Center for Biological Sequence Analysis

  1. 2014
  2. Published
  3. 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

  4. 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

  5. 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

  6. Published
  7. 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

  8. Published
  9. Published
  10. Published
  11. Published
  12. 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

  13. Published
  14. 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

  15. Published
  16. E-pub ahead of print
  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. Published

    Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium. / Koivula, Robert W.; Heggie, Alison; Barnett, Anna; Cederberg, Henna; Hansen, Tue Haldor; Koopman, Anitra D.; Ridderstrale, Martin; Rutters, Femke; Vestergaard, Henrik; Gupta, Ramneek; Herrgard, Sanna; Heymans, Martijn W.; Perry, Mandy H.; Rauh, Simone; Siloaho, Maritta; Teare, Harriet J. A.; Thorand, Barbara; Bell, Jimmy; Brunak, Søren; Frost, Gary; Jablonka, Bernd; Mari, Andrea; McDonald, Tim J.; Dekker, Jacqueline M.; Hansen, Torben; Hattersley, Andrew; Laakso, Markku; Pedersen, Oluf; Koivisto, Veikko; Ruetten, Hartmut; Walker, Mark; Pearson, Ewan; Franks, Paul W.

    In: DIABETOLOGIA, Vol. 57, No. 6, 2014, p. 1132-1142.

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

  24. Published

    DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families. / Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas Salhøj; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

    In: Nucleic Acids Research, Vol. 42, No. 4, 2014, p. 202270-2281.

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

  25. Published

    Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population. / Eriksson, Robert; Werge, Thomas; Jensen, Lars Juhl; Brunak, Søren.

    In: Drug Safety, Vol. 37, No. 4, 2014, p. 237-247.

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

  26. Published

    Effect of subinhibitory concentrations of four commonly used biocides on the conjugative transfer of Tn916 in Bacillus subtilis. / Seier-Petersen, Maria Amalie; Jasni, A.; Aarestrup, Frank Møller; Vigre, Håkan; Mullany, P.; Roberts, A. P.; Agersø, Yvonne.

    In: Journal of Antimicrobial Chemotherapy, Vol. 69, No. 2, 2014, p. 343-348.

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

  27. E-pub ahead of print
  28. Published

    Effects on metabolic markers are modified by PPARG2 and COX2 polymorphisms in infants randomized to fish oil.. / Harsløf, Laurine B. S.; Damsgaard, Camilla T.; Hellgren, Lars I.; Andersen, Anders Daniel; Vogel, Ulla; Lauritzen, Lotte.

    In: Genes & Nutrition, Vol. 9, No. 3, 396, 2014.

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

  29. Published

    Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population. / Eriksson, Robert; Werge, Thomas; Jensen, Lars Juhl; Brunak, Søren.

    In: Drug Safety, Vol. 37, 2014, p. 379.

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

  30. Published

    Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. / Leekitcharoenphon, Pimlapas; Nielsen, Eva M.; Kaas, Rolf Sommer; Lund, Ole; Aarestrup, Frank Møller.

    In: P L o S One, Vol. 9, No. 2, e87991, 2014.

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

  31. Published
  32. Published

    High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions. / Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.; Jacobsen, Carsten Suhr.

    In: Applied and Environmental Microbiology, Vol. 80, No. 12, 2014, p. 3568-3575.

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

  33. Published

    Host genome variations and risk of infections during induction treatment for childhood acute lymphoblastic leukaemia. / Lund, Bendik; Wesolowska-Andersen, Agata; Lausen, Birgitte; Borst, Louise; Rasmussen, Kirsten Kørup; Müller, Klaus; Klungland, Helge; Gupta, Ramneek; Schmiegelow, Kjeld.

    In: European Journal of Haematology, Vol. 92, No. 4, 2014, p. 321-330.

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

  34. Published

    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. / Nielsen, Henrik Bjørn; Almeida, Mathieu; Juncker, Agnieszka; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian Rafal; Gautier, Laurent; Pedersen, Anders Gorm; Emmanuelle, Le Chatelier; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer S.; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf Sommer; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Denis, Le Paslier; Pons, Nicolas; Pedersen, Oluf; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren; Tap, Julien; Tims, Sebastian; Ussery, David; Yamada, Takuji; Renault, Pierre; Sicheritz-Pontén, Thomas; Bork, Peer; Wang, Jun; Brunak, Søren; Ehrlich, S. Dusko.

    In: Nature Biotechnology, 2014.

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

  35. Published

    Identification and HLA-Tetramer-Validation of Human CD4(+) and CD8(+) T Cell Responses against HCMV Proteins IE1 and IE2. / Braendstrup, Peter; Mortensen, Bo Kok; Justesen, Sune Frederik Lamdahl; Osterby, Thomas; Rasmussen, Michael; Hansen, Andreas Martin; Christiansen, Claus Bohn; Hansen, Morten Bagge; Nielsen, Morten; Vindelov, Lars; Buus, Søren; Stryhn, Anette.

    In: PLOS ONE, Vol. 9, No. 4, e94892, 2014.

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

  36. Published

    Identification of Hypoxia-Regulated Proteins Using MALDI-Mass Spectrometry Imaging Combined with Quantitative Proteomics. / Djidja, Marie-Claude; Chang, Joan; Hadjiprocopis, Andreas; Schmich, Fabian; Sinclair, John; Mršnik, Martina; Schoof, Erwin M.; Barker, Holly E.; Linding, Rune; Jørgensen, Claus; Erler, Janine T.

    In: Journal of Proteome Research, Vol. 13, 2014, p. 2297-2313.

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

  37. Published

    Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome. / Audouze, Karine Marie Laure; Tromelin, Anne; Le Bon, Anne Marie; Belloir, Christine; Petersen, Rasmus Koefoed; Kristiansen, Karsten; Brunak, Søren; Taboureau, Olivier .

    In: PLOS ONE, Vol. 9, No. 4, e93037, 2014.

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

  38. Published

    Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment. / Carrasco Pro, S.; Zimic, M.; Nielsen, Morten.

    In: Tissue Antigens, Vol. 83, No. 2, 2014, p. 94-100.

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

  39. E-pub ahead of print

    Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies. / Messih, M. A.; Lepore, R.; Marcatili, Paolo; Tramontano, A.

    In: Bioinformatics, 2014, p. 1-8.

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

  40. E-pub ahead of print

    In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. / Carattoli, Alessandra; Zankari, Ea; García-Fernández, Aurora; Larsen, Mette Voldby; Lund, Ole; Villa, Laura; Aarestrup, Frank Møller; Hasman, Henrik.

    In: Antimicrobial Agents and Chemotherapy, Vol. 58, No. 7, 2014, p. 3895-3903.

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

  41. Published

    Intercorrelations of lipoprotein subfractions and their covariation with lifestyle factors in healthy men. / Parlesak, Alexandr; Eckoldt, Joachim; Winkler, Karl; Bode, Johann Christian.

    In: Journal of Clinical Biochemistry and Nutrition, Vol. 54, No. 3, 2014, p. 174-180.

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

  42. Published

    KinomeXplorer: an integrated platform for kinome biology studies. / Horn, Heiko; Schoof, Erwin; Kim, Jinho; Robin, Xavier; Miller, Martin Lee; Diella, Francesca; Palma, Anita; Cesareni, Gianni; Jensen, Lars Juhl; Linding, Rune.

    In: Nature Methods, Vol. 11, No. 6, 2014, p. 603-604.

