irina; Nielsen, Jens.

    In: Biotechnology Journal, Vol. 9, No. 5, 2014, p. 609-620.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  5. Published

    Ageing of atrazine in manure amended soils assessed by bioavailability to Pseudomonas sp. strain ADP. / Glæsner, Nadia; Bælum, Jacob; Strobel, Bjarne W.; Jacobsen, Carsten S.

    In: Biodegradation, Vol. 25, No. 2, 2014, p. 217-225.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  6. Published

    A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent. / McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A.; Naviaux, Robert K.; Barshop, Bruce A.; Palsson, Bernhard; Feist, Adam.

    In: Biotechnology and Bioengineering, Vol. 111, No. 4, 2014, p. 803-815.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  7. Published

    A new high-throughput LC-MS method for the analysis of complex fructan mixtures.. / Verspreet, Joran; Hansen, Anders Holmgaard; Dornez, Emmie; Courtin, Christophe M.; Harrison, Scott James.

    In: Analytical and Bioanalytical Chemistry, Vol. 406, No. 19, 2014, p. 4785-4788.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  8. E-pub ahead of print
  9. In press
  10. Published

    A sustainable route to produce the scytonemin precursor using Escherichia coli. / Malla, Sailesh; Sommer, Morten O. A.

    In: Green Chemistry, Vol. 16, No. 6, 2014, p. 3255-3265.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  11. Published
  12. E-pub ahead of print

    Bacterial diversity in snow on North Pole ice floes. / Hauptmann, Aviaja Zenia Edna Lyberth; Stibal, Marek ; Bælum, Jacob; Sicheritz-Pontén, Thomas; Brunak, Søren; Bowman, Jeff S.; Hansen, Lars H. ; Jacobsen, Carsten S.; Blom, Nikolaj.

    In: Extremophiles, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  13. Published

    Balanced globin protein expression and heme biosynthesis improve production of human hemoglobin in Saccharomyces cerevisiae. / Liu, Lifang; Martínez, José L.; Liu, Zihe; Petranovic, Dina; Nielsen, Jens.

    In: Metabolic Engineering, Vol. 21, 2014, p. 9-16.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  14. Published

    Biosynthesis of Phenylnannolone A, a Multidrug Resistance Reversal Agent from the Halotolerant Myxobacterium Nannocystis pusilla B150. / Bouhired, Sarah M.; Crüsemann, Max; Almeida, Celso; Weber, Tilmann; Piel, Jörn; Schäberle, Till F.; König, Gabriele M.

    In: ChemBioChem, Vol. 15, No. 5, 2014, p. 757-765.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  15. Published

    Determining the Control Circuitry of Redox Metabolism at the Genome-Scale. / Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali; Lerman, Joshua; Nagarajan, Harish; Cho, Byung-kwan; Zengler, Karsten; Palsson, Bernhard.

    In: P L o S Genetics, Vol. 10, No. 4, e1004264, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  16. Accepted

    Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides. / Bonde, Mads; Kosuri, Sriram; Genee, Hans Jasper; Sarup-Lytzen, Kira; Church, George M.; Sommer, Morten; Wang, Harris H.

    In: A C S Synthetic Biology, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  17. Accepted
  18. Published
  19. Published

    Engineering synergy in biotechnology. / Nielsen, Jens; Fussenegger, Martin; Keasling, Jay; Yup Lee, Sang; Liao, James C.; Prather, Kristala; Palsson, Bernhard.

    In: Nature Chemical Biology, Vol. 10, No. 5, 2014, p. 319-322.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  20. Published

    Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. / Cho, Byung-Kwan; Kim, Donghyuk; Knight, Eric M.; Zengler, Karsten; Palsson, Bernhard.

    In: Journal of Biology (Online), Vol. 12, 4, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  21. Published

    High-throughput screening for industrial enzyme production hosts by droplet microfluidics. / Sjostrom, Staffan L.; Bai, Yunpeng; Huang, Mingtao; Liu, Zihe; Nielsen, Jens; Jönsson, Håkan; Svahn, Helene Andersson.

    In: Lab On a Chip, Vol. 14, No. 4, 2014, p. 806-813.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  22. Published

    How to Fight Back Against Antibiotic Resistance. / Dantas, Gautam; Sommer, Morten.

