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. Published

    Draft genome sequence and chemical profiling of Fusarium langsethiae, an emerging producer of type A trichothecenes. / Lysøe, Erik; Frandsen, Rasmus John Normand; Divon, Hege H.; Terzi, Valeria; Orrù, Luigi; Lamontanara, Antonella; Kolseth, Anna Karin; Nielsen, Kristian Fog; Thrane, Ulf.

    In: International Journal of Food Microbiology, Vol. 221, 2016, p. 29-36.

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

  7. 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

  8. Published

    Effect of Vitamin D3 Supplementation During Pregnancy on Risk of Persistent Wheeze in the Offspring A Randomized Clinical Trial : A Randomized Clinical Trial. / Chawes, Bo L.; Bonnelykke, Klaus; Stokholm, Jakob; Vissing, Nadja H.; Bjarnadottir, Elin; Schoos, Ann-Marie M.; Wolsk, Helene M.; Pedersen, Tine Marie; Vinding, Rebecca K.; Thorsteinsdottir, Sunna; Arianto, Lambang; Hallas, Henrik W.; Heickendorff, Lene; Pedersen, Susanne Brix; Rasmussen, Morten A.; Bisgaard, Hans Flinker.

    In: J A M A: The Journal of the American Medical Association, Vol. 315, No. 4, 2016, p. 353-361.

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

  9. 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

  10. E-pub ahead of print

    Fish oil supplementation from 9 to 18 months of age affects the insulin-like growth factor axis in a sex-specific manner in Danish infants. / Damsgaard, Camilla T.; Harsløf, Laurine B. S.; Andersen, Anders D.; Hellgren, Lars; Michaelsen, Kim F.; Lauritzen, Lotte.

    In: British Journal of Nutrition, 2016.

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

  11. Published

    Gapped sequence alignment using artificial neural networks: application to the MHC class I system. / Andreatta, Massimo; Nielsen, Morten.

    In: Bioinformatics (Online), Vol. 32, No. 4, btv639, 2016, p. 511-517.

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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. Accepted/In press

    Siblings Promote a Type 1/Type 17-oriented immune response in the airways of asymptomatic neonates. / Wolsk, Helene Mygind; Chawes, Bo L.; Følsgaard, Nilofar V.; Rasmussen, Morten A.; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: Allergy, 2016.

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

  21. 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

  22. 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

  23. Published

    The elusive endogenous adipogenic PPARγ agonists: Lining up the suspects. / Hallenborg, Philip; Petersen, Rasmus K.; Kouskoumvekaki, Irene; Newman, John W.; Madsen, Lise; Kristiansen, Karsten.

    In: Progress in Lipid Research, Vol. 61, 2016, p. 149-162.

    Publication: Research - peer-reviewReview – Annual report year: 2016

  24. E-pub ahead of print

    The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. / Trolle, Thomas; McMurtrey, Curtis P.; Sidney, John; Bardet, Wilfried; Osborn, Sean C.; Kaever, Thomas; Sette, Alessandro; Hildebrand, William H.; Nielsen, Morten; Peters, Bjoern.

    In: Journal of Immunology, 2016, p. 1480-1487.

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

  25. 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

  26. 2015
  27. 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

  28. 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

  29. E-pub ahead of print
  30. 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

  31. 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

  32. 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

  33. Published
  34. 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

  35. 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

  36. 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

  37. Published
  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. Published
  47. 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

  48. 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

  49. 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

  50. Published

    A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. / Petrovics, Gyorgy; Li, Hua; Stümpel, Tanja; Tan, Shyh-Han; Young, Denise; Katta, Shilpa; Li, Qiyuan; Ying, Kai; Klocke, Bernward; Ravindranath, Lakshmi; Kohaar, Indu; Chen, Yongmei; Ribli, Dezső; Grote, Korbinian; Zou, Hua; Cheng, Joseph; Dalgard, Clifton L.; Zhang, Shimin; Csabai, Istvan; Kagan, Jacob; Takeda, David; Loda, Massimo; Scherf, Matthias; Seifert, Martin; Gaiser, Timo; McLeod, David G.; Szallasi, Zoltan Imre; Ebner, Reinhard; Werner, Thomas; Sesterhenn, Isabell A; Freedman, Matthew; Dobi, Albert; Srivastava, Shiv.

    In: EBioMedicine, Vol. 2, No. 12, 2015, p. 1957-1964.