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

  43. Published

    LocTree3 prediction of localization. / Goldberg, T.; Hecht, M.; Hamp, T.; Karl, T.; Yachdav, G.; Ahmed, Nadeed; Altermann, U.; Angerer, P.; Ansorge, S.; Balasz, K.; Bernhofer, M.; Betz, A.; Cizmadija, L.; Do, K. T.; Gerke, J.; Greil, R.; Joerdens, V.; Hastreiter, M.; Hembach, K.; Herzog, M.; Kalemanov, M.; Kluge, M.; Meier, A.; Nasir, H.; Neumaier, U.; Prade, V.; Reeb, J.; Sorokoumov, A.; Troshani, I.; Vorberg, S.; Waldraff, S.; Zierer, J.; Nielsen, Henrik; Rost, B.

    In: Nucleic Acids Research, Vol. 42, No. W1, 2014, p. W350-W355.

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

  44. Published

    Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and β-cell protection.. / Christensen, Dan Ploug; Gysemans, Conny; Lundh, Morten; Dahllöf, Mattias Salling; Noesgaard, Daniel; Schmidt, Søren Fisker; Mandrup, Susanne; Birkbak, Nicolai Juul; Workman, Christopher; Piemonti, Lorenzo; Blaabjerg, Lykke; Monzani, Valmen; Fossati, Gianluca; Mascagni, Paolo; Paraskevas, Steven; Aikin, Reid A; Billestrup, Nils; Grunnet, Lars Groth; Dinarello, Charles A; Mathieu, Chantal; Mandrup-Poulsen, Thomas.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 3, 2014, p. 1055-1059.

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

  45. Published

    Multiparametric Bioinformatics Distinguish the CD4/CD8 Ratio as a Suitable Laboratory Predictor of Combined T Cell Pathogenesis in HIV Infection. / Buggert, Marcus; Frederiksen, Juliet Wairimu; Noyan, Kajsa; Svärd, Jenny; Barqasho, Babilonia; Sönnerborg, Anders; Lund, Ole; Nowak, Piotr; Karlsson, Annika C.

    In: Journal of Immunology, Vol. 192, No. 5, 2014, p. 2099-2108.

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

  46. Published

    Natural mannosylation of HIV-1 gp120 imposes no immunoregulatory effects in primary human plasmacytoid dendritic cells. / Søndergaard, Jonas Nørskov; Vinner, Lasse; Pedersen, Susanne Brix.

    In: Molecular Immunology, Vol. 59, No. 2, 2014, p. 180-187.

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

  47. E-pub ahead of print

    NetTepi: an integrated method for the prediction of T cell epitopes. / Trolle, Thomas; Nielsen, Morten.

    In: Immunogenetics, 2014.

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

  48. Published

    Pre‐natal undernutrition and post‐natal overnutrition are associated with permanent changes in hepatic metabolism markers and fatty acid composition in sheep. / Hou, L.; Hellgren, Lars; Kongsted, A. H.; Vaag, A.; Nielsen, M. O.

    In: Acta Physiologica (Print), Vol. 210, No. 2, 2014, p. 317-329.

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

  49. Published

    Probe design for expression arrays using OligoWiz. / Wernersson, Rasmus.

    DNA Microarrays for Biomedical Research: Methods and Protocols. ed. / Martin Dufva. Vol. 529 Humana Press, 2014. p. 23-36 (Methods in Molecular Biology, Vol. 529).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2009

  50. Published

    Proteome reference maps of the Lotus japonicus nodule and root. / Dam, Svend Secher; Dyrlund, Thomas F.; Ussatjuk, Anna; Jochimsen, Bjarne; Nielsen, Kasper; Goffard, Nicolas; Ventosa, Miguel; Lorentzen, Andrea; Gupta, Vikas; Andersen, Stig U. ; Enghild, Jan J.; Ronson, Clive W.; Roepstorff, Peter; Stougaard, Jens.

    In: Journal of Proteomics, Vol. 14, 2014, p. 230-240.

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

  51. Published
  52. Published
  53. Published

    Removal of the phage-shock protein PspB causes reduction of virulence in Salmonella enterica serovar Typhimurium independently of NRAMP1.. / Wallrodt, Inke; Jelsbak, Lotte; Thomsen, Line E.; Brix, Lena; Lemire, Sebastien; Gautier, Laurent; Nielsen, Dennis S.; Jovanovic, Goran; Buck, Martin; Olsen, John E.

    In: Journal of Medical Microbiology, Vol. 63, No. Pt 6, 2014, p. 788-795.

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

  54. Published

    RNA-protein interactions: an overview.. / Re, Angela; Joshi, Tejal; Kulberkyte, Eleonora; Morris, Quaid; Workman, Christopher.

    RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods: Springer Protocols. Vol. 1097 2014. p. 491-521 (Methods in Molecular Biology, Vol. 1097).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2014

  55. Published

    Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling. / Tian, Pengfei; Jónsson, Sigurdur Æ.; Ferkinghoff-Borg, Jesper; Krivov, Sergei V.; Lindorff-Larsen, Kresten; Irbäck, Anders; Boomsma, Wouter.

    In: Journal of Chemical Theory and Computation, Vol. 10, No. 2, 2014, p. 543-553.

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

  56. Published

    Signal peptides and protein localization prediction. / Nielsen, Henrik.

    Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley and Sons, Ltd., 2014.

    Publication: Research - peer-reviewEncyclopedia chapter – Annual report year: 2014

  57. Published

    Size of quorum sensing communities. / Ferkinghoff-Borg, Jesper; Sams, Thomas.

    In: Molecular BioSystems, Vol. 10, No. 103, 2014, p. 103-109.

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

  58. E-pub ahead of print
  59. Published

    Solid‐Phase Synthesis and Biological Evaluation of N‐Dipeptido L‐Homoserine Lactones as Quorum Sensing Activators. / Hansen, Mette Reimert; Le Quement, Sebastian Thordal; Jakobsen, Tim Holm; Skovstrup, Søren; Taboureau, Olivier ; Tolker‐Nielsen, Tim; Givskov, Michael Christian; Nielsen, Thomas Eiland.

    In: ChemBioChem, Vol. 15, No. 3, 2014, p. 460-465.

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

  60. Published

    Studies on genetic diversity of bovine viral diarrhea viruses in Danish cattle herds. / Nagy, Abdou; Fahnøe, Ulrik; Rasmussen, Thomas Bruun; Uttenthal, Åse.

    In: Virus Genes, Vol. 48, No. 2, 2014, p. 376-380.

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

  61. Published

    The comparison of thrombocytosis and platelet-lymphocyte ratio as potential prognostic markers in colorectal cancer. / Baranyai, Zsolt; Krzystanek, Marcin; Josa, Valeria; Dede, Kristof; Ágoston, E.; Szasz, A. Marcell; Sinko, Daniel; Szarvas, Viktor; Salamon, Ferenc; Eklund, Aron Charles; Szallasi, Zoltan Imre; Jakab, Ferenc.

    In: Thrombosis and Haemostasis, Vol. 111, No. 3, 2014, p. 483-490.

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

  62. Published

    The effect of a short-term high-fat overfeeding on plasma levels of amino acids in young, healthy men with low or normal birth weight. / Ribel-Madsen, Amalie; Hellgren, Lars; Brøns , Charlotte; Ribel-Madsen , Rasmus; B. Newgard , Christopher; A. Vaag , Allan.

    2014. Abstract from The Power of Programming Conference, Munich, Germany.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2014

  63. Published

    The effect of a short-term high-fat overfeeding on plasma levels of amino acids in young, healthy men with low or normal birth weight. / Ribel-Madsen, Amalie; Hellgren, Lars; Brøns , Charlotte; Ribel-Madsen , Rasmus; B. Newgard , Christopher; A. Vaag , Allan.