    In: American Scientist, Vol. 102, No. 1, 2014, p. 42-51.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  23. Published

    Human Intestinal Cells Modulate Conjugational Transfer of Multidrug Resistance Plasmids between Clinical Escherichia coli Isolates.. / Machado, Ana Manuel; Sommer, Morten.

    In: P L o S One, Vol. 9, No. 6, 2014, p. e100739.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  24. Published

    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. / Nielsen, Henrik Bjørn; Almeida, Mathieu; Juncker, Agnieszka; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian Rafal; Gautier, Laurent; Pedersen, Anders Gorm; Emmanuelle, Le Chatelier; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer S.; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf Sommer; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Denis, Le Paslier; Pons, Nicolas; Pedersen, Oluf; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren; Tap, Julien; Tims, Sebastian; Ussery, David; Yamada, Takuji; Renault, Pierre; Sicheritz-Pontén, Thomas; Bork, Peer; Wang, Jun; Brunak, Søren; Ehrlich, S. Dusko.

    In: Nature Biotechnology, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  25. Published

    Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens. / Zhang, Tian; Tremblay, Pier-Luc; Chaurasia, Akhilesh Kumar; Smith, Jessica A.; Bain, Timothy S.

    In: Frontiers in Microbiology, Vol. 5, 245, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  26. Published

    In silico tools for the analysis of antibiotic biosynthetic pathways.. / Weber, Tilmann.

    In: International Journal of Medical Microbiology, Vol. 304, 2014, p. 230-235.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  27. Published

    Loss of Social Behaviours in Populations of Pseudomonas aeruginosa Infecting Lungs of Patients with Cystic Fibrosis. / Jiricny, Natalie; Molin, Søren; Foster, Kevin; Diggle, Stephen P.; Scanlan, Pauline D.; Ghoul, Melanie; Johansen, Helle Krogh; Santorelli, Lorenzo A.; Popat, Roman; West, Stuart A.; Griffin, Ashleigh S.

    In: P L o S One, Vol. 9, No. 1, 2014, p. Article No.: e83124.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  28. Published

    Microbiology: Barriers to the spread of resistance. / Sommer, Morten.

    In: Nature, 2014, p. 567–568.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  29. E-pub ahead of print

    MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. / Bonde, Mads; Klausen, Michael S.; Anderson, Mads Valdemar; Nilsson Wallin, Annika; Wang, Harris H.; Sommer, Morten.

    In: Nucleic Acids Research, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  30. Published
  31. Published

    Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. / King, Zachary A.; Feist, Adam.

    In: Metabolic Engineering, Vol. 24, 2014, p. 117-128.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  32. Published

    Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68. / Knuf, Christoph; Nookaew, Intawat; Remmers, Ilse; Khoomrung, Sakda; Brown, Stephen; Berry, Alan; Nielsen, Jens.

    In: Applied Microbiology and Biotechnology, Vol. 98, No. 8, 2014, p. 3517-3527.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  33. Published

    Protein network reconstruction of CHO cell secretory pathway. / Lund, Anne Mathilde; Kaas, Christian Schrøder; Kildegaard, Helene Faustrup; Kristensen, Claus; Andersen, Mikael Rørdam.

    2014. Poster session presented at CHOgenome workshop, Vienna, Austria.

    Publication: Research - peer-reviewPoster – Annual report year: 2014

  34. Published

    Secreted single‐stranded DNA is involved in the initial phase of biofilm formation by Neisseria gonorrhoeae. / Zweig, Maria; Schork, Sabine; Koerdt, Andrea; Siewering, Katja; Sternberg, Claus; Thormann, Kai; Albers, Sonja‐Verena; Molin, Søren; Does, Chris, van der.

    In: Environmental Microbiology, Vol. 16, No. 4, 2014, p. 1040-1052.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  35. Published

    Sequestration, tissue distribution and developmental transmission of cyanogenic glucosides in a specialist insect herbivore. / Zagrobelny, Mika; Olsen, Carl Erik; Pentzold, Stefan; Fürstenberg-Hägg, Joel; Jørgensen, Kirsten; Bak, Søren; Møller, Birger Lindberg; Motawia, Mohammed Saddik.

    In: Insect Biochemistry and Molecular Biology, Vol. 44, 2014, p. 44-53.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  36. E-pub ahead of print
  37. Published

    Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.. / Machado, Daniel; Herrgard, Markus.

