Department of Systems Biology

  1. 2015
  2. E-pub ahead of print

    Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways.. / Ninel Hansen, Stine; Westergaard, David ; Borg Houlberg Thomsen, Mathilde; Vistesen, Mette; Nguyen Do, Khoa; Fogh, Louise; Belling, Kirstine C.; Wang, Jun; Yang, Huanming; Gupta, Ramneek; Ditzel, Henrik Jørn; Moreira, José ; Brünner, Nils; Stenvang, Jan; Schrohl, Anne-Sofie.

    In: Tumor Biology, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  3. Accepted

    Acylcarnitine plasma levels suggest incomplete mitochondrial fatty acid oxidation in young, healthy men with low birth weight. / Ribel-Madsen, Amalie; Ribel-Madsen, Rasmus; Brøns, Charlotte; B. Newgard, Christopher; Vaag, Allan; Hellgren, Lars.

    2015. Abstract from 28th Nordic Lipid Symposium, Reykjavik, Iceland.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  4. E-pub ahead of print
  5. Published

    Airway Mucosal Immune-suppression in Neonates of Mothers Receiving A(H1N1)pnd09 Vaccination During Pregnancy. / Pedersen, Susanne Brix; Bischoff, Anne L.; Folsgaard, Nilofar V.; Vissing, Nadja H.; Birch, Sune; Bisgaard, Hans .

    In: Pediatric Infectious Disease Journal, Vol. 34, No. 1, 2015, p. 84-90.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  6. Published

    Amino acid and glucose metabolism in fed-batch CHO cell culture affects antibody production and glycosylation. / Fan, Yuzhou; Jimenez Del Val, Ioscani; Müller, Christian; Wagtberg Sen, Jette; Rasmussen, Søren Kofoed; Kontoravdi, Cleo; Weilguny, Dietmar; Andersen, Mikael Rørdam.

    In: Biotechnology and Bioengineering, Vol. 112, No. 3, 2015, p. 521-535.

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

  7. Published
  8. Published

    A novel approach for studying programmed cell death in living plant tissues. / Mark, Christina; Dufva, Martin (Supervisor); Finnie, Christine (Supervisor).

    Kgs. Lyngby : Technical University of Denmark (DTU), 2015. 140 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2015

  9. Published

    A novel common variant in DCST2 is associated with length in early life and height in adulthood. / van der Valk, Ralf J.P.; Kreiner-Møller, Eskil; Kooijman, Marjolein N.; Guxens, Mònica; Stergiakouli, Evangelia; Sääf, Annika; Bradfield, Jonathan P.; Geller, Frank; Hayes, M. Geoffrey; Cousminer, Diana L.; Bisgaard, Hans; Chawes, Bo; Stokholm, Jakob; Waage, Johannes; Eriksen, Patrick; Sevelsted, Astrid; Melbye, Mads; Feenstra, Bjarke; Pers, Tune Hannes; Bønnelykke, Klaus.

    In: Human Molecular Genetics, Vol. 24, No. 4, 2015, p. 1155-1168.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  10. Published

    Archival Bone Marrow Samples: Suitable for Multiple Biomarker Analysis?. / Lund, Bendik; Najmi, A. Laeya; Wesolowska, Agata; Landsem, Veslemoy M.; Rasmussen, Kirsten K.; Borst, Louise; Gupta, Ramneek; Schmiegelow, Kjeld; Klungland, Helge.

    In: Applied Immunohistochemistry & Molecular Morphology, Vol. 23, No. 1, 2015, p. 71-77.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  11. Published
  12. Published
  13. Published
  14. Published

    Aspiperidine oxide, a piperidine N-oxide from the filamentous fungus Aspergillus indologenus. / Petersen, Lene Maj; Kildgaard, Sara; Jaspars, Marcel; Larsen, Thomas Ostenfeld.

    In: Tetrahedron Letters, Vol. 56, No. 14, 2015, p. 1847-1850.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  15. Published

    Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides. / Oehlenschlæger, Christian Berg; Løvgreen, Monika Nøhr; Reinauer, Eva; Lehtinen, Emilia; Pind, Marie-Louise Lindberg; Harris, Pernille; Martinussen, Jan; Willemoës, Martin.

    In: Applied and Environmental Microbiology, Vol. 81, No. 10, 2015, p. 3395-3404.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  16. Published

    Bioinformatics prediction of swine MHC class I epitopes from Porcine Reproductive and Respiratory Syndrome Virus. / Welner, Simon; Nielsen, Morten; Lund, Ole; Jungersen, Gregers; Larsen, Lars Erik.

    2015. Abstract from Keystone Symposia on Molecular and Cellular Biology: Accelerating life science discovery, Keystone, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  17. Published

    Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens. / Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian Bille; Ferguson, Gayle C.; Desprat, Nicolas; Buffing, Marieke F.; Sauer, Uwe; Beaumont, Hubertus J. E.; Martinussen, Jan; Kilstrup, Mogens; Rainey, Paul B.