    2014. Abstract from The 11th Biennial ISSFAL Congress 2014, Stockholm, Sweden.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2014

  64. Published

    The genome of a Late Pleistocene human from a Clovis burial site in western Montana.. / Rasmussen, Morten; Anzick, Sarah L.; Waters, Michael R; Skoglund, Pontus; DeGiorgio, Michael; Stafford, Thomas W, Jr; Rasmussen, Simon; Moltke, Ida; Albrechtsen, Anders; Doyle, Shane M; Poznik, G David; Gudmundsdottir, Valborg; Yadav, Rachita; Malaspinas, Anna Sapfo; White, Samuel Stockton, 5th; Allentoft, Morten Erik; Cornejo, Omar E.; Tambets, Kristiina; Eriksson, Anders; Heintzman, Peter D.; Karmin, Monika; Korneliussen, Thorfinn Sand; Meltzer, David J.; Pierre, Tracey Lynn; Stenderup, Jesper; Saag, Lauri; Warmuth, Vera M; Lopes, Margarida C; Malhi, Ripan S.; Brunak, Søren; Sicheritz-Pontén, Thomas; Barnes, Ian; Collins, Matthew; Orlando, Ludovic Antoine Alexandre; Balloux, Francois; Manica, Andrea; Gupta, Ramneek; Metspalu, Mait; Bustamante, Carlos D; Jakobsson, Mattias; Nielsen, Rasmus; Willerslev, Eske.

    In: Nature, Vol. 506, No. 7487, 2014, p. 225-229.

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

  65. Published

    The Role of the st313-td Gene in Virulence of Salmonella Typhimurium ST313. / Herrero-Fresno, Ana; Wallrodt, Inke; Leekitcharoenphon, Pimlapas; Olsen, John Elmerdahl; Aarestrup, Frank Møller; Hendriksen, Rene S.

    In: PLOS ONE, Vol. 9, No. 1, e84566, 2014.

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

  66. Published

    Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution. / Dewhurst, Sally M.; McGranahan, Nicholas; Burrell, Rebecca A.; Rowan, Andrew J.; Grönroos, Eva; Endesfelder, David; Joshi, Tejal; Mouradov, Dmitri; Gibbs, Peter; Ward, Robyn L.; Hawkins, Nicholas J.; Szallasi, Zoltan Imre; Sieber, Oliver M.; Swanton, Charles.

    In: Cancer Discovery, Vol. 4, No. 2, 2014, p. 175-185.

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

  67. Published

    Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. / Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.; Metspalu, Mait; Albrechtsen, Anders; Moltke, Ida; Rasmussen, Simon; Stafford jr., Thomas; Orlando, Ludovic Antoine Alexandre; Metspalu, Ene; Karmin, Monika; Tambets, Kristiina; Rootsi, Siiri; Mägi, Reedik; Campos, Paula; Balanovska, Elena; Balanovsky, Oleg; Khusnutdinova, Elza; Litvinov, Sergey; Osipova, Ludmila P; Fedorova, Sardana A; Voevoda, Mikhail I; Degiorgio, Michael; Sicheritz-Pontén, Thomas; Brunak, Søren; Demeshchenko, Svetlana; Kivisild, Toomas; Villems, Richard; Nielsen, Rasmus; Jakobsson, Mattias; Willerslev, Eske.

    In: Nature, Vol. 505, No. 7481, 2014, p. 87–91.

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

  68. Published

    Use of "one-pot, mix-and-read" peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle. / Svitek, Nicholas; Hansen, Andreas Martin; Steinaa, Lucilla; Saya, Rosemary; Awino, Elias; Nielsen, Morten; Buus, Søren; Nene, Vishvanath.

    In: Veterinary Research, Vol. 45, No. 1, 2014.

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

  69. Published

    Vibrio chromosome-specific families. / Lukjancenko, Oksana; Ussery, David.

    In: Frontiers in Microbiology, Vol. 5, 2014.

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

  70. 2013
  71. 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

  72. Published
  73. Published
  74. Published

    A computational approach to chemical etiologies of diabetes.. / Audouze, Karine Marie Laure; Brunak, Søren; Grandjean, Philippe.

    In: Scientific Reports, Vol. 3, 2013, p. 2712.

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

  75. Published
  76. Published

    Adipose tissue trans fatty acids and changes in body weight and waist circumference. / Hansen, C.P.; Berentzen, T.L.; Østergaard, J.N.; Dahm, C.C.; Hellgren, Lars; Schmidt, E.B.; Tjønneland, A.; Sørensen, T.I.A.; Overvad, K.; Jakobsen, M.U.

    2013. Abstract from European Congress on Obesity 2013, Liverpool, United Kingdom.

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

  77. Published

    Adipose tissue trans fatty acids and changes in body weight and waist circumference. / Hansen, Camilla P.; Berentzen, Tina L.; Østergaard, Jane N.; Dahm, Christina C.; Hellgren, Lars; Schmidt, Erik B.; Tjønneland, Anne; Sørensen, Thorkild I. A.; Overvad, Kim; Jakobsen, Marianne U.

    In: The British Journal of Nutrition, 2013.

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

  78. Published
  79. Published

    A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations.. / Bønnelykke, Klaus; Sleiman, Patrick; Nielsen, Kasper; Kreiner-Møller, Eskil; Mercader, Josep M; Belgrave, Danielle; den Dekker, Herman T; Husby, Anders; Sevelsted, Astrid; Faura-Tellez, Grissel; Mortensen, Li Juel; Paternoster, Lavinia; Flaaten, Richard; Mølgaard, Anne; Smart, David E; Thomsen, Philip Francis; Rasmussen, Morten; Bonàs-Guarch, Silvia; Holst, Claus; Nohr, Ellen A; Yadav, Rachita; March, Michael E; Blicher, Thomas Holberg; Lackie, Peter M; Jaddoe, Vincent W V; Simpson, Angela; Holloway, John W; Duijts, Liesbeth; Custovic, Adnan; Davies, Donna E; Torrents, David; Gupta, Ramneek; Hollegaard, Mads Vilhelm; Hougaard, David M; Hakonarson, Hakon; Bisgaard, Hans Flinker.

    In: Nature Genetics, 2013.

    Publication: Research - peer-reviewLetter – Annual report year: 2013

  80. Published

    Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes.. / Bohlin, Jon; Brynildsrud, Ola Brønstad; Vesth, Tammi Camilla; Skjerve, Eystein; Ussery, David.

    In: PLoS ONE, Vol. 8, No. 7, e69878, 2013.

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

  81. 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.

    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

  82. 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; Thomas, M.; Gilbert, P.; Lusingu, John; Theander, Thor G.; Lavstsen, Thomas.

    In: Tropical Medicine & International Health, Vol. 18, No. Supplement 1 , 2013, p. 67-67.

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

  83. Published

    A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk. / Blair, David R.; Lyttle, Christopher S.; Mortensen, Jonathan M.; Bearden, Charles F.; Jensen, Anders Boeck; Khiabanian, Hossein; Melamed, Rachel; Rabadan, Raul; Bernstam, Elmer V.; Brunak, Søren; Jensen, Lars Juhl; Nicolae, Dan; Shah, Nigam H.; Grossman, Robert L.; Cox, Nancy J.; White, Kevin P.; Rzhetsky, Andrey.

    In: Cell, Vol. 155, No. 1, 2013, p. 70-80.