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

  51. 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

  52. 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

  53. 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

  54. 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

  55. Published
  56. 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

  57. Published
  58. Published
  59. 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

  60. 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

  61. Published

    Automated benchmarking of peptide-MHC class I binding predictions. / Trolle, Thomas; Metushi, Imir G.; Greenbaum, Jason; Kim, Yohan; Sidney, John; Lund, Ole; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten.

    In: Bioinformatics, Vol. 31, No. 13, 2015, p. 2174-2181.

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

  62. 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

  63. Published

    Bacteriocin-mediated competition in cystic fibrosis lung infections. / Ghoul, Melanie; West, Stuart A.; Johansen, Helle Krogh; Molin, Søren; Harrison, Odile B.; Maiden, Martin C. J.; Jelsbak, Lars; Bruce, John B.; Griffin, Ashleigh S.

    In: Royal Society of London. Proceedings B. Biological Sciences, Vol. 282, No. 1814, 20150972, 2015.

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

  64. Published
  65. Published

    Bioactivities by a crude extract from the Greenlandic Pseudomonas sp. In5 involves the nonribosomal peptides, nunamycin and nunapeptin. / Frydenlund Michelsen, Charlotte; Jensen, Helle; Venditto, Vincent J.; Hennessy, Rosanna C.; Stougaard, Peter.

    In: PeerJ, Vol. 3, e1476, 2015.

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

  66. 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

  67. Published

    Biosensor-based genome screening platform for the production of Biosynthetic Precursors and coFactors in E. coli.. / Cardinale, Stefano; Ye, Lumeng; Sommer, Morten.

    Book of Abstracts. DTU's Sustain Conference 2015. Lyngby : Technical University of Denmark, 2015. B-14.

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

  68. 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

  69. Published

    Carbon Source Influences Population Heterogeneity In Pseudomonas Putida Kt2440 Biofilms. / Juel Christensen, Anne-Mette; Sternberg, Claus; Molin, Søren.

    The Danish Microbiological Society Annual Congress 2015: Programme & Abstracts. Copenhagen, 2015. p. 41-41.

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

  70. Published

    CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.. / Spisák, Sándor; Lawrenson, Kate; Fu, Yanfang; Csabai, Istvan; Cottman, Rebecca T.; Seo, Ji-Heui; Haiman, Christopher; Han, Ying; Lenci, Romina; Li, Qiyuan; Tisza, Viktória; Szallasi, Zoltan Imre; Herbert, Zachery T.; Chabot, Matthew; Pomerantz, Mark; Solymosi, Norbert; Gayther, Simon A.; Joung, J. Keith; Freedman, Matthew L.

    In: Nature Medicine, Vol. 21, No. 11, 2015, p. 1357-1363.

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

  71. Published

    Characterising interactions between alginates of different sizes and beta-lactoglobulin. / Stender, Emil G. P.; Khan, Sanaullah; Mäkinen, Outi E.; Almdal, Kristoffer; Westh, Peter; Ibsen, Richard; Abou Hachem, Maher ; Svensson, Birte.

    In: Protein Science, Vol. 24, No. S1, PL-070, 2015, p. 303-303.

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

  72. 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

  73. Published

    Characterization of Chinese Hamster Ovary Cells Producing Coagulation Factor VIII Using Multi-omics Tools. / Kaas, Christian Schrøder; Andersen, Mikael Rørdam (Supervisor); Kristensen, Claus (Supervisor); Bolt, Gert (Supervisor).

    Kgs. Lyngby : Department of Systems Biology, DTU, 2015. 219 p.

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

  74. Published
  75. Published
  76. Published

    Chemical intolerance. / Dantoft, Thomas Meinertz; Andersson, Linus; Nordin, Steven; Skovbjerg, Sine.

    In: Current Rheumatology Reviews, Vol. 11, No. 2, 2015, p. 167-184.

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

  77. Published

    Chemodiversity in the genus Aspergillus. / Frisvad, Jens Christian; Larsen, Thomas Ostenfeld.

    In: Applied Microbiology and Biotechnology, Vol. 99, No. 19, 2015, p. 7859-7877.

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

  78. Published

    Chitin Degradation In Marine Bacteria. / Paulsen, Sara; Machado, Henrique; Gram, Lone.

    The Danish Microbiological Society Annual Congress 2015: Programme & Abstracts. Copenhagen, 2015. p. 65-66.

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

  79. Published
  80. Published

    Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. / Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Laroche, Jérôme; Larose, Stéphane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Jelsbak, Lars; Thrane, Sandra Wingaard.

    In: Frontiers in Microbiology, Vol. 6, 1036, 2015.

