Department of Systems Biology

  1. 2016
  2. Published

    A Bacteriophage-Acquired O-Antigen Polymerase (Wzyβ) from P. aeruginosa Serotype O16 Performs a Varied Mechanism Compared to Its Cognate Wzyα. / Taylor, Veronique L.; Hoage, Jesse F. J.; Thrane, Sandra Wingaard; Huszczynski, Steven M.; Jelsbak, Lars; Lam, Joseph S.

    In: Frontiers in Microbiology, Vol. 7, 393, 2016.

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

  3. Published

    A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01. / Pedersen, Lasse Eggers; Rasmussen, Michael; Harndahl, Mikkel; Nielsen, Morten; Buus, Søren; Jungersen, Gregers.

    In: Immunogenetics, Vol. 68, No. 2, 2016, p. 157-165.

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

  4. Published

    A fast and robust method for whole genome sequencing of the Aleutian Mink Disease Virus (AMDV) genome. / Hagberg, Emma Elisabeth; Krarup, Anders; Fahnøe, Ulrik; Larsen, Lars Erik; Dam-Tuxen, Rebekka; Pedersen, Anders Gorm.

    In: Journal of Virological Methods, Vol. 234, 2016, p. 43-51.

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

  5. Published

    Alcohol dehydrogenase gene ADH3 activates glucose alcoholic fermentation in genetically engineered Dekkera bruxellensis yeast. / Schifferdecker, Anna Judith; Siurkus, Juozas; Andersen, Mikael Rørdam; Jørck-Ramberg, Dorte; Ling, Zhihao; Zhou, Nerve; Blevins, James E.; Sibirny, Andriy A.; Piškur, Jure; Ishchuk, Olena P.

    In: Applied Microbiology and Biotechnology, Vol. 100, No. 7, 2016, p. 3219-3231.

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

  6. E-pub ahead of print
  7. Published

    An investigation on the application of ohmic heating of cold water shrimp and brine mixtures. / Pedersen, Søren Juhl; Feyissa, Aberham Hailu; Brøkner Kavli, Sissel Therese; Frosch, Stina.

    In: Journal of Food Engineering, Vol. 179, 2016, p. 28-35.

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

  8. 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

  9. Published

    A robust prognostic gene expression signature for early stage lung adenocarcinoma. / Krzystanek, Marcin; Moldvay, Judit; Szüts, David; Szallasi, Zoltan Imre; Eklund, Aron Charles.

    In: Biomarker Research, Vol. 4, No. 4, 2016.

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

  10. Published

    Benchtop Whole-Genome Sequencing for Identification of Nosocomial Outbreaks in Tanzania. / Sonda, Tolbert; Kumburu, Happiness; Zwetselaar, Marco van; Ahrenfeldt, Johanne; Alifrangis, Michael; Lund, Ole; Kibiki, Gibson; Aarestrup, Frank Møller.

    In: Infection Control & Hospital Epidemiology, Vol. 37, No. 5, 2016, p. 622-623.

    Publication: Research - peer-reviewComment/debate – Annual report year: 2016

  11. 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

  12. Published

    Chemical Diversity, Origin, and Analysis of Phycotoxins. / Rasmussen, Silas Anselm; Andersen, Aaron John Christian; Andersen, Nikolaj Gedsted; Nielsen, Kristian Fog; Hansen, Per Juel; Larsen, Thomas Ostenfeld.

    In: Journal of Natural Products, Vol. 79, No. 3, 2016, p. 662-673.

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

  13. 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

  14. Published

    ChemProt-3.0: a global chemical biology diseases mapping. / Kringelum, Jens Vindahl; Kjærulff, Sonny Kim; Brunak, Søren; Lund, Ole; Oprea, Tudor I.; Taboureau, Olivier .

    In: Database, Vol. 2016, bav123, 2016.

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

  15. Published

    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, Vol. 12, No. 3, 2016, p. 499-514.

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

  16. 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, 2016, p. 60-69.