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

  84. Published

    A Novel Domain Cassette Identifies Plasmodium falciparum PfEMP1 Proteins Binding ICAM-1 and Is a Target of Cross-Reactive, Adhesion-Inhibitory Antibodies. / Bengtsson, Anja; Jørgensen, Louise; Rask, Thomas Salhøj; Olsen, Rebecca W.; Andersen, Marianne A.; Turner, Louise; Theander, Thor G.; Hviid, Lars; Higgins, Matthew K.; Craig, Alister; Brown, Alan; Jensen, Anja T. R.

    In: Journal of Immunology, Vol. 190, No. 1, 2013, p. 240-249.

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

  85. Published

    ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.. / Jensen, Michael Krogh; Lindemose, Søren; De Masi, Federico; Reimer, Julia J; Nielsen, Michael; Perera, Venura; Workman, Christopher; Turck, Franziska; Grant, Murray R; Mundy, John; Petersen, Morten; Skriver, Karen.

    In: FEBS Open Bio, Vol. 3, 2013, p. 321-327.

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

  86. Published

    Ataxia, Dementia, and Hypogonadotropism Caused by Disordered Ubiquitination. / Margolin, David H.; Kousi, Maria; Chan, Yee-Ming; Lim, Elaine T.; Schmahmann, Jeremy D.; Hadjivassiliou, Marios; Hall, Janet E.; Adam, Ibrahim; Dwyer, Andrew; Plummer, Lacey; Aldrin, Stephanie V.; O'Rourke, Julia; Kirby, Andrew; Hansen, Kasper Lage; Milunsky, Aubrey; Milunsky, Jeff M.; Chan, Jennifer; Hedley-Whyte, E. Tessa; Daly, Mark J.; Katsanis, Nicholas; Seminara, Stephanie B.

    In: New England Journal of Medicine, Vol. 368, No. 21, 2013, p. 1992-2003.

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

  87. 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

  88. Published

    Bacterial natural transformation by highly fragmented and damaged DNA.. / Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre; Mayar, J. Victor Moreno; Rasmussen, Simon; Dahl, Tais Wittchen; Rosing, Minik Thorleif; Poole, Anthony M; Sicheritz-Pontén, Thomas; Brunak, Søren; Inselmann, Sabrina; de Vries, Johann; Wackernagel, Wilfried; Pybus, Oliver G; Nielsen, Rasmus; Johnsen, Pål Jarle; Nielsen, Kaare Magne; Willerslev, Eske.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 49, 2013, p. 19860-19865.

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

  89. 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

  90. Published
  91. 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.

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

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

  92. Published

    BlockLogo: Visualization of peptide and sequence motif conservation. / Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L.; Zhang, Guang Lan; Brusic, Vladimir.

    In: Journal of Immunological Methods, Vol. 400-401, 2013, p. 37-44.

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

  93. Published

    Cancer signaling networks and their implications for personalized medicine. / Creixell, Pau; Linding, Rune (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 113 p.

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

  94. Published
  95. Published

    ChemProt: A disease chemical biology database. / Taboureau, Olivier ; Oprea, Tudor I.

    Computational Chemogenomics. Pan Stanford Publishing, 2013.

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

  96. 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

  97. Published

    Colorectal cancer cell lines made resistant to SN38-and Oxaliplatin: Roles of altered ion transporter function in resistance?. / Sandra, Christensen; Jensen, Niels Frank; Stoeckel, Johanne Danmark; Belling, Kirstine C.; Romer, Maria Unni; Gupta, Ramneek; Brunner, Nils; Pedersen, Stine Helene Falsig; Stenvang, Jan.

    In: F A S E B Journal, Vol. 27, lb452, 2013.

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

  98. Published

    Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus. / Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun.

    ABSTRACTS: 7th Annual Meeting EPIZONE. 2013. p. 124 D 2.

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

  99. Published

    Comparison of typing by whole genome sequencing (WGS) and pulsed field gel electrophoresis (PFGE) of isolates from a hospital outbreak with a CTX-M-15 producing Klebsiella pneumoniae. / Hansen, D. S.; Kaas, Rolf Sommer; Nielsen, E. M.; Aarestrup, Frank Møller; Hasman, Henrik.

    10th International Meeting on Microbial Epidemiological Markers (IMMEM-10) - Abstract Book. Paris, France, 2013. p. 154.

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

  100. Published

    Complete genes may pass from food to human blood. / Spisák, Sándor; Solymosi, Norbert; Ittzés, Péter; Bodor, András; Kondor, Dániel; Vattay, Gábor; Barták, Barbara K; Sipos, Ferenc; Galamb, Orsolya; Tulassay, Zsolt; Szállási, Zoltán; Rasmussen, Simon; Sicheritz-Ponten, Thomas; Brunak, Søren; Molnár, Béla; Csabai, István.

    In: PloS one., Vol. 8, No. 7, e69805, 2013, p. 11.

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

  101. Published

    Computational approaches to identify functional genetic variants in cancer genomes.. / Gonzalez-Perez, Abel; Mustonen, Ville; Reva, Boris; Ritchie, Graham R S; Creixell, Pau; Karchin, Rachel; Vazquez, Miguel; Fink, J Lynn; Kassahn, Karin S; Pearson, John V; Bader, Gary D; Boutros, Paul C; Muthuswamy, Lakshmi; Ouellette, B F Francis; Reimand, Jüri; Linding, Rune; Shibata, Tatsuhiro; Valencia, Alfonso; Butler, Adam; Dronov, Serge; Flicek, Paul; Shannon, Nick B; Carter, Hannah; Ding, Li; Sander, Chris; Stuart, Josh M; Stein, Lincoln D; Lopez-Bigas, Nuria.

    In: Nature Methods, Vol. 10, No. 8, 2013, p. 723-729.

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

  102. Published

    Computational optimisation of targeted DNA sequencing for cancer detection.. / Martinez, Pierre; McGranahan, Nicholas; Birkbak, Nicolai Juul; Gerlinger, Marco; Swanton, Charles.

    In: Scientific Reports, Vol. 3, 2013, p. 3309.

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

  103. Published

    Concordance of gene expression in human protein complexes reveals tissue specificity and pathology. / Börnigen, Daniela; Pers, Tune Hannes; Thorrez, Lieven; Huttenhower, Curtis; Moreau, Yves; Brunak, Søren.

    In: Nucleic Acids Research, Vol. 41, No. 18, e171, 2013.

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

  104. 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

  105. Published
  106. 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

  107. Published

    Deep phenotyping of the unselected COPSAC2010 birth cohort study. / Bisgaard, Hans Flinker; Vissing, Nadja Hawwa; Carson, C. G.; Bischoff, Anne Louise; Følsgaard, Nilofar Vahman; Kreiner‐Møller, E.; Chawes, Bo Lund Krogsgaard; Stokholm, J.; Pedersen, L.; Bjarnadóttir, E.; Thysen, Anna Hammerich; Nilsson, E.; Mortensen, L. J.; Olsen, S. F.; Schjørring, S.; Krogfelt, Karen Angeliki; Lauritzen, L.; Pedersen, Susanne Brix; Bønnelykke, K.

    In: Clinical & Experimental Allergy, Vol. 43, No. 12, 2013, p. 1384-1394.

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

  108. Published

    Detection of serological biomarkers by proximity extension assay for detection of colorectal neoplasias in symptomatic individuals. / Buch Thorsen, Stine ; Lundberg, Martin ; Villablanca, Andrea ; Christensen, Sarah Louise T.; Belling, Kirstine C.; Sander Nielsen, Birgitte ; Knowles, Mick ; Gee, Nick; Nielsen, Hans Jørgen ; Brünner, Nils; Jarle Christensen, Ib ; Fredriksson, Simon ; Stenvang, Jan ; Assarsson, Erika.