    In: P L o S Computational Biology, Vol. 10, No. 4, e1003580, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  38. Published

    Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. / Hwang, Kyu-Sang; Kim, Hyun Uk; Charusanti, Pep; Palsson, Bernhard; Yup Lee, Sang.

    In: Biotechnology Advances, Vol. 32, No. 2, 2014, p. 255-268.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  39. Published

    The impact of bioaugmentation on dechlorination kinetics and on microbial dechlorinating communities in subsurface clay till. / Bælum, Jacob; Scheutz, Charlotte; Chambon, Julie Claire Claudia; Jensen, Christine Mosegaard; Brochmann, Rikke P.; Dennis, Philip; Laier, Troels; Broholm, Mette Martina; Bjerg, Poul Løgstrup; Binning, Philip John; Jacobsen, Carsten.

    In: Environmental Pollution, Vol. 186, 2014, p. 149-157.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  40. Published

    Trash to treasure: Production of biofuels and commodity chemicals via syngas fermenting microorganisms. / Latif, Haythem; Zeidan, Ahmad; Nielsen, Alex Toftgaard; Zengler, Karsten.

    In: Current Opinion in Biotechnology, Vol. 27, 2014, p. 79-87.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  41. Published

    Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. / Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.; Metspalu, Mait; Albrechtsen, Anders; Moltke, Ida; Rasmussen, Simon; Stafford jr., Thomas; Orlando, Ludovic Antoine Alexandre; Metspalu, Ene; Karmin, Monika; Tambets, Kristiina; Rootsi, Siiri; Mägi, Reedik; Campos, Paula; Balanovska, Elena; Balanovsky, Oleg; Khusnutdinova, Elza; Litvinov, Sergey; Osipova, Ludmila P; Fedorova, Sardana A; Voevoda, Mikhail I; Degiorgio, Michael; Sicheritz-Pontén, Thomas; Brunak, Søren; Demeshchenko, Svetlana; Kivisild, Toomas; Villems, Richard; Nielsen, Rasmus; Jakobsson, Mattias; Willerslev, Eske.

    In: Nature, Vol. 505, No. 7481, 2014, p. 87–91.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  42. 2013
  43. Published
  44. Published

    Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose. / Hong, Kuk-Ki; Nielsen, Jens.

    In: Metabolic Engineering, Vol. 16, No. 1, 2013, p. 78-86.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  45. Published

    Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks. / Chen, Yun; Nielsen, Jens.

    In: Current Opinion in Biotechnology, Vol. 24, No. 6, 2013, p. 965-972.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  46. Published

    Amphipol trapping of a functional CYP system. / Laursen, Tomas; Naur, Peter; Møller, Birger Lindberg.

    In: Biotechnology and Applied Biochemistry, Vol. 60, No. 1, 2013, p. 119-127.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  47. Published

    Anaerobic α-Amylase Production and Secretion with Fumarate as the Final Electron Acceptor in Saccharomyces cerevisiae. / Liu, Zihe; Österlund, Tobias; Hou, Jin; Petranovic, Dina; Nielsen, Jens.

    In: Applied and Environmental Microbiology, Vol. 79, No. 9, 2013, p. 2962-2967.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  48. Published

    A validated system for ligation-free USER™ -based assembly of expression vectors for mammalian cell engineering. / Lund, Anne Mathilde; Kildegaard, Helene Faustrup; Hansen, Bjarne Gram; Holm, Dorte Koefoed; Andersen, Mikael Rørdam; Mortensen, Uffe Hasbro.

    2013. Poster session presented at 23rd ESACT meeting, Lille, France.

    Publication: Research - peer-reviewPoster – Annual report year: 2013

  49. Published

    Bacterial natural transformation by highly fragmented and damaged DNA.. / Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre; Mayar, J. Victor Moreno; Rasmussen, Simon; Dahl, Tais Wittchen; Rosing, Minik Thorleif; Poole, Anthony M; Sicheritz-Pontén, Thomas; Brunak, Søren; Inselmann, Sabrina; de Vries, Johann; Wackernagel, Wilfried; Pybus, Oliver G; Nielsen, Rasmus; Johnsen, Pål Jarle; Nielsen, Kaare Magne; Willerslev, Eske.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 49, 2013, p. 19860-19865.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  50. Published

    Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. / McCloskey, Douglas; Palsson, Bernhard; Feist, Adam.