    In: P L o S Biology, Vol. 13, No. 3, e1002109, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  18. Published

    Characterization of Alternaria strains from Argentinean blueberry, tomato, walnut and wheat. / Andersen, Birgitte; Nielsen, Kristian Fog; Fernández Pinto, Virginia; Patriarca, Andrea.

    In: International Journal of Food Microbiology, Vol. 196, 2015, p. 1-10.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  19. Published
  20. Published
  21. Published
  22. Published

    Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. / McGranahan, Nicholas; Favero, Francesco; de Bruin, Elza C.; Birkbak, Nicolai Juul; Szallasi, Zoltan Imre; Swanton, Charles.

    In: Science Translational Medicine, Vol. 7, No. 283, 283ra54, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  23. Published
  24. Published

    Complementing DIGE proteomics and DNA subarray analyses to shed light on Oenococcus oeni adaptation to ethanol in wine-simulated conditions. / Costantini, Antonella; Rantsiou, Kalliopi; Majumder, Avishek; Jacobsen, Susanne; Pessione, Enrica; Svensson, Birte; Garcia-Moruno, Emilia; Cocolin, Luca.

    In: Journal of Proteomics, Vol. 123, 2015, p. 114-127.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  25. Published

    Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a. / Schmitz-Esser, Stephan; Gram, Lone; Wagner, Martin.

    In: Genome Announcements, Vol. 3, No. 2, e00150-15, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  26. Published
  27. Published
  28. Published

    CTX-M-1 β-lactamase expression in Escherichia coli is dependent on cefotaxime concentration, growth phase and gene location.. / Kjeldsen, Thea S. B.; Overgaard, Martin; Nielsen, Søren S.; Bortolaia, Valeria; Jelsbak, Lotte; Sommer, Morten Otto Alexander; Guardabassi, Luca; Olsen, John E.

    In: Journal of Antimicrobial Chemotherapy, Vol. 70, No. 1, 2015, p. 62-70.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  29. Published

    Current state of genome-scale modeling in filamentous fungi. / Brandl, Julian; Andersen, Mikael Rørdam.

    In: Biotechnology Letters, Vol. 37, No. 6, 2015, p. 1131-1139.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  30. Published

    Defining the microbial effluxome in the content of the host-microbiome interaction. / Ioannidis, Anastasios; Magana, Maria; Bologa, Cristian G.; Oprea, Tudor I.; Paulsen, Ian T.; Tegos, George P.

    In: Frontiers in Pharmacology, Vol. 6, 31, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  31. Published

    Dereplication-guided isolation of depsides thielavins S-T and lecanorins D-F from the endophytic fungus Setophoma sp.. / de Medeiros, Livia S.; Abreu, Lucas M.; Nielsen, Anita; Ingmer, Hanne; Larsen, Thomas Ostenfeld; Nielsen, Kristian Fog; Rodrigues-Filho, Edson.

    In: Phytochemistry, Vol. 111, 2015, p. 154-162.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  32. Published

    Developing a Molecular Roadmap of Drug-Food Interactions. / Jensen, Kasper; Ni, Yueqiong; Panagiotou, Gianni; Kouskoumvekaki, Irene.

    In: P L o S Computational Biology (Online), Vol. 11, No. 2, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  33. Published
  34. Published
  35. Published

    Dynamic single-cell analysis of Saccharomyces cerevisiae under process perturbation: Comparison of different methods for monitoring the intensity of population heterogeneity. / Delvigne, Frank; Baert, Jonathan; Gofflot, Sébastien; Lejeune, Annick; Telek, Samuel; Johanson, Ted; Eliasson Lantz, Anna.

    In: Journal of Chemical Technology and Biotechnology, Vol. 90, No. 2, 2015, p. 314–323.

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

  36. Published

    Electrochemical detection of pyocyanin as a biomarker for bacterial infections. / Al Atraktchi, Fatima Al-Zahraa; Svendsen, Winnie Edith; Breum Andersen, Sandra; Molin, Søren; Johansen, Helle Krogh.

    2015. Poster session presented at 25th European Society of Clinical Microbiology and Infectious Diseases, Copenhagen, Denmark.

    Publication: ResearchPoster – Annual report year: 2015

  37. Published

    Establishment and characterization of models of chemotherapy resistance in colorectal cancer: Towards a predictive signature of chemoresistance. / Jensen, Niels F.; Stenvang, Jan; Beck, Mette Kristina; Hanáková, Barbora; Belling, Kirstine C.; Nguyen Do, Khoa; Viuff, Birgitte; Nygård, Sune B.; Gupta, Ramneek; Rasmussen, Mads H.; Tarpgaard, Line S.; Hansen, Tine P.; Budinská, Eva; Pfeiffer, Per; Bosman, Fred; Tejpar, Sabine; Roth, Arnaud; Delorenzi, Mauro; Andersen, Claus L.; Rømer, Maria U.; Brünner, Nils; Moreira, José M.A.