    In: Journal of Translational Medicine, Vol. 11, 253, 2013.

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

  109. Published
  110. Published
  111. 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

  112. Published

    Docosahexaenoic acid status at 9 months is inversely associated with communicative skills in 3-year-old girls. / Engel, Sara; Tronhjem, Kathrine Marie Hagerup; Hellgren, Lars; Michaelsen, Kim F.; Lauritzen, Lotte.

    In: Maternal and Child Nutrition, Vol. 9, No. 4, 2013, p. 499-510.

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

  113. Published

    Effect of gestation on obesity-induced hepatic and placental inflammation in mice. / Ingvorsen, Camilla; Thysen, Anna Hammerich; Fernandez-Twinn , Denise ; Ozanne, Susan E.; Pedersen, Susanne Brix; Hellgren, Lars.

    2013. Abstract from Abcam Symposium: Programming Obesity, Cambridge, United Kingdom.

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

  114. Published

    Effects of butter from mountain-pasture grazing cows on risk markers of the metabolic syndrome compared with conventional Danish butter: a randomized controlled study.. / Werner, Louise Bruun; Hellgren, Lars; Raff, Marianne; Jensen, Søren K.; Petersen, Rikke A.; Drachmann, Tue; Tholstrup, Tine.

    In: Lipids in Health and Disease, Vol. 12, No. 99, 2013.

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

  115. Published

    Effects of maternal energy intake during gestation and lactation on leptin levels in the young and adult pups. / Ingvorsen, Camilla; Hellgren, Lars.

    2013. Abstract from Annual meeting in Dansk Selskab for Adipositasforskning, Odense, Denmark.

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

  116. Published
  117. Published

    Emerging trends in the discovery of natural product antibacterials. / Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor; Melançon, Charles E, III; Tegos, George P.

    In: Current Opinion in Pharmacology, Vol. 13, No. 5, 2013, p. 678-687.

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

  118. Published

    NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. / Karosiene, Edita; Rasmussen, Michael; Blicher, Thomas; Lund, Ole; Buus, S.; Nielsen, Morten Munch.

    In: Immunogenetics, Vol. 65, No. 10, 2013, p. 711-724.

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

  119. Published
  120. Published

    Epitope prediction methods. / Karosiene, Edita; Nielsen, Morten (Main supervisor); Lund, Ole (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 127 p.

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

  121. Published

    Evaluation of peptide selection approaches for epitope‐based vaccine design. / Schubert, B.; Lund, Ole; Nielsen, Morten.

    In: Tissue Antigens, Vol. 82, No. 4, 2013, p. 243–251.

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

  122. Published

    Exome mutation burden predicts clinical outcome in ovarian cancer carrying mutated BRCA1 and BRCA2 genes. / Birkbak, Nicolai Juul; Kochupurakkal, Bose; Gonzalez-Izarzugaza, Jose Maria; Li, Yang; Liu, Joyce; Szallasi, Zoltan Imre; Matulonis, Ursula; Richardson, Andrea L.; Iglehart, J. Dirk; Wang, Zhigang C.

    In: Cancer Research, Vol. 73, No. S1, 2013.

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

  123. E-pub ahead of print

    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. / Kouskoumvekaki, Irene; Shublaq, Nour ; Brunak, Søren.

    In: Briefings in Bioinformatics, 2013.

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

  124. Published

    FADS genotype and diet are important determinants of DHA status: a cross-sectional study in Danish infants1-3. / 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

  125. 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

  126. Published

    From viral genome to specific peptide epitopes: methods for identifying porcine T cell epitopes based on in silico predictions, in vitro identification and ex vivo verification. / Pedersen, Lasse Eggers; Rasmussen, Michael; Harndah, Mikkel; Patch, Jared; Nielsen, Morten; Buus, Søren; Golde, William; Jungersen, Gregers.

    In: Journal of Immunology, Vol. 190, 2013.

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

  127. Published

    Functional Similarities and Disparities in Inflammation-Promoting Abilities of Gut-Derived Escherichia coli Strains from Patients with Inflammatory Bowel Diseases and Healthy Individuals. / Jensen, Stina Rikke; Mirsepasi, H.; Thysen, A.H.; Brynskov, J.; Krogfelt, K.; Petersen, A. M.; Pedersen, A. E.; Pedersen, Susanne Brix.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 266-267.

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

  128. Published

    Genetic and antigenic characterization of influenza A virus circulating in Danish swine during the past decade. / Fobian, Kristina; Kirk, Isa Kristina; Breum, Solvej Østergaard; Lewis, Nicola; Hjulsager, Charlotte Kristiane; Larsen, Lars Erik.

    2013. Abstract from Influenza2013, Oxford, United Kingdom.

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

  129. Published

    Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. / Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon; Nielsen, Henrik Bjørn; Mundy, John; Bones, Atle M.

    In: BMC Genomics, Vol. 14, No. 1, 2013, p. 722.

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

  130. Published
  131. 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

  132. Published

    Genome-wide meta-analysis identifies new susceptibility loci for migraine.. / Anttila, Verneri; Winsvold, Bendik S; Gormley, Padhraig; Kurth, Tobias; Bettella, Francesco; McMahon, George; Kallela, Mikko; Malik, Rainer; de Vries, Boukje; Terwindt, Gisela; Medland, Sarah E; Todt, Unda; McArdle, Wendy L; Quaye, Lydia; Koiranen, Markku; Ikram, M Arfan; Lehtimäki, Terho; Stam, Anine H; Ligthart, Lannie; Wedenoja, Juho; Dunham, Ian; Neale, Benjamin M; Palta, Priit; Hamalainen, Eija; Schürks, Markus; Rose, Lynda M; Buring, Julie E; Ridker, Paul M; Steinberg, Stacy; Stefansson, Hreinn; Jakobsson, Finnbogi; Lawlor, Debbie A; Evans, David M; Ring, Susan M; Färkkilä, Markus; Artto, Ville; Kaunisto, Mari A; Freilinger, Tobias; Schoenen, Jean; Frants, Rune R; Pelzer, Nadine; Weller, Claudia M; Zielman, Ronald; Heath, Andrew C; Madden, Pamela A F; Montgomery, Grant W; Martin, Nicholas G; Borck, Guntram; Göbel, Hartmut; Heinze, Axel; Heinze-Kuhn, Katja; Williams, Frances M K; Hartikainen, Anna-Liisa; Pouta, Anneli; van den Ende, Joyce; Uitterlinden, Andre G; Hofman, Albert; Amin, Najaf; Hottenga, Jouke-Jan; Vink, Jacqueline M; Heikkilä, Kauko; Alexander, Michael; Muller-Myhsok, Bertram; Schreiber, Stefan; Meitinger, Thomas; Wichmann, Heinz Erich; Aromaa, Arpo; Eriksson, Johan G; Traynor, Bryan J; Trabzuni, Daniah; Rossin, Elizabeth; Hansen, Kasper Lage; Jacobs, Suzanne B R; Gibbs, J Raphael; Birney, Ewan; Kaprio, Jaakko; Penninx, Brenda W; Boomsma, Dorret I; van Duijn, Cornelia; Raitakari, Olli; Jarvelin, Marjo-Riitta; Zwart, John-Anker; Cherkas, Lynn; Strachan, David P; Kubisch, Christian; Ferrari, Michel D; van den Maagdenberg, Arn M J M; Dichgans, Martin; Wessman, Maija; Smith, George Davey; Stefansson, Kari; Daly, Mark J; Nyholt, Dale R; Chasman, Daniel I; Palotie, Aarno.

    In: Nature Genetics, Vol. 45, No. 8, 2013.