    In: Molecular Systems Biology, Vol. 9, 2013, p. 661.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  51. Published

    Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. / Klatt, Christian G.; Inskeep, William P. ; Herrgard, Markus; Jay, Zackary J. ; Rusch, Douglas B. ; Tringe, Susannah G.; Parenteau, M. Niki; Ward, DavidM.; Boomer, Sarah M.; Bryant, Donald A.; Miller, Scott R.

    In: Frontiers in Microbiology, Vol. 4, 106, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  52. Published
  53. Published

    Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae. / Liu, Zihe; Hou, Jin; Martínez, José L.; Petranovic, D.; Nielsen, Jens.

    In: Applied Microbiology and Biotechnology, Vol. 97, No. 20, 2013, p. 8955-8962.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  54. Published

    Crystal ball - 2013.. / Curtis, Tom; Daran, Jean-Marc; Pronk, Jack T; Frey, Joachim; Jansson, Janet K; Robbins-Pianka, Adam; Knight, Rob; Schnürer, Anna; Smets, Barth F.; Smid, E J; Abee, T; Vicente, Miguel; Zengler, Karsten.

    In: Microbial Biotechnology, Vol. 6, No. 1, 2013, p. 3-16.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  55. Published

    Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut. / Dantas, Gautam; Sommer, Morten; Degnan, Patrick H. ; Goodman, Andrew L.

    In: Annual Review of Microbiology, Vol. 67, 2013, p. 459-475.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  56. E-pub ahead of print

    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. / Kouskoumvekaki, Irene; Shublaq, Nour ; Brunak, Søren.

    In: Briefings in Bioinformatics, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  57. Published

    From flavors and pharmaceuticals to advanced biofuels: Production of isoprenoids in Saccharomyces cerevisiae. / Tippmann, S.; Chen, Y.; Siewers, V.; Nielsen, Jens.

    In: Biotechnology Journal, Vol. 8, No. 12, 2013, p. 1435-1444.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  58. Published

    From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. / Gaspar, Paula; Carvalho, Ana L.; Vinga, Susana; Santos, Helena; Neves, Ana Rute.

    In: Biotechnology Advances, Vol. 31, No. 6, 2013, p. 764-788.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  59. Published

    Genome-scale modeling of the protein secretory machinery in yeast. / Feizi, Amir; Österlund, Tobias; Petranovic, Dina; Bordel, Sergio; Nielsen, Jens.

    In: PloS one., Vol. 8, No. 5, 2013, p. e63284.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  60. Published

    Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa. / Gómez Lozano, María; Molin, Søren (Main supervisor); Long, Katherine (Supervisor).

    Novo Nordisk Foundation Center for Biosustainability, 2013. 176 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2013

  61. Published

    Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.. / Lewis, Nathan E; Liu, Xin; Li, Yuxiang; Nagarajan, Harish; Yerganian, George; O'Brien, Edward; Bordbar, Aarash; Roth, Anne M; Rosenbloom, Jeffrey; Bian, Chao; Xie, Min; Chen, Wenbin; Li, Ning; Baycin-Hizal, Deniz; Latif, Haythem; Förster, Jochen; Betenbaugh, Michael; Famili, Iman; Xu, Xun; Wang, Jun; Palsson, Bernhard O.

    In: Nature biotechnology, Vol. 31, 2013, p. 759-765.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  62. Published

    Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae. / Hou, Jin; Österlund, Tobias; Liu, Zihe; Petranovic, Dina; Nielsen, Jens.

    In: Applied Microbiology and Biotechnology, Vol. 97, No. 8, 2013, p. 3559-3568.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  63. Published

    Heterologous expression and purification of an active human TRPV3 ion channel. / Kol, Stefan; Braun, Christian; Thiel, Gerhard; Doyle, Declan A.; Sundström, Michael; Gourdon, Pontus; Nissen, Poul.

    In: F E B S Journal, Vol. 280, No. 23, 2013, p. 6010-6021.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  64. Published
  65. Published

    Improved production of membrane proteins in Escherichia coli by selective codon substitutions. / Nørholm, Morten H.H.; Toddo, Stephen; Virkki, Minttu T.I.; Light, Sara; von Heijne, Gunnar; Daley, Daniel O.

