Department of Systems Biology

  1. 2015
  2. Published
  3. 2014
  4. Published
  5. Published
  6. Published
  7. Published

    A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.. / Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van; O'Shea, Charlotte; Heyndrickx, Ken S.; Workman, Christopher; Vandepoele, Klaas; Skriver, Karen; De Masi, Federico.

    In: Nucleic Acids Research, Vol. 42, No. 12, 2014, p. 7681-7693.

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

  8. Published

    Adsorption and nanowear properties of bovine submaxillary mucin films on solid surfaces: Influence of solution pH and substrate hydrophobicity. / Sotres, Javier; Madsen, Jan Busk; Arnebrant, Thomas; Lee, Seunghwan.

    In: Journal of Colloid and Interface Science, Vol. 428, 2014, p. 242-250.

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

  9. Published

    Ageing of atrazine in manure amended soils assessed by bioavailability to Pseudomonas sp. strain ADP. / Glæsner, Nadia; Bælum, Jacob; Strobel, Bjarne W.; Jacobsen, Carsten S.

    In: Biodegradation, Vol. 25, No. 2, 2014, p. 217-225.

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

  10. Published

    A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy. / Bruhn, Sören; Fang, Yu; Barrenäs, Fredrik; Gustafsson, Mika; Zhang, Huan; Konstantinell, Aelita; Krönke, Andrea; Sönnichsen, Birte; Bresnick, Anne; Dulyaninova, Natalya; Wang, Hui; Zhao, Yelin; Klingelhöfer, Jörg; Ambartsumian, Noona; Beck, Mette Kristina; Nestor, Colm; Bona, Elsa; Xiang, Zou; Benson, Mikael.

    In: Science Translational Medicine, Vol. 6, No. 218, 2014, p. 20218ra4-218ra4.

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

  11. Published
  12. E-pub ahead of print

    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, 2014.

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

  13. Published

    Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 : — a mini-review. / Cockburn, Darrell; Wilkens, Casper; Ruzanski, Christian; Andersen, Susan; Willum Nielsen, Jonas; Smith, Alison M.; Field, Robert A.; Willemoes, Martin; Abou Hachem, Maher ; Svensson, Birte.

    In: Biologia, Vol. 69, No. 6, 2014, p. 705-712.

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

  14. Published
  15. Published

    An elevated pro-inflammatory cytokine profile in multiple chemical sensitivity. / Dantoft, Thomas Meinertz; Elberling, J.; Pedersen, Susanne Brix; Szecsi, P.B.; Vesterhauge, S.; Skovbjerg, S.

    In: Psychoneuroendocrinology, Vol. 40, 2014, p. 140-150.

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

  16. Published
  17. Published
  18. Published

    A novel platform for heterologous gene expression in Trichoderma reesei (Teleomorph Hypocrea jecorina). / Jørgensen, Mikael Skaanning; Skovlund, Dominique Aubert; Johannesen, Pia Francke; Mortensen, Uffe Hasbro.

    In: Microbial Cell Factories, Vol. 13, No. 1, 2014, p. 33.

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

  19. E-pub ahead of print

    Antibiofilm Properties of Acetic Acid. / Bjarnsholt, Thomas; Alhede, Morten; Jensen, Peter Østrup; Nielsen, Anne K.; Johansen, Helle Krogh; Homøe, Preben; Høiby, Niels; Givskov, Michael Christian; Kirketerp-Møller, Klaus.

    In: Advances in Wound Care, 2014.

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

  20. Published

    Antibody informatics for drug discovery. / Shirai, Hiroki; Prades, Catherine; Vita, Randi; Marcatili, Paolo; Popovic, Bojana; Xu, Jianqing; Overington, John P.; Hirayama, Kazunori; Soga, Shinji; Tsunoyama, Kazuhisa; Clark, Dominic; Lefranc, Marie-Paule; Ikeda, Kazuyoshi.

    In: B B A - Proteins and Proteomics, Vol. 1844, No. 11, 2014, p. 2002-2015.

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

  21. Published
  22. Published
  23. E-pub ahead of print
  24. Published

    Assessment of aflatoxigenicAspergillusand other fungi in millet and sesame from Plateau State, Nigeria. / Ezekiel, C.N.; Udom, I.E.; Frisvad, Jens Christian; Adetunji, M.C.; Houbraken, J.; Fapohunda, S.O.; Samson, R.A.; Atanda, O.O.; Agi-Otto, M.C.; Onashile, O.A.