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

  133. Published
  134. Published
  135. Published

    Gestation reverses obesity-induced hepatic inflammation in mice. / Ingvorsen, Camilla; Thysen, Anna Hammerich; Fernandez-Twinn , Denise ; Ozanne, Susan E.; Pedersen, Susanne Brix; Hellgren, Lars.

    2013. Poster session presented at Joint Symposium of Centre for Fetal programming and Early Nutrition Consortium, Hellerup, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2013

  136. Published

    Gestation reverses obesity-induced hepatic inflammation in mice. / Ingvorsen, Camilla; Thysen, Anna Hammerich; Fernandez-Twinn , Denise ; Ozanne, Susan E.; Pedersen, Susanne Brix; Hellgren, Lars.

    In: Acta Obstetricia et Gynecologica Scandinavica, Vol. 92, No. SI 160, 2013, p. 19-20.

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

  137. Published

    Global characterization of signalling networks associated with tamoxifen resistance in breast cancer. / Browne, Brigid C.; Hochgräfe, Falko; Wu, Jianmin; Millar, Ewan K. A.; Barraclough, Jane; Stone, Andrew; McCloy, Rachael A.; Lee, Christine S.; Roberts, Caroline; Ali, Naveid A.; Boulghourjian, Alice; Schmich, Fabian; Linding, Rune; Farrow, Lynn; Gee, Julia M. W.; Nicholson, Robert I.; O'Toole, Sandra A.; Sutherland, Robert L.; Musgrove, Elizabeth A.; Butt, Alison J.; Daly, Roger J.

    In: F E B S Journal, Vol. 280, No. 21, 2013, p. 5237-5257.

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

  138. Published

    Glucagon-Like Peptide-1 Protects Human Islets against Cytokine-Mediated β-Cell Dysfunction and Death: A Proteomic Study of the Pathways Involved. / Rondas, Dieter; Bugliani, Marco; D’Hertog, Wannes; Hansen, Kasper Lage; Masini, Mathilde; Waelkens, Etienne; Marchetti, Piero; Mathieu, Chantal; Overbergh, Lut.

    In: Journal of Proteome Research, Vol. 12, No. 9, 2013, p. 204193-4206.

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

  139. Published

    Gut Mucosal Regulation of Distinct Macrophage and Dendritic Cell Subsets During Early Stage Salmonella Infection. / Sørensen, Rikke Brandt; Petersen, A.; Larsen, Jeppe Madura; Licht, Tine Rask; Pedersen, Susanne Brix.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 262-263.

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

  140. Published

    HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis. / Adelman, Carrie A.; Lolo, Rafal L.; Birkbak, Nicolai Juul; Murina, Olga; Matsuzaki, Kenichiro; Horejsi, Zuzana; Parmar, Kalindi; Borel, Valérie; Skehel, J. Mark; Stamp, Gordon; D'Andrea, Alan; Sartori, Alessandro A; Swanton, Charles; Boulton, Simon J.

    In: Nature, Vol. 502, 2013, p. 381-384.

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

  141. Published
  142. Published

    High-Mannose Glycosylation of Infectious HIV-1 gp120 and Immune Regulation in Human Plasmacytoid Dendritic Cells. / Søndergaard, Jonas Nørskov; Vinner, L.; Pedersen, Susanne Brix.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 264-265.

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

  143. Published

    Identification of a novel immunoregulatory signaling pathway exploited by M. tuberculosis in dendritic cells. / Laursen, Janne Marie; Schoof, Erwin; Søndergaard, Jonas Nørskov; Linding, Rune; Pedersen, Susanne Brix.

    2013. Abstract from 15th International Congress of Immunology, Milan, Italy.

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

  144. Published

    Identification of a novel immunoregulatory signaling pathway exploited by M. tuberculosis in dendritic cells. / Laursen, Janne Marie; Schoof, Erwin; Søndergaard, Jonas Nørskov; Linding, Rune; Pedersen, Susanne Brix.

    2013. Abstract from 14th International conference on Systems Biology, Copenhagen, Denmark.

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

  145. Published
  146. Published
  147. 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

  148. 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

  149. 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

  150. 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: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 317-318.

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

  151. Published

    Improving data and knowledge management to better integrate health care and research. / Cases, M.; Furlong, L. I.; Albanell, J.; Altman, R. B.; Bellazzi, R.; Boyer, S.; Brand, A.; Brookes, A. J.; Brunak, Søren; Clark, T.W.; Gea, J.; Ghazal, P.; Graf, N.; Guigó, R.; Klein, T. E.; López‐Bigas, N.; Maojo, V.; Mons, B.; Musen, M.; Oliveira, J. L.; Rowe, A.; Ruch, P.; Shabo, A.; Shortliffe, E. H.; Valencia, A.; Lei, J., van der; Mayer, M. A.; Sanz, F.

    In: Journal of Internal Medicine, Vol. 274, No. 4, 2013, p. 321-328.

    Publication: Research - peer-reviewEditorial – Annual report year: 2013

  152. Published

    Inconsistency in large pharmacogenomic studies. / Haibe-Kains, Benjamin; El-Hachem, Nehme; Birkbak, Nicolai Juul; Jin, Andrew C.; Beck, Andrew H; Aerts, Hugo J. W. L.; Quackenbush, John.

    In: Nature, Vol. 504, No. 7480, 2013, p. 389–393.

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

  153. Published

    In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function. / Follin, Elna; Karlsson, Maria; Lundegaard, Claus; Nielsen, Morten; Wallin, Stefan; Paulsson, Kajsa Maria; Westerdahl, Helena.

    In: Immunogenetics, Vol. 65, No. 4, 2013, p. 299-311.

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

  154. Published

    Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. / Khurana, Ekta; Fu, Yao; Colonna, Vincenza; Mu, Xinmeng Jasmine; Kang, Hyun Min; Lappalainen, Tuuli; Sboner, Andrea; Lochovsky, Lucas; Chen, Jieming; Harmanci, Arif; Das, Jishnu; Abyzov, Alexej; Balasubramanian, Suganthi; Beal, Kathryn; Chakravarty, Dimple; Challis, Daniel; Chen, Yuan; Clarke, Declan; Clarke, Laura; Cunningham, Fiona; Evani, Uday S.; Flicek, Paul; Fragoza, Robert; Garrison, Erik; Gibbs, Richard; Gümüş, Zeynep H.; Herrero, Javier; Kitabayashi, Naoki; Kong, Yong; Lage, Kasper; Liluashvili, Vaja; Lipkin, Steven M.; MacArthur, Daniel G.; Marth, Gabor; Muzny, Donna; Pers, Tune Hannes; Ritchie, Graham R. S.; Rosenfeld, Jeffrey A.; Sisu, Cristina; Wei, Xiaomu; Wilson, Michael; Xue, Yali; Yu, Fuli; Dermitzakis, Emmanouil T.; Yu, Haiyuan; Rubin, Mark A.; Tyler-Smith, Chris; Gerstein, Mark.

    In: Science, Vol. 342, No. 6154, 1235587, 2013.

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

  155. Published

    Internet-Based Solutions for Analysis of Next-Generation Sequence Data. / Larsen, Mette Voldby.

    In: Journal of Clinical Microbiology, Vol. 51, No. 9, 2013, p. 3162-3162.

    Publication: Research - peer-reviewLetter – Annual report year: 2013

  156. 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

  157. Published

    Kinetic Model for Signal Binding to the Quorum Sensing Regulator LasR. / Claussen, Anetta; Jakobsen, Tim Holm; Bjarnsholt, Thomas; Givskov, Michael; Welch, Martin; Ferkinghoff-Borg, Jesper; Sams, Thomas.