    In: FEBS Letters, Vol. 587, No. 15, 2013, p. 2352-2358.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  66. Published

    Influence of natural substrates and co-occurring marine bacteria on the production of secondary metabolites by Photobacterium halotolerans. / Månsson, Maria; Giobergia, Sonia; Møller, Kirsten A.; Dorrestein, Pieter C. ; Gram, Lone.

    2013. Poster session presented at 14th International Symposium on Marine Natural Products, Island of la Toja, Galicia, Spain.

    Publication: Research - peer-reviewPoster – Annual report year: 2013

  67. Published

    Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast. / Hou, Jin; Tang, Hongting; Liu, Zihe; Østerlund, Tobias; Nielsen, Jens; Petranovic, Dina.

    In: F E M S Immunology and Medical Microbiology, Vol. 14, No. 3, 2013, p. 481-494.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  68. Published

    Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. / Österlund, Tobias; Nookaew, Intawat; Bordel, Sergio; Nielsen, Jens.

    In: BMC Systems Biology, Vol. 7, No. 36, 2013, p. 36.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  69. Published

    Mathematical model of fructan biosynthesis and polymer length distribution in plants. / Rasmussen, Gitte Susanne; Thornley, John H. M.; Parsons, Anthony J.; Harrison, Scott James.

    In: Annals of Botany, Vol. 111, No. 6, 2013, p. 1219-1231.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  70. Published

    Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.. / Takacs-Vesbach, Cristina; Inskeep, William P; Jay, Zackary J; Herrgard, Markus; Rusch, Douglas B; Tringe, Susannah G; Kozubal, Mark A; Hamamura, Natsuko; Macur, Richard E; Fouke, Bruce W; Reysenbach, Anna-Louise; McDermott, Timothy R; Jennings, Ryan deM; Hengartner, Nicolas W; Xie, Gary.

    In: Frontiers in Microbiology, Vol. 4, 84, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  71. Published

    Metagenomic Analysis of the Human Gut Microbiome. / dos Santos, Marcelo Bertalan Quintanilha; Nielsen, Henrik Bjørn (Supervisor); Sicheritz-Pontén, Thomas (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 117 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2013

  72. Published

    Metagenomic species profiling using universal phylogenetic marker genes. / Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg; Izquierdo-Carrasco, Fernando; Berger, Simon A; Kultima, Jens Roat; Coelho, Luis Pedro; Arumugam, Manimozhiyan; Tap, Julien; Nielsen, Henrik Bjørn; Rasmussen, Simon; Brunak, Søren; Pedersen, Oluf; Guarner, Francisco; de Vos, Willem M; Wang, Jun; Li, Junhua; Doré, Joël; Ehrlich, S Dusko; Stamatakis, Alexandros; Bork, Peer.

    In: Nature Methods, Vol. 10, No. 12, 2013, p. 1196–1199.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  73. Published

    Microorganisms for the production of 5-hydroxytryptophan. / Knight, Eric Michael (Inventor); Zhu, Jiangfeng (Inventor); Förster, Jochen (Inventor); Luo, Hao (Inventor).

    IPC No.: C12N1/21; C12N15/53; C12N15/55. Patent No.: WO2013127914. Sep 06, 2013.

    Publication: ResearchPatent – Annual report year: 2013

  74. Published

    Microorganisms for the production of melatonin. / Knight, Eric Michael (Inventor); Zhu, Jiangfeng (Inventor); Förster, Jochen (Inventor); Luo, Hao (Inventor).

    IPC No.: C12N1/21; C12N15/53; C12N15/54. Patent No.: WO2013127915. Sep 06, 2013.

    Publication: ResearchPatent – Annual report year: 2013

  75. Published

    Multi-scale modeling for sustainable chemical production. / Zhuang, Kai; Bakshi, Bhavik R.; Herrgard, Markus.

    In: Biotechnology Journal, Vol. 8, No. 9, 2013, p. 973-984.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  76. Published

    Nucleic Acid Aptamers as Novel Class of Therapeutics to Mitigate Alzheimer's Disease Pathology. / K. Tannenberg, Rudi; Al. Shamaileh, Hadi; Lauridsen, Lasse Holm; R. Kanwar, Jagat; R. Dodd, Peter; N. Veedu, Rakesh.

    In: Current Alzheimer Research, Vol. 10, No. 4, 2013, p. 442.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  77. Published

    Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap. / King, Zachary A.; Feist, Adam.