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

  17. E-pub ahead of print
  18. Published

    Divergent Response Profile in Activated Cord Blood T cells from First-born Child Implies Birth-order-associated in Utero Immune Programming. / Kragh, Marie; Larsen, Jeppe Madura; Thysen, Anna Hammerich; Rasmussen, Morten Arendt; Wolsk, Helene Mygind; Bisgaard, Hans Flinker; Pedersen, Susanne Brix.

    In: Allergy, Vol. 71, No. 3, 2016.

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

  19. 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

  20. 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

  21. 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

  22. Published

    Evolution of NADPH-cytochrome P450 oxidoreductases (POR) in Apiales - POR 1 is missing. / Andersen, Trine Bundgaard; Hansen, Niels Bjørn; Laursen, Tomas; Weitzel, Corinna; Simonsen, Henrik Toft.

    In: Molecular Phylogenetics and Evolution, Vol. 98, 2016, p. 21-28.

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

  23. Published
  24. Published

    Extraction, characterization and application of antioxidants from the Nordic brown alga Fucus vesiculosus. / Hermund, Ditte Baun; Jacobsen, Charlotte (Supervisor); Nielsen, Kristian Fog (Supervisor).

    Kgs. Lyngby : National Food Institute, Technical University of Denmark, 2016. 111 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2016

  25. 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

  26. Published
  27. Published

    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, Vol. 115, No. 5, 2016, p. 782-790.

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

  28. E-pub ahead of print

    Free Amino Acids in Human Milk and Associations with Maternal Anthropometry and Infant Growth. / Larnkjær, Anni; Bruun, Signe; Pedersen, Dorthe; Zachariassen, Gitte; Barkholt, Vibeke; Agostoni, Carlo; Mølgaard, Christian; Husby, Steffen; Michaelsen, Kim F.

    In: Journal of Pediatric Gastroenterology and Nutrition, 2016.

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

  29. E-pub ahead of print

    Functional Analysis of a Novel Genome-Wide Association Study Signal in SMAD3 That Confers Protection From Coronary Artery Disease. / Turner, Adam W.; Martinuk, Amy; Silva, Anada; Lau, Paulina; Nikpay, Majid; Eriksson, Per; Folkersen, Lasse; Perisic, Ljubica; Hedin, Ulf; Soubeyrand, Sebastien; McPherson, Ruth.

    In: Arteriosclerosis, Thrombosis, and Vascular Biology, 2016.

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

  30. Published

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

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

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

  31. Published

    Genome Sequence of Pseudomonas aeruginosa Strain DK1-NH57388A, a Stable Mucoid Cystic Fibrosis Isolate. / Norman, Anders; Ciofu, Oana; Amador Hierro, Cristina Isabel; Høiby, Niels; Jelsbak, Lars.

    In: Genome Announcements, Vol. 4, No. 1, e00008-16, 2016.

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

  32. Published

    Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104. / Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon; Weill, François-Xavier; Baggesen, Dorte Lau; Jun, Se-Ran; Ussery, David; Lund, Ole; Crook, Derrick W; Wilson, Daniel J; Aarestrup, Frank Møller.

    In: Applied and Environmental Microbiology, Vol. 82, No. 8, 2016, p. 2516-2526.

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

  33. 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

  34. Published

    Highlights from the eleventh ISCB Student Council Symposium 2015. / Wilkins, Katie; Hassan, Mehedi; Francescatto, Margherita; Jespersen, Jakob Berg; Gonzalo Parra, R.; Cuypers, Bart; DeBlasio, Dan; Junge, Alexander; Jigisha, Anupama; Rahman, Farzana.

    In: B M C Bioinformatics, Vol. 17, No. Suppl. 3, 2016, p. 203-205.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2016

  35. E-pub ahead of print

    How compelling are the data for Epstein-Barr virus being a trigger for systemic lupus and other autoimmune diseases?. / Draborg, Anette; Gonzalez-Izarzugaza, Jose Maria; Houen, Gunnar.

    In: Current Opinion in Rheumatology, 2016.

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

  36. E-pub ahead of print

    Aspergillus europaeus sp. nov., a widely distributed soil-borne species related to A. wentii (section Cremei). / Hubka, Vit; Nováková, Alena; Samson, Robert A.; Houbraken, Jos; Frisvad, Jens Christian; Sklenář, František; Varga, Janos; Kolařík, Miroslav.

