Department of Systems Biology

  1. 2013
  2. Published

    31P gain of chromosomal region 15q26 cause increased expression of blm and fanci, and is associated with sensitivity to platinum chemotherapy in triple negative breast cancer. / Birkbak, Nicolai Juul; Li, Y.; Bowman-Collin, C.; Iglehart, J.D.; Silver, D.; Wang, Z.C.; Szallasi, Zoltan Imre; Richardson, A.

    In: Annals of Oncology, Vol. 24, No. suppl 3, 2013, p. iii22.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  3. Published
  4. Published
  5. Published
  6. Published

    Analyzing Plasmodium falciparum erythrocyte membrane protein 1 gene expression by a next generation sequencing based method. / Jespersen, Jakob S.; Petersen, Bent; Seguin-Orlando, Andaine; Willerslev, Eske; Gilbert, M. Thomas P.; Lusingu, John; Theander, Thor G.; Lavstsen, Thomas.

    In: The nature of parasitism: Joint Spring Symposium 2013, Danish Society for Parasitology and Danish Society for Tropical Medicine & International Health. 2013. p. 8.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2013

  7. Published

    Applying mechanistic models in bioprocess development.. / Lencastre Fernandes, Rita; Bodla, Vijaya Krishna; Carlquist, Magnus; Heins, Anna-Lena; Eliasson Lantz, Anna; Sin, Gürkan; Gernaey, Krist V.

    In: Advances in Biochemical Engineering/Biotechnology . Springer, 2013. p. 137–166 (Advances in Biochemical Engineering. Biotechnology, Vol. 132).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  8. Published

    Aquaculture application and ecophysiology of marine bacteria from the Roseobacter clade. / D'Alvise, Paul; Gram, Lone (Main supervisor).

    Søborg : DTU Food, 2013. 79 p.

    Publication: ResearchPh.d. thesis – Annual report year: 2013

  9. Published

    A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites. / Kongsbak, Kristine Grønning; Bergmann, Rikke; Sørensen, Pernille Louise; Sander, Tommy; Balle, Thomas.

    In: P L o S One, Vol. 8, No. 1, 2013, p. e52323.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  10. Published

    A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study. / Eijsden, Rudy G. E. van; Stassen, Catherine; Daenen, Luk; Mulders, Sebastiaan E. Van; Bapat, Prashant Madhusudhan; Siewers, Verena; Goossens, Katty V. Y.; Nielsen, Jens; Delvaux, Freddy R.; Hummelen, Paul Van; Devreese, Bart; Willaert, Ronnie G.

    In: Biotechnology Letters, Vol. 35, No. 6, 2013, p. 891-900.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  11. Accepted

    Bacillus amyloliquefaciens ssp. plantarum strains as potential protective starter cultures for the production of Bikalga, an alkaline fermented food. / Compaor, C.S.; Nielsen, D.S.; Sawadogo-Lingani, H.; Berner, T.S.; Nielsen, Kristian Fog; Adimpong, David Bichala; Diawara, B.; Ouedraogo, G.A.; Jakobsen, M.; Thorsen, L.

    In: Journal of Applied Microbiology, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  12. Published

    Biasogram: visualization of confounding technical bias in gene expression data.. / Krzystanek, Marcin; Szallasi, Zoltan Imre; Eklund, Aron Charles.

    In: P L o S One, Vol. 8, No. 4, 2013, p. e61872.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  13. Published

    Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players.. / Lund, Ole; Karosiene, Edita; Lundegaard, Claus; Larsen, Mette Voldby; Nielsen, Morten.

    In: Antigen Processing : Methods and Protocols. 2013. p. 247-260 (Methods in Molecular Biology, Vol. 960).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  14. Published

    Cell mass and cell cycle dynamics of an asynchronous budding yeast population : Experimental observations, flow cytometry data analysis, and multi-scale modeling. / Lencastre Fernandes, Rita; Carlquist, Magnus; Lundin, Luisa; Heins, Anna-Lena; Dutta, Abhishek; Sørensen, Søren J.; Jensen, Anker Degn; Nopens, Ingmar; Eliasson Lantz, Anna; Gernaey, Krist.