    In: Industrial Biotechnology, Vol. 9, No. 4, 2013, p. 236.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  78. Published

    Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. / Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas; Nakjang, Sirintra; Martin Embley, T; Hirt, Robert P.

    In: Genome Biology, Vol. 14, No. 2, 2013, p. R19.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  79. Published

    Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.. / Inskeep, William P; Jay, Zackary J; Herrgard, Markus; Kozubal, Mark A; Rusch, Douglas B; Tringe, Susannah G; Macur, Richard E; Jennings, Ryan deM; Boyd, Eric S; Spear, John R; Roberto, Francisco F.

    In: Frontiers in Microbiology, Vol. 4, 2013, p. 95.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  80. Published

    Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. / Steentoft, Catharina; Vakhrushev, Sergey; Joshi, Hiren Jitendra; Kong, Yun; Vester-Christensen, Malene B; Schjoldager, Katrine T-BG; Lavrsen, Kirstine; Dabelsteen, Sally Anne Malene; Pedersen, Nis Borbye; Marcos-Silva, Lara; Gupta, Ramneek; Paul Bennett, Eric; Mandel, Ulla; Brunak, Søren; Wandall, Hans H.; Levery, Steven Bruce; Clausen, Henrik.

    In: EMBO Journal, Vol. 32, No. 10, 2013, p. 1478-1488.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  81. Published
  82. Published

    Production of 3-O-xylosyl quercetin in Escherichia coli. / Pandey, Ramesh Prasad; Malla, Sailesh; Simkhada, Dinesh; Kim, Byung-Gee; Sohng, Jae Kyung.

    In: Applied Microbiology and Biotechnology, Vol. 97, No. 5, 2013, p. 1889-1901.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  83. Published

    Production of biopharmaceutical proteins by yeast: Advances through metabolic engineering.. / Nielsen, Jens.

    In: Bioengineered Bugs, Vol. 4, No. 4, 2013, p. 207-211.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  84. Published

    Pseudomonas aeruginosa adaptation to lungs of cystic fibrosis patients leads to lowered resistance to phage and protist enemies.. / Friman, Ville-Petri; Ghoul, Melanie; Molin, Søren; Johansen, Helle Krogh; Buckling, Angus.

    In: PloS one., Vol. 8, No. 9, 2013, p. e75380.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  85. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. / Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Johnson, Philip L F; Fumagalli, Matteo; Vilstrup, Julia T; Raghavan, Maanasa; Korneliussen, Thorfinn Sand; Malaspinas, Anna Sapfo; Vogt, Josef Korbinian; Szklarczyk, Damian; Kelstrup, Christian; Vinther, Jakob; Dolocan, Andrei; Stenderup, Jesper; Velazquez, Amhed M. V.; Cahill, James; Rasmussen, Morten; Wang, Xiaoli; Min, Jiumeng; Zazula, Grant D; Seguin-Orlando, Andaine; Mortensen, Cecilie; Magnussen, Kim; Thompson, John F; Weinstock, Jacobo; Gregersen, Magnus Kristian; Røed, Knut H; Eisenmann, Véra; Rubin, Carl J; Miller, Donald C; Antczak, Douglas F; Bertelsen, Mads; Brunak, Søren; Al-Rasheid, Khaled A S; Ryder, Oliver; Andersson, Leif; Mundy, John; Krogh, Anders; Gilbert, Marcus Thomas Pius; Kjær, Kurt H.; Sicheritz-Pontén, Thomas; Jensen, Lars Juhl; Olsen, Jesper; Hofreiter, Michael; Nielsen, Rasmus; Shapiro, Beth; Wang, Jun; Willerslev, Eske.

    In: Nature, Vol. 499, 2013, p. 74-78.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  86. Published
  87. Published

    Richness of human gut microbiome correlates with metabolic markers.. / Le Chatelier, Emmanuelle; Nielsen, Trine; Qin, Junjie; Prifti, Edi; Hildebrand, Falk; Falony, Gwen; Almeida, Mathieu; Arumugam, Manimozhiyan; Batto, Jean-Michel; Kennedy, Sean; Leonard, Pierre; Li, Junhua; Burgdorf, Kristoffer; Grarup, Niels; Jørgensen, Torben; Brandslund, Ivan; Nielsen, Henrik Bjørn; Juncker, Agnieszka; dos Santos, Marcelo Bertalan Quintanilha; Levenez, Florence; Pons, Nicolas; Rasmussen, Simon; Sunagawa, Shinichi; Tap, Julien; Tims, Sebastian; Zoetendal, Erwin G; Brunak, Søren; Clément, Karine; Doré, Joël; Kleerebezem, Michiel; Kristiansen, Karsten; Renault, Pierre; Sicheritz-Pontén, Thomas; de Vos, Willem M.; Zucker, Jean-Daniel; Raes, Jeroen; Hansen, Torben; Bork, Peer; Wang, Jun; Ehrlich, S Dusko; Pedersen, Oluf.