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

  81. 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

  82. Published
  83. Published
  84. Published
  85. Published

    Comparative Evaluation of the Antimicrobial Activity of Different Antimicrobial Peptides against a Range of Pathogenic Bacteria. / Ebbensgaard, Anna Elisabeth; Mordhorst, Hanne; Overgaard, Michael Toft; Nielsen, Claus Gyrup; Aarestrup, Frank Møller; Hansen, Egon Bech; Mergaert, Peter (Editor).

    In: P L o S One, Vol. 10, No. 12, e0144611, 2015.

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

  86. 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

  87. 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

  88. Published

    Continuous Exposure Of Vibrio Anguillarum To Tropodithietic Acid: Genetic Changes And Influence On Virulence. / Rasmussen, Bastian Barker; D'Alvise, Paul; Grotkjær, Torben; Bentzon-Tilia, Mikkel; Gram, Lone.

    The Danish Microbiological Society Annual Congress 2015: Programme & Abstracts. Copenhagen, 2015. p. 72-72.

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

  89. Published
  90. Published

    Convolutional LSTM Networks for Subcellular Localization of Proteins. / Sønderby, Søren Kaae; Sønderby, Casper Kaae; Nielsen, Henrik; Winther, Ole.

    Algorithms for Computational Biology: Second International Conference, AlCoB 2015, Mexico City, Mexico, August 4-5, 2015, Proceedings. ed. / Adrian-Horia Dediu; Francisco Hernández-Quiroz; Carlos Martín-Vide; David A. Rosenblueth. Vol. 9199 Springer International Publishing, 2015. p. 68-80 (Lecture Notes in Computer Science).

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

  91. Published

    Convolutional LSTM Networks for Subcellular Localization of Proteins. / Nielsen, Henrik; Sønderby, Søren Kaae; Sønderby, Casper Kaae; Winther, Ole.

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

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

  92. Published

    Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction. / Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin; Orton, Richard J; Blome, Sandra; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun.

    In: P L o S One, Vol. 10, No. 10, e0140912, 2015.

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

  93. Published
  94. 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

  95. 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

  96. Published

    Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. / Santos Delgado, Alberto; Wernersson, Rasmus; Jensen, Lars Juhl.

    In: Nucleic Acids Research, Vol. 43, No. D1, gku1092, 2015, p. D1140-D1144.

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

  97. Published

    Danger in the reef : proteome, toxicity, and neutralization of the venom of the olive sea snake, Aipysurus laevis. / Laustens, Andreas H.; Gutiérrez, José Maria; Redsted Rasmussen, Arne; Engmark, Mikael; Gravlund, Peter; Sanders, Kate L.; Lohse, Brian; Lomonte, Bruno.

    In: Toxicon, Vol. 107, No. Part B, 2015, p. 187-196.

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

  98. Published

    Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. / Udatha, D. B. R. K. Gupta; Topakas, Evangelos; Salazar, Margarita Pena; Olsson, Lisbeth; Andersen, Mikael Rørdam; Panagiotou, Gianni.

    In: B M C Systems Biology, Vol. 9, No. 77, 2015.

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

  99. Published

    Deep sequencing reveals different compositions of mRNA transcribed from the F8 gene in a panel of FVIII-producing CHO cell lines. / Kaas, Christian Schrøder; Bolt, Gert; Hansen, Jens J; Andersen, Mikael Rørdam; Kristensen, Claus.

    In: Biotechnology Journal, Vol. 10, No. 7, 2015, p. 1082-1089.

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

  100. Published

    Defining Starch Binding by Glucan Phosphatases. / Auger, Kyle; Raththagala, Madushi; Wilkens, Casper; Svensson, Birte; Gentry, Matthew.

    In: Faseb Journal, Vol. 29, No. no. 1 Supplement, LB205, 2015.

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

  101. Published

    Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells. / Ternette, Nicola; Yang, Hongbing; Partridge, Thomas; Llano, Anuska; Cedeño, Samandhy; Fischer, Roman; Charles, Philip D.; Dudek, Nadine L.; Mothe, Beatriz; Crespo, Manuel; Fischer, William M.; Korber, Bette T. M.; Nielsen, Morten; Borrow, Persephone; Purcell, Anthony W.; Brander, Christian; Dorrell, Lucy; Kessler, Benedikt M.; Hanke, Tomáš.

    In: European Journal of Immunology, Vol. 46, No. 1, 2015, p. 60-69.

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

  102. 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-reviewComment/debate – Annual report year: 2015

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