    In: Biotechnology and Bioengineering (Print), Vol. 110, No. 3, 2013, p. 812-826.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  15. Published

    Characterization of microbial communities and fungal metabolites on field grown strawberries from organic and conventional production. / Jensen, Birgit; Knudsen, Inge M.B.; Andersen, Birgitte; Nielsen, Kristian Fog; Thrane, Ulf; Jensen, Dan Funck; Larsen, John.

    In: International Journal of Food Microbiology, Vol. 160, No. 3, 2013, p. 313-322.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  16. Published
  17. Published

    CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics.. / Vesth, Tammi Camilla; Lagesen, Karin; Acar, Öncel; Ussery, David.

    In: P L o S One, Vol. 8, No. 4, 2013, p. e60120.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  18. Published

    Comparative fermentation of insoluble carbohydrates in an in vitro human feces model spiked with Lactobacillus acidophilus NCFM. / Knudsen, Anne; van Zanten, Gabriella C.; Jensen, Susanne L.; Forssten, Sofia D.; Saarinen, Markku; Lahtinen, Sampo J.; Bandsholm, Ole; Svensson, Birte; Jespersen, Lene; Blennow, Andreas.

    In: Starch, Vol. 65, No. 3‐4, 2013, p. 346-353.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  19. Published

    Content and distribution of phytanic acid diastereomers in organic milk as affected by feed composition. / Che, Brita Ngum; Kristensen, Troels; Nebel, Caroline; Dalsgaard, Trine; Hellgren, Lars; Young, Jette Feveile; Larsen, Mette K.

    In: Journal of Agricultural and Food Chemistry, Vol. 61, No. 1, 2013, p. 225-230.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  20. Published

    Co-production of surfactin and a novel bacteriocin by Bacillus subtilis subsp. subtilis H4 isolated from bikalga, an African alkaline Hibiscus sabdariffa seed fermented condiment.. / Compaore, C. S.; Nielsen, Dennis S.; Ouoba, L. I. I.; Berner, Torben Sune; Nielsen, Kristian Fog; Sawadogo-Lingani, H.; Diawara, B.; Ouedraogo, G. A.; Jakobsen, Mogens; Thorsen, Line.

    In: International Journal of Food Microbiology, Vol. 162, No. 3, 2013, p. 297-307.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  21. Published

    Covalent Immobilization of β-Glucosidase on Magnetic Particles for Lignocellulose Hydrolysis. / Alftrén, Johan; Hobley, Timothy John.

    In: Applied Biochemistry and Biotechnology, Vol. 169, No. 7, 2013, p. 2076-2087.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  22. Published

    Deconvoluting complex tissues for expression quantitative trait locus-based analyses. / Seo, Ji-Heui; Li, Qiyuan; Fatima, Aquila; Eklund, Aron Charles; Szallasi, Zoltan Imre; Polyak, Kornelia; Richardson, Andrea L.; Freedman, Matthew L.

    In: Royal Society of London. Philosophical Transactions B. Biological Sciences, Vol. 368, No. 1620, 2013, p. 20120363-20120363.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  23. Published

    Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks. / Macé, Sabrina; Mamlouk, Kelthoum; Chipchakova, Stoyka; Prévost, Hervé; Joffraud, Jean-Jacques; Dalgaard, Paw; Pilet, Marie-France; Dousset, Xavier.

    In: Applied and Environmental Microbiology, Vol. 79, No. 8, 2013, p. 2612-2619.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  24. Published

    Discovery of a novel selective PPARγ ligand with partial agonist binding properties by integrated in silico / in vitro work flow. / Kouskoumvekaki, Irene; Petersen, Rasmus K.; Fratev, Filip Filipov ; Taboureau, Olivier ; Nielsen, Thomas Eiland; Oprea, Tudor; Sonne, Si Brask; Flindt, Esben N.; Jonsdottir, Svava Osk; Kristiansen, Karsten.

