Department of Systems Biology

  1. 2016
  2. Published

    Antibiotic combination therapy can select for broad-spectrum multidrug resistance in Pseudomonas aeruginosa. / Vestergaard, Martin; Paulander, Wilhelm; Marvig, Rasmus L.; Clasen, Julie; Jochumsen, Nicholas; Molin, Søren; Jelsbak, Lars; Ingmer, Hanne; Folkesson, Sven Anders.

    In: International Journal of Antimicrobial Agents, Vol. 47, 2016, p. 48-55.

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

  3. Published

    Cellulolytic and xylanolytic activities of common indoor fungi. / Andersen, Birgitte; Poulsen, Rehab; Hansen, Gustav Hammerich.

    In: International Biodeterioration and Biodegradation, Vol. 107, 2016, p. 111-116.

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

  4. Published

    Chemosensory perception, symptoms and autonomic responses during chemical exposure in multiple chemical sensitivity. / Andersson, Linus; Claeson, Anna Sara; Dantoft, Thomas Meinertz; Skovbjerg, Sine; Lind, Nina; Nordin, Steven.

    In: International Archives of Occupational and Environmental Health, Vol. 89, No. 1, 2016, p. 79-88.

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

  5. E-pub ahead of print

    Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in Drosophila melanogaster. / Tognon, Emiliana; Kobia, Francis; Busi, Ilaria; Fumagalli, Arianna; De Masi, Federico; Vaccari, Thomas.

    In: Autophagy, 2016.

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

  6. E-pub ahead of print

    Dynamics of immature mAb glycoform secretion during CHO cell culture: An integrated modelling framework. / Jimenez del Val, Ioscani; Fan, Yuzhou; Weilguny, Dietmar.

    In: Biotechnology Journal, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  7. Published

    Extrolites of Aspergillus fumigatus and Other Pathogenic Species in Aspergillus Section Fumigati. / Frisvad, Jens Christian; Larsen, Thomas Ostenfeld.

    In: Frontiers in Microbiology, Vol. 6, 1485, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  8. Published

    Glycoprofiling effects of media additives on IgG produced by CHO cells in fed-batch bioreactors. / Kildegaard, Helene Faustrup; Fan, Yuzhou; Wagtberg Sen, Jette; Larsen, Bo; Andersen, Mikael Rørdam.

    In: Biotechnology and Bioengineering (Print), Vol. 113, No. 2, 2016, p. 359-366.

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

  9. Published

    Immunogenicity of HLA Class I and II Double Restricted Influenza A-Derived Peptides. / Pedersen, Sara Ram; Christensen, Jan Pravsgaard; Buus, Søren; Rasmussen, Michael; Korsholm, Karen Smith; Nielsen, Morten; Claesson, Mogens Helweg.

    In: P L o S One, Vol. 11, No. 1, e0145629, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  10. Accepted/In press

    Propionibacterium acnes – disease causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing. / Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse; Richter, Stine Raith; Fridholm, Helena; Herrera, Jose Romero; Lund, Ole; Brunak, Søren; Gonzalez-Izarzugaza, Jose Maria; Mourier, Tobias; Nielsen, Lars Peter; Hansen, Anders Johannes.

    In: Journal of Clinical Microbiology, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  11. Published

    LOX1 inhibition with small molecules. / Gousiadou, Chryssoula; Kouskoumvekaki, Irene.

    In: Journal of Molecular Graphics and Modelling, Vol. 63, 2016, p. 99-109.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  12. Published

    MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. / Neupane, Manish; Clark, Allison P.; Landini, Serena; Birkbak, Nicolai Juul; Eklund, Aron Charles; Lim, Elgene; Culhane, Aedin C.; Barry, William T.; Schumacher, Steven E.; Beroukhim, Rameen; Szallasi, Zoltan Imre; Vidal, Marc; Hill, David E.; Silver, Daniel P.

    In: Cancer Discovery, Vol. 6, No. 1, 2016, p. 45-58.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  13. E-pub ahead of print

    Plant α-glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose. / Wilkens, Casper; Auger, Kyle D.; Anderson, Nolan T.; Meekins, David A.; Raththagala, Madushi; Abou Hachem, Maher ; Payne, Christina M.; Gentry, Matthew S.; Svensson, Birte.