    In: Plant Systematics and Evolution, 2016.

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

  37. Published

    Aspergillus mulundensis sp. nov., a new species for the fungus producing the antifungal echinocandin lipopeptides, mulundocandins. / Bills, Gerald F.; Yue, Qun; Chen, Li; Li, Yan; An, Zhiqiang; Frisvad, Jens Christian.

    In: Journal of Antibiotics, Vol. 69, No. 3, 2016, p. 141-148.

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

  38. Published

    Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. / Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Asplund, Maria ; Mourier, Tobias ; Holm Jensen, Randi ; Arn Hansen, Thomas; Rey-Iglesia, Alba ; Vinner, Lasse ; Fridholm, Helena ; Nielsen, Lars Peter; Willerslev, Eske; Sicheritz-Pontén, Thomas; Lund, Ole; Hansen, Anders Johannes ; Gonzalez-Izarzugaza, Jose Maria; Brunak, Søren.

    In: Viruses, Vol. 8, No. 53, 2016.

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

  39. E-pub ahead of print

    Identification of the non-ribosomal peptide synthetase responsible for biosynthesis of the potential anti-cancer drug sansalvamide in Fusarium solani. / Romans-Fuertes, Patricia; Sondergaard, Teis Esben; Sandmann, Manuela Ilse Helga; Wollenberg, Rasmus Dam; Nielsen, Kristian Fog; Hansen, Frederik T.; Giese, Henriette; Brodersen, Ditlev Egeskov; Sørensen, Jens Laurids.

    In: Current Genetics, 2016.

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

  40. Published

    Iminosugar inhibitors of carbohydrate-active enzymes that underpin cereal grain germination and endosperm metabolism. / Andriotis, Vasilios M. E.; Rejzek, Martin; Rugen, Michael D.; Svensson, Birte; Smith, Alison M.; Field, Robert A.

    In: Biochemical Society Transactions, Vol. 44, No. 1, 2016, p. 159-165.

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

  41. 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

  42. Published

    Improved in vitro evaluation of novel antimicrobials: potential synergy between human plasma and antibacterial peptidomimetics, AMPs and antibiotics against human pathogenic bacteria. / Citterio, Linda; Franzyk, Henrik; Palarasah, Yaseelan; Andersen, Thomas Emil; Mateiu, Ramona Valentina; Gram, Lone.

    In: Research in Microbiology, Vol. 167, No. 2, 2016, p. 72-82.

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

  43. Published

    Phaeobacter inhibens as biocontrol agent against Vibrio vulnificus in oyster models. / Porsby, Cisse Hedegaard; Gram, Lone.

    In: Food Microbiology, Vol. 57, 2016, p. 63-70.

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

  44. Published

    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, Vol. 54, No. 4, 2016, p. 980-987.

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

  45. E-pub ahead of print
  46. Published

    Staphylococcus aureus Transcriptome Architecture : From Laboratory to Infection-Mimicking Conditions. / Mäder, Ulrike; Nicolas, Pierre; Depke, Maren; Pané-Farré, Jan; Debarbouille, Michel; van der Kooi-Pol, Magdalena M; Guérin, Cyprien; Dérozier, Sandra; Hiron, Aurelia; Jarmer, Hanne Østergaard; Leduc, Aurélie; Michalik, Stephan; Reilman, Ewoud; Schaffer, Marc; Schmidt, Frank; Bessières, Philippe; Noirot, Philippe; Hecker, Michael; Msadek, Tarek; Völker, Uwe; van Dijl, Jan Maarten.

    In: P L o S Genetics, Vol. 12, No. 4, e1005962, 2016.

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

  47. Published

    Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove. / McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany; Remesh, Soumya G.; Kaever, Thomas; Bardet, Wilfried; Jackson, Kenneth; McLeod, Rima; Sette, Alessandro; Nielsen, Morten; Zajonc, Dirk M.; Blader, Ira J.; Peters, Bjoern; Hildebrand, William.

    In: eLife, Vol. 5, e12556, 2016.