    In: Journal of Chemical Information and Modeling, Vol. 53, No. 4, 2013, p. 923-937.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  25. Published
  26. Published
  27. Published
  28. Published
  29. Published

    FADS genotype and diet are important determinants of DHA status: a cross-sectional study in Danish infants123. / Harsløf, Laurine Bente Schram; Larsen, Lesli Hingstrup; Ritz, Christian; Hellgren, Lars; Michaelsen, Kim Fleischer; Vogel, Ulla; Lauritzen, Lotte.

    In: American Journal of Clinical Nutrition, Vol. 97, No. 6, 2013, p. 1403-1410.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  30. Published

    Filtering apparatus and method for mixing, extraction and/or separation. / Stubbe, Peter Reimer (Inventor); Hansen, Preben Bøje (Inventor).

    IPC No.: A23L1/221. Feb 21, 2013.

    Publication: ResearchPatent – Annual report year: 2013

  31. Published

    From essential to persistent genes: a functional approach to constructing synthetic life. / Acevedo-Rocha, Carlos G.; Fang, Gang; Schmidt, Markus; Ussery, David; Danchin, Antoine.

    In: Trends in Genetics, Vol. 29, No. 5, 2013, p. 273-279.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  32. Published

    Fusarium graminearum and Its Interactions with Cereal Heads: Studies in the Proteomics Era.. / Yang, Fen; Jacobsen, Susanne; Jørgensen, Hans J L; Collinge, David B.; Svensson, Birte; Finnie, Christine.

    In: Frontiers in Plant Science, Vol. 4, 2013, p. 37.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  33. Published
  34. Published

    Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer.. / Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils; Wesolowska, Agata; Rajpert-De Meyts, Ewa; Ottesen, Anne Marie; Juul, Anders; Skakkebæk, Niels Erik; Jensen, Thomas Skøt; Gupta, Ramneek; Leffers, Henrik; Brunak, Søren.

    In: Frontiers in Endocrinology, Vol. 4, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  35. Published
  36. Published
  37. Published

    High beta-Lactamase Levels Change the Pharmacodynamics of beta-Lactam Antibiotics in Pseudomonas aeruginosa Biofilms. / Wang, Hengzhuang; Ciofu, Oana; Yang, Liang; Wu, Hong; Song, Zhijun; Oliver, Antonio; Hoiby, Niels.

    In: Antimicrobial Agents and Chemotherapy, Vol. 57, No. 1, 2013, p. 196-204.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  38. Published
  39. Published

    Identification of LasR Ligands through a Virtual Screening Approach. / Skovstrup, Søren; Le Quement, Sebastian Thordal; Hansen, Thomas; Jakobsen, Tim Holm; Harmsen, Morten; Tolker‐Nielsen, Tim; Nielsen, Thomas Eiland; Givskov, Michael Christian; Taboureau, Olivier .

    In: ChemMedChem, Vol. 8, No. 1, 2013, p. 157-163.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  40. Published

    Identification of peptides from foot‐and‐mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA‐1*0401 and SLA‐2*0401. / Pedersen, Lasse Eggers; Harndahl, M.; Nielsen, Morten; Patch, J. R.; Jungersen, Gregers; Buus, S.; Golde, W. T.

    In: Animal Genetics, Vol. 44, No. 3, 2013, p. 251-258.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  41. Published

    Identification of the Receptor-Binding Protein in Lytic Leuconostoc pseudomesenteroides Bacteriophages. / Kot, Witold Piotr; Hammer, Karin; Neve, Horst; Vogensen, Finn Kvist.

    In: Applied and Environmental Microbiology, Vol. 79, No. 10, 2013, p. 203311-3314.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  42. Published

    Identification of Y-Chromosomally Encoded Minor Histocompatibility Antigens Using a Reverse Immunology Approach. / Mortensen, Bo Kok; Brændstrup, Peter; Larsen, Malene Erup; Larsen, Mette Voldby; Lund, Ole; Rasmussen, Michael; Buus, Søren; Stryhn, Anette; Vindeløv, Lars.