    In: International Journal of Molecular Sciences (Online), Vol. 14, No. 7, 2013, p. 13360-13376.

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

  158. Published

    LC-MS at core of university-industry link. / Linding, Rune.

    In: Trends in Analytical Chemistry, Vol. 51, 2013, p. VIII-IX.

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

  159. 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

  160. 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 - peer-reviewConference abstract for conference – Annual report year: 2013

  161. Published

    Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads. / Gautier, Laurent; Lund, Ole.

    In: P L o S One, Vol. 8, No. 12, e83784, 2013.

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

  162. Published

    Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae.. / Jewett, Michael Christopher; Workman, Christopher; Nookaew, Intawat; Pizarro, Francisco A; Agosin, Eduardo; Hellgren, Lars; Nielsen, Jens.

    In: G3 Defence, Vol. 3, No. 11, 2013, p. 1979-1995.

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

  163. Published

    Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.. / Bønnelykke, Klaus; Matheson, Melanie C; Pers, Tune Hannes; Granell, Raquel; Strachan, David P; Alves, Alexessander Couto; Linneberg, Allan René; Curtin, John A; Warrington, Nicole M; Standl, Marie; Kerkhof, Marjan; Jonsdottir, Ingileif; Bukvic, Blazenka K; Kaakinen, Marika; Sleimann, Patrick; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Schramm, Katharina; Baltic, Svetlana; Kreiner-Møller, Eskil; Simpson, Angela; Pourcain, Beate St; Coin, Lachlan; Hui, Jennie; Walters, Eugene H; Tiesler, Carla M T; Duffy, David L; Jones, Graham; Ring, Susan M; McArdle, Wendy L; Price, Loren; Robertson, Colin F; Pekkanen, Juha; Tang, Clara S; Thiering, Elisabeth; Montgomery, Grant W; Hartikainen, Anna-Liisa; Dharmage, Shyamali C; Husemoen, Lise Lotte Nystrup; Herder, Christian; Kemp, John P; Elliot, Paul; James, Alan; Waldenberger, Melanie; Abramson, Michael J; Fairfax, Benjamin P; Knight, Julian C; Gupta, Ramneek; Thompson, Philip J; Holt, Patrick; Sly, Peter; Hirschhorn, Joel N; Blekic, Mario; Weidinger, Stephan; Hakonarsson, Hakon; Stefansson, Kari; Heinrich, Joachim; Postma, Dirkje S; Custovic, Adnan; Pennell, Craig E; Jarvelin, Marjo-Riitta; Koppelman, Gerard H; Timpson, Nicholas; Ferreira, Manuel A; Bisgaard, Hans; Henderson, A John.

    In: Nature Genetics, 2013.

    Publication: Research - peer-reviewLetter – Annual report year: 2013

  164. Published

    Metagenomic Analysis of the Human Gut Microbiome. / dos Santos, Marcelo Bertalan Quintanilha; Nielsen, Henrik Bjørn (Supervisor); Sicheritz-Pontén, Thomas (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 117 p.

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

  165. Published

    Metagenomic species profiling using universal phylogenetic marker genes. / Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg; Izquierdo-Carrasco, Fernando; Berger, Simon A; Kultima, Jens Roat; Coelho, Luis Pedro; Arumugam, Manimozhiyan; Tap, Julien; Nielsen, Henrik Bjørn; Rasmussen, Simon; Brunak, Søren; Pedersen, Oluf; Guarner, Francisco; de Vos, Willem M; Wang, Jun; Li, Junhua; Doré, Joël; Ehrlich, S Dusko; Stamatakis, Alexandros; Bork, Peer.

    In: Nature Methods, Vol. 10, No. 12, 2013, p. 1196–1199.

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

  166. Published

    MetaRanker 2.0: a web server for prioritization of genetic variation data. / Pers, Tune Hannes; Dworzynski, Piotr; Thomas, Cecilia Engel; Hansen, Kasper Lage; Brunak, Søren.

    In: Nucleic Acids Research, Vol. 41, No. Web Server issue, 2013, p. W104-W108.

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

  167. Published

    Methods for predicting anti-cancer response. / Szallasi, Zoltan Imre (Inventor); Eklund, Aron Charles (Inventor); Birkbak, Nicolai Juul (Inventor); Richardson, Andrea L. (Inventor); Silver, Daniel P. (Inventor); Wang, Zhigang (Inventor).

    IPC No.: C12Q1/68. Patent No.: WO2013130347. Sep 06, 2013.

    Publication: ResearchPatent – Annual report year: 2012

  168. Published

    MHCcluster, a method for functional clustering of MHC molecules. / Thomsen, Martin Christen Frølund; Lundegaard, Claus; Buus, Søren; Lund, Ole; Nielsen, Morten.

    In: Immunogenetics, Vol. 65, No. 9, 2013, p. 655-665.

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

  169. Published

    MicroRNA profiling in ocular adnexal lymphoma: a role for MYC and NFKB1 mediated dysregulation of microRNA expression in aggressive disease. / Hother, Christoffer; Rasmussen, Peter Kristian; Joshi, Tejal; Reker, Ditte; Ralfkiær, Ulrik; Workman, Christopher; Heegaard, Steffen; Ralfkiær, Elisabeth; Grønbæk, Kirsten.

    In: Investigative Ophthalmology & Visual Science, Vol. 54, No. 8, 2013, p. 5169-5175.

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

  170. Published

    MISTIC: mutual information server to infer coevolution. / Simonetti, Franco L.; Teppa, Elin; Chernomoretz, Ariel; Nielsen, Morten; Marino Buslje, Cristina.

    In: Nucleic Acids Research, Vol. 41, No. W1, 2013, p. 20W8-W14.

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

  171. Published

    Molecular signaling networks in regulation of immunity and disease. / Laursen, Janne Marie; Jensen, Stina Rikke; Sørensen, Morten; Pedersen, Susanne Brix.

    2013. Abstract from Copenhagen Bioscience Conference – Genomics in metabolism, Snekkersten, Denmark.

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

  172. Published

    Monitoring Expansion of T Cell Specifities Against Foot-and-Mpouth-Disease Virus (FMDV) in Swine With MHC Class I Tetramers Following a Prime/Boost Vaccination. / Pedersen, Lasse Eggers; Patch, J.; Glabman, R.; Kenney, M.; Nielsen, Morten; Buus, S.; Jungersen, Gregers; Golde, W. T.

    10th International Veterinary Immunology Symposium - IVIS 2013. 2013. p. 72 CS05.5.

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

  173. 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

  174. Published

    NetFCM: A Tool for Automated Flow Cytometric Data Analysis. / Frederiksen, Juliet Wairimu; Lund, Ole; Buggert, M.; Karlsson, A.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 44, 2013, p. 325.

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

  175. Published

    NETMHCSTAB - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. / Jørgensen, Kasper W.; Rasmussen, Michael; Buus, Søren; Nielsen, Morten.

    In: Immunology, Vol. 141, No. 1, 2013, p. 18-26.

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

  176. Published

    Obesity-induced hepatic and placental inflammation are absent in obese gestating mice compared to control fed dams. / Ingvorsen, Camilla; Thysen, Anna Hammerich; Fernandez-Twinn, Denise; Ozanne, Susan E.; Pedersen, Susanne Brix; Hellgren, Lars.

    2013. Abstract from 15th European Congress of Endocrinology 2013, Copenhagen, Denmark.

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

  177. Published

    Offspring from rat mothers fed a high-fat/high-sucrose diet during gestation and lactation accumulate free fatty acids in the liver when exposed to high fat diet as adults.. / Hellgren, Lars; Ingvorsen, Camilla.