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

  48. Published

    Linking Hydrolysis Performance to Trichoderma reesei Cellulolytic Enzyme Profile. / Lehmann, Linda Olkjær; Petersen, Nanna; I. Jørgensen, Christian; Olsson, Lisbeth; Stocks, Stuart M.; Jørgensen, Henrik S.; Hobley, Timothy John.

    In: Biotechnology and Bioengineering, Vol. 113, No. 5, 2016, p. 1001-1010.

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

  49. 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

  50. Published

    Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. / Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo; Pagnani, Andrea.

    In: P L o S Computational Biology (Online), Vol. 12, No. 4, e1004870, 2016.

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

  51. 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

  52. E-pub ahead of print

    Model studies of lipid flip-flop in membranes. / Parisio, Giulia; Ferrarini, Alberta; Sperotto, Maria Maddalena.

    In: International Journal of Advances in Engineering Sciences and Applied Mathematics, 2016.

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

  53. E-pub ahead of print

    Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis. / Walter, Stephanie; Ali, Sajid; Kemen, Eric; Nazari, Kumarse; Bahri, Bochra A.; Enjalbert, Jérôme; Hansen, Jens G.; Brown, James K.M.; Sicheritz-Pontén, Thomas; Jones, Jonathan; de Vallavieille-Pope, Claude; Hovmøller, Mogens S.; Justesen, Annemarie Fejer.

    In: Ecology and Evolution, 2016.

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

  54. E-pub ahead of print

    NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. / Nielsen, Morten; Andreatta, Massimo.

    In: Genome Medicine, Vol. 8, No. 1, 33, 2016.

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

  55. Published

    Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans. / Donkin, Ida; Versteyhe, Soetkin; Ingerslev, Lars R.; Qian, Kui; Mechta, Mie; Nordkap, Loa; Mortensen, Brynjulf; Appel, Emil Vincent R; Jørgensen, Niels; Kristiansen, Viggo B.; Hansen, Torben; Workman, Christopher; Zierath, Juleen R.; Barrès, Romain.

    In: Cell Metabolism, Vol. 23, No. 2, 2016, p. 369–378.

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

  56. Published

    Occurrence of Aspergillus section Flavi and section Nigri and aflatoxins in raw cashew kernels (Anacardium occidentale L.) from Benin. / Lamboni, Yendouban; Frisvad, Jens Christian; Hell, Kerstin; Linnemann, Anita R.; Nout, Rob M. J.; Tamo, Manuele; Nielsen, Kristian Fog; van Boekel, Martinus A. J. S.; Smid, Eddy J.

    In: L W T- Food Science and Technology, Vol. 70, 2016, p. 71-77.

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

  57. Published

    PD-1 Blockade Expands Intratumoral Memory T Cells. / Ribas, Antoni; Shin, Daniel Sanghoon; Zaretsky, Jesse; Frederiksen, Juliet Wairimu; Cornish, Andrew; Avramis, Earl; Seja, Elizabeth; Kivork, Christine; Siebert, Janet; Kaplan-Lefko, Paula; Wang, Xiaoyan; Chmielowski, Bartosz; Glaspy, John A.; Chodon, Thinle; Tumeh, Paul C.; Pe'er, Dana; Comin-Anduix, Begoña.

    In: Cancer Immunology Research , Vol. 4, No. 3, 2016, p. 194-203.

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

  58. Published

    Picornavirus-Induced Airway Mucosa Immune Profile in Asymptomatic Neonates. / Wolsk, Helene M.; Følsgaard, Nilofar V.; Birch, Sune; Pedersen, Susanne Brix; Hansel, Trevor T.; Johnston, Sebastian L.; Kebadze, Tatiana; Chawes, Bo L.; Bønnelykke, Klaus; Bisgaard, Hans Flinker.

    In: Journal of Infectious Diseases, Vol. 213, No. 8, 2016, p. 1262-1270.

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

  59. 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

  60. Accepted/In press
  61. E-pub ahead of print
  62. 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

  63. Published

    Principles of Systems Biology, No. 2. / Klausen, Michael Schantz; Sommer, Morten Otto Alexander.

    In: Cell Systems, Vol. 2, No. 2, 2016, p. 60-61.