    In: Molecular Oncology, Vol. 9, No. 6, 2015, p. 1169-1185.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  38. Published

    Evidence of interactions between aroma compounds and the CB1 receptor opens new routes for regulation of food intake. / Le Bon, Anne-Marie; Audouze, Karine Marie Laure; Taboureau, Olivier ; Burton, Kathryn; Belloir, Christine; Desmetz, Catherine; Brunak, Søren; Guichard, Elisabeth; Tromelin, Anne.

    In: Chemical Senses, Vol. 40, No. 3, 2015, p. 280-280.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2015

  39. Published

    Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients. / Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Jelsbak, Lars; Molin, Søren; Johansen, Helle Krogh.

    In: Future Microbiology, Vol. 10, No. 4, 2015, p. 599-611.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  40. Published
  41. E-pub ahead of print
  42. Published

    Extended spectrum beta-lactamase-producing Escherichia coli forms filaments as an initial response to cefotaxime treatment. / Kjeldsen, Thea S. B.; Sommer, Morten Otto Alexander; Olsen, John E.

    In: B M C Microbiology, Vol. 15, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  43. Published

    Gene expression analysis identifies global gene dosage sensitivity in cancer. / Fehrmann, Rudolf S. N.; Karjalainen, Juha M.; Krajewska, Malgorzata; Westra, Harm-Jan; Maloney, David; Simeonov, Anton; Pers, Tune Hannes; Hirschhorn, Joel N.; Jansen, Ritsert C.; Schultes, Erik A.; van Haagenl, Herman H. H. B. M.; de Vries, Elisabeth G. E.; Meerman, Gerard J. te; Wijmenga, Cisca; van Vugt, Marcel A. T. M.; Franke, Lude.

    In: Nature Genetics, Vol. 47, No. 2, 2015, p. 115-125.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  44. Published

    Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria. / Machado, Henrique; Sonnenschein, Eva; Melchiorsen, Jette; Gram, Lone.

    In: B M C Genomics, Vol. 16, 158, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  45. Published

    Genomic Dissection of Travel-Associated Extended-Spectrum-Beta-Lactamase-Producing Salmonella enterica Serovar Typhi Isolates Originating from the Philippines: a One-Off Occurrence or a Threat to Effective Treatment of Typhoid Fever?. / Hendriksen, Rene S.; Leekitcharoenphon, Pimlapas; Mikoleit, Matthew; Jensen, Jacob Dyring; Kaas, Rolf Sommer; Roer, Louise; Joshi, Heena B.; Pornruangmong, Srirat; Pulsrikarn, Chaiwat; Gonzalez-Aviles, Gladys D.; Reuland, E. Ascelijn; Al Naiemi, Nashwan; Wester, Astrid Louise; Aarestrup, Frank Møller; Hasman, Henrik.

    In: Journal of Clinical Microbiology, Vol. 53, No. 2, 2015, p. 677-680.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  46. Published

    Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients. / Wesolowska, Agata; Borst, L.; Dalgaard, Marlene Danner; Yadav, Rachita; Rasmussen, K. K. ; Wehner, Peder Skov; Rasmussen, M.; Ørntoft, T.F.; Nordentoft, I.; Koehler, R.; Sicheritz-Pontén, Thomas; Gautier, Laurent; Brunak, Søren; Gupta, Ramneek.

    In: Leukemia, Vol. 29, 2015, p. 297-303.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  47. Published

    Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012.. / Hendriksen, Rene S.; Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Lukwesa-Musyani, Chileshe; Tambatamba, Bushimbwa; Mwaba, John; Kalonda, Annie; Nakazwe, Ruth; Kwenda, Geoffrey; Jensen, Jacob Dyring; Svendsen, Christina Aaby; Dittmann, Karen K.; Kaas, Rolf Sommer; Cavaco, Lina; Aarestrup, Frank Møller; Hasman, Henrik; Mwansa, James C. L.

    In: Journal of Clinical Microbiology, Vol. 53, No. 1, 2015, p. 262-272.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  48. Published
  49. Published
  50. Published

    Gliadin affects glucose homeostasis and intestinal metagenome in C57BL6 mice fed a high-fat diet. / Zhang, Li; Hansen, Axel Kornerup; Bahl, Martin Iain; Hansen, Camilla Hartmann Friis; Andersen, Daniel; Pedersen, Susanne Brix; Hellgren, Lars; Licht, Tine Rask.

    2015. Abstract from Keystone Symposia - Gut Microbiota Modulation of Host Physiology: The Search for Mechanism, Keystone, Colorado, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  51. Published

    Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. / Favero, Francesco; McGranahan, N.; Salm, M.; Birkbak, Nicolai Juul; Sanborn, J. Z.; Benz, S. C.; Becq, J.; Peden, J. F.; Kingsbury, Z.; Grocok, R. J.; Eklund, Aron Charles; Szallasi, Zoltan Imre.

    In: Annals of Oncology, Vol. 26, No. 5, 2015, p. 880-887.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

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