    In: Mycology, Vol. 5, No. 1, 2014, p. 16-22.

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

  25. Published

    A sustainable route to produce the scytonemin precursor using Escherichia coli. / Malla, Sailesh; Sommer, Morten O. A.

    In: Green Chemistry, Vol. 16, No. 6, 2014, p. 3255-3265.

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

  26. Published

    A taxonomic and phylogenetic revision of Penicillium section Aspergilloides. / Houbraken, J.; Visagie, C.M.; Meijer, M.; Frisvad, Jens Christian; Busby, P.E.; Pitt, J.I.; Seifert, K.A.; Louis-Seize, G.; Demirel, R.; Yilmaz, N.; Jacobs, K.; Christensen, M.; Samson, R.A.

    In: Studies in Mycology, Vol. 78, 2014, p. 373-451.

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

  27. Published
  28. E-pub ahead of print

    Bacterial diversity in snow on North Pole ice floes. / Hauptmann, Aviaja Zenia Edna Lyberth; Stibal, Marek ; Bælum, Jacob; Sicheritz-Pontén, Thomas; Brunak, Søren; Bowman, Jeff S.; Hansen, Lars H. ; Jacobsen, Carsten S.; Blom, Nikolaj.

    In: Extremophiles, 2014.

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

  29. Published
  30. Published
  31. Published
  32. Published

    Brazil nuts are subject to infection with B and G aflatoxin-producing fungus, Aspergillus pseudonomius. / Massi, Fernanda Pelisson; Cameiro Vieira, Maria Lucia; Sartori, Daniele; Silva Penha, Rafael Elias; Munhoz, Carla de Freitas; Ferreira, Josue Maldonado; Iamanaka, Beatriz Thie; Taniwaki, Marta Hiromi; Frisvad, Jens Christian; Pelegrinelli Fungaro, Maria Helena.

    In: INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, Vol. 186, 2014, p. 14-21.

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

  33. Published

    Cesarean section imprints cord blood immune cell distributions. / Thysen, Anna Hammerich; Larsen, Jeppe Madura; Rasmussen, Mette Annelie; Stokholm, J.; Bønnelykke, K.; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: ALLERGY, Vol. 69, No. Supplement s99, 438, 2014, p. 192-192.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

  34. Published
  35. Published

    Characterisation of the Ara h 1-specific IgE repertoire in peanut allergic patients using phage display technology and next generation sequencing. / Christiansen, Anders; Bøgh, Katrine Lindholm; Kringelum, Jens Vindahl; Hansen, Christian Skjødt; Rigby, N. M.; Eiwegger, T.; Szepfalusi, Z.; Lund, Ole; Dufva, Martin.

    In: ALLERGY, Vol. 69, No. Supplement, 297, 2014, p. 140-140.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

  36. Published

    Children developing asthma by school-age display aberrant immune responses to pathogenic airway bacteria as infants. / Larsen, Jeppe Madura; Pedersen, Susanne Brix; Thysen, Anna Hammerich; Birch, S.; Rasmussen, M.A.; Bisgaard, H.

    In: ALLERGY, Vol. 69, No. s99, 404, 2014, p. 179-179.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

  37. Published

    Children with asthma by school age display aberrant immune responses to pathogenic airway bacteria as infants. / Larsen, Jeppe Madura; Pedersen, Susanne Brix; Thysen, Anna Hammerich; Birch, Sune; Rasmussen, Morten Arendt; Bisgaard, Hans Flinker.

    In: Journal of Allergy and Clinical Immunology, Vol. 133, No. 4, 2014, p. 1008-1013.

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

  38. Published
  39. Published

    Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds. / Geertz-Hansen, Henrik Marcus; Blom, Nikolaj; Feist, Adam; Brunak, Søren; Petersen, Thomas Nordahl.

    In: Proteins, Vol. 82, No. 9, 2014, p. 1819-1828.

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

  40. E-pub ahead of print
  41. Published

    Combining Experiments and Simulations Using the Maximum Entropy Principle. / Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten.

