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

  28. Published

    Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain. / Zhang, Yiming; Liu, Guodong; Engqvist, Martin K. M.; Krivoruchko, Anastasia; Hallström, Björn M.; Chen, Yun; Siewers, Verena; Nielsen, Jens.

    In: Microbial Cell Factories, Vol. 14, 116, 2015.

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

  29. Published

    A global reference for human genetic variation. / Auton, Adam; Abecasis, Goncalo R.; M. Altshuler, David; M. Durbin, Richard; R. Bentley, David; Chakravarti, Aravinda; G. Clark, Andrew; Donnelly, Peter; E. Eichler, Evan; Flicek, Paul; Wang, Jun; Feng, Qiang; Fang, Xiaodong; Guo, Xiaosen; Jian, Min; Jiang, Hui; Liu, Xiao; Fang, Lin; Cao, Hongzhi; Jespersen, Jakob Berg.

    In: Nature, Vol. 526, 2015, p. 68-74.

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

  30. Published
  31. 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

  32. Published

    AllelicImbalance: An R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. / Gådin, Jesper R.; van't Hooft, Ferdinand M.; Eriksson, Per; Folkersen, Lasse.

    In: BMC Bioinformatics, Vol. 16, No. 194, 2015.

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

  33. 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

  34. Published

    A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules. / Pandya, Mital; Rasmussen, Michael; Hansen, Andreas; Nielsen, Morten; Buus, Søren; Golde, William; Barlow, John.

    In: Immunogenetics, Vol. 67, No. 11-12, 2015, p. 691-703.

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

  35. Published

    Amphibian antimicrobial peptide fallaxin analogue FL9 affects virulence gene expression and DNA replication in Staphylococcus aureus. / Gottschalk, Sanne; Gottlieb, Caroline Trebbien; Vestergaard, Martin; Hansen, Paul R.; Gram, Lone; Ingmer, Hanne; Thomsen, Line Elnif.

    In: Journal of Medical Microbiology, Vol. 64, No. 12, 2015, p. 1504-1513.

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

  36. Published

    A multi-pronged investigation into the effect of glucose starvation and culture duration on fed-batch CHO cell culture. / Fan, Yuzhou; Jimenez Del Val, Ioscani; Müller, Christian; Lund, Anne Mathilde; Wagtberg Sen, Jette; Rasmussen, Søren Kofoed; Kontoravdi, Cleo; Baycin-Hizal, Deniz; Betenbaugh, Michael J.; Weilguny, Dietmar; Andersen, Mikael Rørdam.

    In: Biotechnology and Bioengineering (Print), Vol. 112, No. 10, 2015, p. 2172-2184.

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

  37. Published

    Analysis artefacts of the INS-IGF2 fusion transcript. / Wernersson, Rasmus; Frogne, Thomas; Rescan, Claude; Hansson, Lena; Bruun, Christine; Grønborg, Mads; Jensen, Jan Nygaard; Madsen, Ole Dragsbæk.

    In: B M C Molecular Biology, Vol. 16, No. 13, 2015.

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

  38. Published

    Analysis of gene essentiality in Escherichia coli across strains and growth conditions. / Bonde, Ida; Lennen, Rebecca; Cardoso, Joao; Koza, Anna; Herrgard, Markus.

    2015. Abstract from First Annual Danish Bioinformatics Conference, Odense, Denmark.

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

  39. Published
  40. Published

    Analysis of Surface Binding Sites (SBS) within GH62, GH13, and GH77. / Wilkens, Casper; Cockburn, Darrell; Andersen, Susan; Ole Petersen, Bent; Ruzanski, Christian; A. Field, Robert; Hindsgaul, Ole; Nakai, Hiroyuki; McCleary, Barry; M. Smith, Alison; Abou Hachem, Maher ; Svensson, Birte.

    In: Journal of Applied Glycoscience, Vol. 62, No. 3, 2015, p. 87-93.

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

  41. 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

  42. 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

  43. Published

    A novel in vitro wound biofilm model used to evaluate low-frequency ultrasonic-assisted wound debridement. / Crone, S.; Garde, Christian; Bjarnsholt, T.; Alhede, Morten.

    In: Journal of Wound Care, Vol. 24, No. 2, 2015, p. 64-72.

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

  44. Published

    Applying genetics in inflammatory disease drug discovery. / Folkersen, Lasse; Biswas, Shameek; Frederiksen, Klaus Stensgaard; Keller, Pernille; Fox, Brian; Fleckner, Jan.

    In: Drug Discovery Today, Vol. 20, No. 10, 2015, p. 1176-1181.

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

  45. Published

    A proteomic study of the regulatory role for STAT-1 in cytokine-induced beta-cell death. / Rondas, Dieter; Gudmundsdottir, Valborg; D’Hertog, Wannes; Crèvecoeur, Inne; Waelkens, Etienne; Brunak, Søren; Mathieu, Chantal; Overbergh, Lut.

    In: Proteomics - Clinical Applications, Vol. 9, No. 9-10, 2015, p. 938-952.

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

  46. 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

  47. Published
  48. Published

    A retrospective metagenomics approach to studying Blastocystis. / Andersen, Lee O'Brien; Bonde, Ida; Nielsen, Henrik Bjørn; Stensvold, Christen Rune.

    In: F E M S Microbiology Reviews, Vol. 91, No. 7, fiv072, 2015.

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

  49. Published
  50. Published
  51. 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

  52. Published

    A taxonomic revision of the Wallemia sebi species complex. / Jančič, Sašo; Nguyen, Hai D. T.; Frisvad, Jens Christian; Zalar, Polona; Schroers, Hans-Josef; Seifert, Keith A.; Gunde-Cimerman, Nina.

    In: P L o S One, Vol. 10, No. 5, e0125933, 2015.

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

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