    Publication: Research - peer-reviewComment/debate – Annual report year: 2016

  64. 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

  65. Published

    Relation between tetR and tetA expression in tetracycline resistant Escherichia coli. / Møller, Thea S. B.; Overgaard, Martin; Nielsen, Søren S.; Bortolaia, Valeria; Sommer, Morten Otto Alexander; Guardabassi, Luca; Olsen, John E.

    In: B M C Microbiology, Vol. 16, No. 1, 649, 2016.

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

  66. Published

    Sæsonens mykolog. / Thrane, Ulf.

    In: Svampe, Vol. 73, 2016, p. 11-15.

    Publication: CommunicationJournal article – Annual report year: 2016

  67. Published

    Scale-down of continuous protein producing Saccharomyces cerevisiae cultivations using a two compartment system. / Wright, Naia Risager; Rønnest, Nanna Petersen; Thykær, Jette.

    In: Biotechnology Progress, Vol. 32, No. 1, 2016, p. 152–159.

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

  68. Published

    Season of birth shapes neonatal immune function. / Thysen, Anna Hammerich; Rasmussen, Morten Arendt; Kreiner-Møller, Eskil; Larsen, Jeppe Madura; Følsgaard, Nilofar Vahman; Bønnelykke, Klaus; Stokholm, Jakob; Bisgaard, Hans Flinker; Pedersen, Susanne Brix.

    In: Journal of Allergy and Clinical Immunology, Vol. 137, No. 4, 2016, p. 1238-1246.e13.

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

  69. E-pub ahead of print

    Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions : in silico peptide binding prediction identifies distinct functional clusters. / Obara, Isaiah; Nielsen, Morten; Jeschek, Marie; Nijhof, Ard; Mazzoni, Camila J.; Svitek, Nicholas; Steinaa, Lucilla; Awino, Elias; Olds, Cassandra; Jabbar, Ahmed; Clausen, Peter Henning; Bishop, Richard P.

    In: Immunogenetics, 2016.

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

  70. 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

  71. E-pub ahead of print

    Susceptibility to Lower Respiratory Infections in Childhood is Associated with Perturbation of the Cytokine Response to Pathogenic Airway Bacteria. / Vissing, Nadja Hawwa; Larsen, Jeppe Madura; Rasmussen, Morten Arendt; Chawes, Bo Lund Krogsgaard; Thysen, Anna Hammerich; Bønnelykke, Klaus; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: Pediatric Infectious Disease Journal, 2016.

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

  72. 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

  73. Published

    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, Vol. 148, No. 1, 2016, p. 34-39.

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

  74. 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

  75. 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

  76. Published

    Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations. / Aslan, Derya; Garde, Christian; Nygaard, Mette Katrine; Helbo, Alexandra Søgaard; Dimopoulos, Konstantinos; Hansen, Jakob Werner; Severinsen, Marianne Tang; Treppendahl, Marianne Bach; Sjø, Lene Dissing; Grønbæk, Kirsten; Kristensen, Lasse Sommer.

    In: OncoTarget, Vol. 7, No. 9, 2016, p. 9951-9963.

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

  77. Published

    Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data. / Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.; Day, Karen P.; Pedersen, Anders Gorm.

    In: B M C Bioinformatics, Vol. 17, No. 1, 176, 2016.

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

  78. Published
  79. 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

  80. 2015
  81. Published

    Statin resistance and export. / Frandsen, Rasmus John Normand (Inventor); Ley, Ane (Inventor); Naesby, Michael (Inventor).

    IPC No.: A61K 31/ 20 A N. Patent No.: WO2015161856. Oct 29, 2015.

    Publication: ResearchPatent – Annual report year: 2016

  82. 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

  83. 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

  84. 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

  85. 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

  86. 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

  87. Published
  88. 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

  89. 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

  90. 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

  91. Published
  92. 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

  93. 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

  94. Published

    Allergic sensitization at school age is a systemic low-grade inflammatory disorder. / Chawes, B. L. K.; Stokholm, J.; Malby-Schoos, A.-M.; Kreiner-Moller, L.; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: Allergy, Vol. 70, No. Suppl. 101, 1632, 2015, p. 512-512.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2016

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. Published
  102. 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

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