Department of Systems Biology
- 2013
- 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-review › Journal article – Annual report year: 2013
- Published
45p deciphering patterns of chromosomal aberrations in breast cancer patients: how defects in specific dna repair genes affect the accumulation of gross dna aberrations in the cancer genome. / Marquard, Andrea Marion; Birkbak, Nicolai Juul; Eklund, Aron Charles; Varga, A.; Szüts, D.; Szallasi, Zoltan Imre.
In: Annals of Oncology, Vol. 24, No. suppl 3, 2013, p. iii26.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Accurate prediction of secondary metabolite gene clusters in filamentous fungi.. / Andersen, Mikael Rørdam; Nielsen, Jakob Blæsbjerg; Klitgaard, Andreas; Petersen, Lene Maj; Zachariasen, Mia; Hansen, Tilde J; Holberg Blicher, Lene; Gotfredsen, Charlotte Held; Larsen, Thomas Ostenfeld; Nielsen, Kristian Fog; Mortensen, Uffe Hasbro.
In: National Academy of Sciences. Proceedings, Vol. 110, No. 1, 2013, p. E99-E107.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. / Bælum, Jacob; Chambon, Julie Claire Claudia; Scheutz, Charlotte; Binning, Philip John; Laier, Troels; Bjerg, Poul Løgstrup; Jacobsen, Carsten.
In: Water Research, Vol. 47, No. 7, 2013, p. 2467-2478.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Conference abstract in proceedings – Annual report year: 2013
- 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-review › Book chapter – Annual report year: 2013
- 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: Research › Ph.d. thesis – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Book chapter – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2013
- Published
ChemProt-2.0: visual navigation in a disease chemical biology database. / Kjærulff, Sonny Kim; Wich, Louis; Kringelum, Jens Vindahl; Jacobsen, Ulrik Plesner; Kouskoumvekaki, Irene; Audouze, Karine Marie Laure; Lund, Ole; Brunak, Søren; Oprea, Tudor; Taboureau, Olivier .
In: Nucleic Acids Research, Vol. 41, No. D1, 2013, p. D464-D469.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- Published
Effect of natural microbiota on growth of Salmonella spp. in fresh pork – A predictive microbiology approach. / Møller, Cleide; Ilg, Y.; Aabo, Søren; Christensen, Bjarke Bak; Dalgaard, Paw; Hansen, Tina Beck.
In: Food Microbiology, Vol. 34, No. 2, 2013, p. 284-295.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Engineering strategies aimed at control of acidification rate of lactic acid bacteria. / Martinussen, Jan; Solem, Christian; Holm, Anders Koefoed; Jensen, Peter Ruhdal.
In: Current Opinion in Biotechnology, Vol. 24, No. 2, 2013, p. 124-129.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts. / Pedersen, Søren Damkiær; Yang, Lei; Molin, Søren; Jelsbak, Lars.
In: National Academy of Sciences. Proceedings, Vol. 110, No. 19, 2013, p. 7766-7771.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Expression and functional studies of genes involved in transport and metabolism of glycerol in Pachysolen tannophilus.. / Liu, Xiaoying; Mortensen, Uffe Hasbro; Workman, Mhairi.
In: Microbial Cell Factories, Vol. 12, 2013, p. 27.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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: Research › Patent – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- Published
Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart. / Holch, Anne; Webb, Kristen; Lukjancenko, Oksana; Ussery, David; Rosenthal, Benjamin M.; Gram, Lone.
In: Applied and Environmental Microbiology, Vol. 79, No. 9, 2013, p. 2944-2951.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- Published
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. / Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller.
In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 4, 2013, p. 771-777.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
HExpoChem: a systems biology resource to explore human exposure to chemicals. / Taboureau, Olivier ; Jacobsen, Ulrik Plesner; Kalhauge, Christian Gram; Edsgard, Stefan Daniel; Rigina, Olga; Gupta, Ramneek; Audouze, Karine Marie Laure.
In: Bioinformatics, Vol. 29, No. 9, 2013, p. 1231-1232.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- Published
High in vitro antimicrobial activity of β-peptoid-peptide hybrid oligomers against planktonic and biofilm cultures of Staphylococcus epidermidis.. / Liu, Yang; Knapp, Kolja Michael; Yang, Liang; Molin, Søren; Franzyk, Henrik; Folkesson, Anders.
In: International Journal of Antimicrobial Agents, Vol. 41, No. 1, 2013, p. 20-27.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Conference abstract in journal – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2012
- Published
In vitro growth of four individual human gut bacteria on oligosaccharides produced by chemoenzymatic synthesis.. / Vigsnæs, Louise Kristine; Nakai, Hiroyuki; Hemmingsen, Lene; Andersen, Joakim Mark; Lahtinen, Sampo J; Rasmussen, Louise Enggaard; Abou Hachem, Maher ; Petersen, Bent O.; Duus, Jens Øllgaard; Meyer, Anne S.; Licht, Tine Rask; Svensson, Birte.
In: Food & Function, Vol. 4, No. 5, 2013, p. 784-793.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Conference abstract for conference – Annual report year: 2013
- 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: Research › Conference abstract for conference – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013