    In: Febs Letters, 2016.

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

  14. E-pub ahead of print

    Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms. / Nielsen, Henrik.

    Protein Export in Gram-positive Bacteria. ed. / F. Bagnoli; R. Rappuoli. 2016. (Current Topics in Microbiology and Immunology).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2016

  15. Published

    Quantification of oxidative stress phenotypes based on high-throughput growth profiling of protein kinase and phosphatase knockouts. / Altıntaş, Ali; Martini, Jacopo; Mortensen, Uffe Hasbro; Workman, Christopher T.

    In: Fems Yeast Research, Vol. 16, No. 1, fov101, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  16. Published

    Taichunamides: Prenylated Indole Alkaloids from Aspergillus taichungensis (IBT 19404). / Kagiyama, Ippei; Kato, Hikaru; Nehira, Tatsuo; Frisvad, Jens Christian; Sherman, David H.; Williams, Robert M.; Tsukamoto, Sachiko.

    In: Angewandte Chemie (International Edition), Vol. 55, No. 3, 2016, p. 1128-1132.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  17. Accepted/In press

    T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome. / Bresciani, Anne Gøther; Paul, Sinu; Schommer, Nina; Dillon, Myles B.; Bancroft, Tara; Greenbaum, Jason; Sette, Alessandro; Nielsen, Morten; Peters, Bjoern.

    In: Immunology, 2016.

    Publication: Research - peer-reviewJournal article – Annual report year: 2016

  18. Published

    wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases. / Vazquez, Miguel; Pons, Tirso; Brunak, Søren; Valencia, Alfonso; Gonzalez-Izarzugaza, Jose Maria.

    In: Human Mutation, Vol. 37, No. 1, 2016, p. 36-42.

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

  19. 2015
  20. Published

    A catalog of the mouse gut metagenome. / Xiao, Liang; Feng, Qiang; Liang, Suisha; Sonne, Si Brask; Xia, Zhongkui; Qiu, Xinmin; Li, Xiaoping; Long, Hua; Zhang, Jianfeng; Zhang, Dongya; Liu, Chuan; Fang, Zhiwei; Chou, Joyce; Glanville, Jacob; Hao, Qin; Kotowska, Dorota; Colding, Camilla; Licht, Tine Rask; Wu, Donghai; Yu, Jun; Sung, Joseph Jao Yiu; Liang, Qiaoyi; Li, Junhua; Jia, Huijue; Lan, Zhou; Tremaroli, Valentina; Dworzynski, Piotr; Nielsen, H Bjørn; Bäckhed, Fredrik; Doré, Joël; Le Chatelier, Emmanuelle; Ehrlich, S. Dusko; Lin, John C.; Arumugam, Manimozhiyan; Wang, Jun; Madsen, Lise; Kristiansen, Karsten.

    In: Nature Biotechnology, Vol. 33, No. 10, 2015, p. 1103-1108.

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

  21. Published

    Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. / Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten.

    In: Immunogenetics, Vol. 67, No. 11-12, 2015, p. 641-650.

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

  22. E-pub ahead of print
  23. Published

    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, Vol. 36, No. 6, 2015, p. 4327-4338.

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

  24. Published

    A CRISPR/Cas9 system for genetic engineering of filamentous fungi. / Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Kogle, Martin Engelhard; Mortensen, Uffe Hasbro.

    Book of Abstracts. DTU's Sustain Conference 2015. Lyngby : Technical University of Denmark, 2015. B-16.

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

  25. Published

    A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi. / Nødvig, Christina Spuur; Nielsen, Jakob B.; Kogle, Martin Engelhard; Mortensen, Uffe Hasbro.

    In: P L o S One, Vol. 10, No. 7, e0133085, 2015.

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

  26. Published
  27. Published

    Adaptive Laboratory Evolution Of Escherichia Coli Reveals Arduous Resistance Development To A Combination Of Three Novel Antimicrobial Compounds And To The Short Amp P9-4. / Citterio, Linda; Franzyk, Henrik; Gram, Lone.

    The Danish Microbiological Society Annual Congress 2015: Programme & Abstracts. Copenhagen, 2015. p. 29-29.

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

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