    In: Nature, Vol. 500, No. 7464, 2013, p. 541-546.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  88. Published

    RNA-seq based expression analysis of the CHO cell protein secretion pathway. / Lund, Anne Mathilde; Kaas, Christian Schrøder; Kildegaard, Helene Faustrup; Kristensen, Claus; Andersen, Mikael Rørdam.

    2013. Poster session presented at 3rd Annual Next Generation Sequencing Asia Congress, Singapore, Singapore.

    Publication: Research - peer-reviewPoster – Annual report year: 2013

  89. Published

    Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli. / Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk; Li, Zhanwen; Godzik, Adam; Palsson, Bernhard.

    In: Science, Vol. 340, No. 6137, 2013, p. 1220-1223.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  90. Published

    Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs). / Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas; Panagiotou, Gianni.

    Systems Metabolic Engineering : Methods and Protocols. Springer, 2013. p. 409-428 (Methods in Molecular Biology, Vol. 985).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  91. Published
  92. Published

    The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology. / Kildegaard, Helene Faustrup; Baycin-Hizal, Deniz; Lewis, Nathan E.; Betenbaugh, Michael.

    In: Current Opinion in Biotechnology, Vol. 24, No. 6, 2013, p. 1102-1107.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  93. Published

    The Uses and Future Prospects of Metabolomics and Targeted Metabolite Profiling in Cell Factory Development. / Harrison, Scott James; Herrgard, Markus.

    In: Industrial Biotechnology, Vol. 9, No. 4, 2013, p. 196-202.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  94. Published

    The YNP metagenome project : Environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. / Inskeep, William P.; Jay, Zackary J.; Tringe, Susannah G.; Herrgard, Markus; B. Rusch, Douglas.

    In: Frontiers in Microbiology, Vol. 4, 67, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  95. Published

    Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels. / Caspeta, Luis; Nielsen, Jens.

    In: Biotechnology Journal, Vol. 8, No. 5, 2013, p. 534-544.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  96. Published

    Understanding the 3-hydroxypropionic acid tolerance mechanism in Saccharomyces cerevisiae. / Kildegaard, Kanchana Rueksomtawin; Juncker, Agnieszka; Hallstrom, Bjorn; Jensen, Niels Bjerg; Maury, Jerome; Nielsen, Jen; Förster, Jochen; Borodina, Irina.

    In: Yeast, Vol. 30, No. S1, 2013.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

  97. Published

    Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development.. / Imamovic, Lejla; Sommer, Morten.

    In: Science Translational Medicine, Vol. 5, No. 204, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  98. 2012
  99. Published

    A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). / Hildebrand, Falk; Ebersbach, Tine; Nielsen, Henrik Bjørn; Li, Xiaoping; Sonne, Si Brask; dos Santos, Marcelo Bertalan Quintanilha; Dimitrov, Peter; Madsen, Lise; Qin, Junjie; Wang, Jun; Raes, Jeroen; Kristiansen, Karsten; Licht, Tine Rask.

    In: B M C Genomics, Vol. 13, No. 514, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  100. 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-reviewJournal article – Annual report year: 2012

  101. Published

    A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. / Nookaew, Intawat; Papini, Marta; Pornputtapong, Natapol; Scalcinati, Gionata; Fagerberg, Linn; Uhlén, Matthias; Nielsen, Jens.

    In: Nucleic Acids Research, Vol. 40, No. 20, 2012, p. 10084-10097.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  102. 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-reviewJournal article – Annual report year: 2012

  103. Published

    Amplification and Re-Generation of LNA-Modified Libraries. / Doessing, Holger; Hansen, Lykke H.; Veedu, Rakesh N.; Wengel, Jesper; Vester, Birte.

    In: Molecules, Vol. 17, No. 11, 2012, p. 13087.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

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