    In: Biology of Blood and Marrow Transplantation, Vol. 19, No. 2, 2013, p. S335.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2013

  43. Published

    Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.. / Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon Guldberg; Olsson, Lisbeth; Nielsen, Jens.

    In: P L o S One, Vol. 8, No. 1, 2013, p. e54144.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  44. Published

    Influence of Temperature on Mechanical Properties of Jute/Biopolymer Composites. / Løvdal, Alexandra ; Laursen, Louise Løcke; Løgstrup Andersen, Tom; Madsen, Bo; Mikkelsen, Lars Pilgaard.

    In: Journal of Applied Polymer Science, Vol. 128, No. 3, 2013, p. 2038-2045.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  45. Published
  46. Published

    In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis. / Zanivan, Sara; Meves, Alexander; Behrendt, Kristina; Schoof, Erwin; Neilson, Lisa J.; Cox, Jürgen; Tang, Hao R.; Kalna, Gabriela; van Ree, Janine H.; van Deursen, Jan M.; Trempus, Carol S.; Machesky, Laura M.; Linding, Rune; Wickström, Sara A.; Fässler, Reinhard; Mann, Matthias.

    In: Cell Reports, Vol. 3, No. 2, 2013, p. 552-566.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  47. Published

    Lipid hydrolysis products affect the composition of microbiota isolated from infant fecal samples after in vitro fermentation. / Bennike, Rikke Mette Guldhammer; Licht, Tine Rask; Hellgren, Lars.

    2013. Abstract from Cell Symposia, Lisbon, Portugal.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2013

  48. Published

    Lipid hydrolysis products affect the composition of microbiota isolated from infant fecal samples after in vitro fermentation. / Bennike, Rikke Mette Guldhammer; Licht, Tine Rask; Hellgren, Lars.

    2013. Abstract from 27th Nordic Lipid Symposium, Helsinki, Finland.

    Publication: ResearchConference abstract for conference – Annual report year: 2013

  49. Published

    Multilocus phylogeny and MALDI-TOF analysis of the plant pathogenic species Alternaria dauci and relatives. / Brun, Sophie; Madrid, Hugo; Gerrits Van Den Ende, Bert; Andersen, Birgitte; Marinach-Patrice, Carine; Mazier, Dominique; De Hoog, G. Sybren.

    In: Fungal Biology, Vol. 117, No. 1, 2013, p. 32-40.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  50. Published

    Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 Are Identified in Individuals with Congenital Hypogonadotropic Hypogonadism. / Miraoui, Hichem; Dwyer, Andrew A.; Sykiotis, Gerasimos P.; Plummer, Lacey; Chung, Wilson; Feng, Bihua; Beenken, Andrew; Clarke, Jeff; Pers, Tune Hannes; Dworzynski, Piotr; Keefe, Kimberley; Niedziela, Marek; Raivio, Taneli; Crowley, William F., Jr.; Seminara, Stephanie B.; Quinton, Richard; Hughes, Virginia A.; Kumanov, Philip; Young, Jacques; Yialamas, Maria A.; Hall, Janet E.; Van Vliet, Guy; Chanoine, Jean-Pierre; Rubenstein, John; Mohammadi, Moosa; Tsai, Pei-San; Sidis, Yisrael; Hansen, Kasper Lage; Pitteloud, Nelly.

    In: American Journal of Human Genetics, Vol. 92, No. 5, 2013, p. 725-743.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  51. Published

    Penicillium subrubescens, a new species efficiently producing inulinase. / Mansouri, S.; Houbraken, J.; Samson, R.A.; Frisvad, Jens Christian; Christensen, M.; Tuthill, D. E.; Koutaniemi, S.; Hatakka, A.; Lankinen, P.

    In: Antonie van Leeuwenhoek, Vol. 103, No. 6, 2013, p. 1343-1357.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

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