    In: P L o S Computational Biology, Vol. 10, No. 2, e1003406, 2014.

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

  42. Published

    Comparative Genomic and Metabolomic Analysis of Twelve Strains of Pseudoalteromonas luteoviolacea. / Månsson, Maria; Vynne, Nikolaj Grønnegaard; Klitgaard, Andreas; Melchiorsen, Jette; Dorrestein, Pieter C.; Gram, Lone.

    2014. Poster session presented at Gordon Conference on Marine Natural Products, Venture, CA, United States.

    Publication: Research - peer-reviewPoster – Annual report year: 2014

  43. Published

    Comparison of the Web Tools ARG-ANNOT and ResFinder for Detection of Resistance Genes in Bacteria. / Zankari, Ea.

    In: Antimicrobial Agents and Chemotherapy, Vol. 58, No. 8, 2014, p. 4986-4986.

    Publication: Research - peer-reviewLetter – Annual report year: 2014

  44. Published

    Compass: A hybrid method for clinical and biobank data mining. / Krysiak-Baltyn, Konrad; Petersen, Thomas Nordahl; Audouze, Karine Marie Laure; Jørgensen, Niels; Ängquist, L.; Brunak, Søren.

    In: Journal of Biomedical Informatics, Vol. 47, 2014, p. 160-170.

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

  45. Published

    Complete Genome Sequence of Border Disease Virus Genotype 3 Strain Gifhorn. / Fahnøe, Ulrik; Höper, Dirk ; Beer, Martin; Rasmussen, Thomas Bruun.

    In: Genome Announcements, Vol. 2, No. 1, e01142-13, 2014.

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

  46. Published

    Complete Genome Sequence of Classical Swine Fever Virus Genotype 2.2 Strain Bergen. / Fahnøe, Ulrik; Lohse, Louise; Becher, Paul ; Rasmussen, Thomas Bruun.

    In: Genome Announcements, Vol. 2, No. 3, 2014, p. e00483-14.

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

  47. Published

    CoreFlow: A computational platform for integration, analysis and modeling of complex biological data. / Pasculescu, Adrian; Schoof, Erwin; Creixell, Pau; Zheng, Yong; Olhovsky, Marina; Tian, Ruijun; So, Jonathan; Vanderlaan, Rachel D.; Pawson, Tony; Linding, Rune; Colwill, Karen.

    In: Journal of Proteomics, Vol. 100, 2014, p. 167-173.

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

  48. Published
  49. Published

    Database-driven primary analysis of raw sequencing data. / Gautier, Laurent (Inventor); Lund, Ole (Inventor).

    IPC No.: G06F19/22. Patent No.: WO2014060305. Apr 24, 2014.

    Publication: ResearchPatent – Annual report year: 2014

  50. Published

    Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. / Kim, Yohan; Sidney, John; Buus, Søren; Sette, Alessandro; Nielsen, Morten; Peters, Bjoern.

    In: B M C Bioinformatics, Vol. 15, No. 1, 241, 2014.

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

  51. Published

    Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. / Olalde, Inigo; Allentoft, Morten E.; Sanchez-Quinto, Federico; Santpere, Gabriel; Chiang, Charleston W. K.; DeGiorgio, Michael; Prado-Martinez, Javier; Rodriguez, Juan Antonio; Rasmussen, Simon; Quilez, Javier; Ramirez, Oscar; Marigorta, Urko M.; Fernandez-Callejo, Marcos; Prada, Maria Encina; Encinas, Julio Manuel Vidal; Nielsen, Rasmus; Netea, Mihai G.; Novembre, John; Sturm, Richard A.; Sabeti, Pardis; Marques-Bonet, Tomas; Navarro, Arcadi; Willerslev, Eske; Lalueza-Fox, Carles.

    In: NATURE, Vol. 507, No. 7491, 2014, p. 225-228.

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

  52. Published

    Detection of a caspase-3 cleaved tau fragment in the serum of alzheimer's patients by using immunoprecipitation and lc-ms/ms. / Inekci, Dilek; Hägglund, Per; Linemann, Thomas; Jacobsen, Susanne; Svensson, Birte; Vilholm, Ole; Henriksen, Kim.

    In: Alzheimer's & Dementia, Vol. 10, No. 4, 2014, p. P272-P273.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

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