    2013. Abstract from 11th Euro Fed Lipid Congress, Antalya, Turkey.

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

  178. Published

    Parallel evolution of tumor subclones mimics diversity between tumors. / Martinez, Pierre; Birkbak, Nicolai Juul; Gerlinger, Marco; McGranahan, Nicholas; Burrell, Rebecca; Rowan, Andrew; Joshi, Tejal; Fisher, Rosalie; Larkin, James; Szallasi, Zoltan Imre; Swanton, Charles.

    In: Journal of Pathology, Vol. 230, No. 4, 2013, p. 356-364.

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

  179. Published

    PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data.. / Cosentino, Salvatore; Larsen, Mette Voldby; Aarestrup, Frank Møller; Lund, Ole.

    In: PloS one., Vol. 8, No. 10, 2013, p. e77302.

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

  180. Published

    Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release.. / Følsgaard, Nilofar Vahman; Schjørring, Susanne; Chawes, Bo Lund Krogsgaard; Rasmussen, Morten; Krogfelt, Karen Angeliki; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: American Journal of Respiratory and Critical Care Medicine, Vol. 187, No. 6, 2013, p. 589-595.

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

  181. Published

    Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. / Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas; Nakjang, Sirintra; Martin Embley, T; Hirt, Robert P.

    In: Genome Biology, Vol. 14, No. 2, 2013, p. R19.

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

  182. Published

    Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. / Mothé, Bianca R.; Southwood, Scott; Sidney, John; English, A. Michelle; Wriston, Amanda; Hoof, Ilka; Shabanowitz, Jeffrey; Hunt, Donald F.; Sette, Alessandro.

    In: Immunogenetics, Vol. 65, No. 5, 2013, p. 371-386.

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

  183. Published

    Perinatal programming of metabolic dysfunction and obesity-induced inflammation. / Ingvorsen, Camilla; Hellgren, Lars; Pedersen, Susanne Brix.

    Kgs. Lyngby : Technical University of Denmark, 2013. 184 p.

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

  184. Published

    Personalized Network-Based Treatments in Oncology. / Robin, Xavier; Creixell, Pau; Radetskaya, Oxana; Santina, Cristina Costa; Longden, James; Linding, Rune.

    In: Clinical Pharmacology and Therapeutics, Vol. 94, No. 6, 2013, p. 646-650.

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

  185. Published

    PHAISTOS : A framework for Markov chain Monte Carlo simulation and inference of protein structure. / Boomsma, Wouter; Frellsen, Jes; Harder, Tim; Bottaro, Sandro; Johansson, Kristoffer E.; Tian, Pengfei; Stovgaard, Kasper; Andreetta, Christian; Olsson, Simon; Valentin, Jan B.; Antonov, Lubomir D.; Christensen, Anders; Borg, Mikael; Jensen, Jan H.; Lindorff‐Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas.

    In: Journal of Computational Chemistry, Vol. 34, No. 19, 2013, p. 1697-1705.

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

  186. Published

    Pharmacological profiling of drugs by linking chemoinformatics and bioinformatics data. / Taboureau, Olivier .

    In: Abstracts of Papers of the American Chemical Society, Vol. 245, 71-CINF, 2013.

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

  187. Published

    Phytanic acid stimulates glucose uptake in a model of skeletal muscles, the primary porcine myotubes. / Che, Brita Ngum; Oksbjerg, Niels; Hellgren, Lars; Nielsen, Jacob H; Young, Jette F.

    In: Lipids in Health and Disease, Vol. 12, No. 1, 2013, p. 14.

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

  188. Published

    Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1.. / Wohlfahrt-Veje, Christine; Audouze, Karine Marie Laure; Brunak, Søren; Antignac, Jean Philippe; le Bizec, Bruno; Juul, Anders ; Skakkebæk, Niels E.; Main, Katharina Maria.

    In: Reproduction, Vol. 147, No. 4, 2013, p. 391-399.

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

  189. Published

    Polymorphism in the fatty acid desaturase genes and diet are important determinants of infant n-3 fatty acid status.. / Harsløf, L.B.S.; Larsen, L.H.; Ritz, C.; Hellgren, Lars; Michaelsen, K. F.; Vogel, U.; Lauritzen, L.

    2013. Abstract from IUNS 20th International Congress of Nutrition, Granada, Spain.

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

  190. Published

    Polymorphisms in the fatty acid desaturase genes and diet are important determinants of infant docosahexaenoic acid status. / Lauritzen, L.; Harsløf, L.; Larsen, L.H.; Ritz, C.; Hellgren, Lars; Michaelsen, K. F.; Vogel, U.

    In: Annals of Nutrition and Metabolism, Vol. 63, No. Suppl. 1, PO133, 2013, p. 320-321.

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

  191. Published

    Postnatal amniotic fluid intake reduces gut inflammatory responses and necrotizing enterocolitis in preterm neonates. / Siggers, Jayda; Østergaard, Mette V.; Siggers, Richard H.; Skovgaard, Kerstin; Mølbak, Lars; Thymann, Thomas; Schmidt, Mette; Møller, Hanne Kristine; Purup, Stig; Fink, Lisbeth Nielsen; Frøkiær, Hanne; Boye, Mette; Sangild, Per T.; Bering, Stine B.

    In: American Journal of Physiology: Gastrointestinal and Liver Physiology, Vol. 304, No. 10, 2013, p. G864-G875.

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

  192. Published

    Pre- and early-postnatal nutrition modify gene and protein expressions of muscle energy metabolism markers and phospholipid fatty acid composition in a muscle type specific manner in sheep.. / Hou, Lei; Kongsted, Alice; Ghoreishi, S. M.; Takhtsabzy, T. K.; Friedrichsen, Martin; Hellgren, Lars; Kadarmideen, Haja; Vaag, Allan; Nielsen, Mette O.

    In: PLoS ONE, Vol. 8, No. 6, 2013, p. e65452 .

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

  193. Published

    Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. / Steentoft, Catharina; Vakhrushev, Sergey; Joshi, Hiren Jitendra; Kong, Yun; Vester-Christensen, Malene B; Schjoldager, Katrine T-BG; Lavrsen, Kirstine; Dabelsteen, Sally Anne Malene; Pedersen, Nis Borbye; Marcos-Silva, Lara; Gupta, Ramneek; Paul Bennett, Eric; Mandel, Ulla; Brunak, Søren; Wandall, Hans H.; Levery, Steven Bruce; Clausen, Henrik.

    In: EMBO Journal, Vol. 32, No. 10, 2013, p. 1478-1488.

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

  194. Published
  195. Published

    Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field. / Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena; Laradji, Mohamed.

    In: Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Vol. 117, No. 15, 2013, p. 4072-4080.

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

  196. Published

    Prognostic and Predictive Markers in Metastatic Renal Cell Carcinoma. / Khattak, Muhammad A.; Bakr, Farrah; Krzystanek, Marcin; Szallasi, Zoltan Imre; Gerlinger, Marco; Santos, Claudio; Swanton, Charles; Pickering, Lisa M.; Gore, Martin E.; Larkin, James M.G.

    In: Journal of Clinical Oncology, Vol. 31, No. 7, 2013, p. 20971-972.

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

  197. Published

    PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development. / Martin, Sarah F.; Falkenberg, Heiner; Dyrlund, Thomas Franck; Khoudoli, Guennadi A.; Mageean, Craig J.; Linding, Rune.

    In: Journal of Proteomics, Vol. 88, 2013, p. 41-46.

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

  198. Published

    Real-Time WGS-based Typing of VTEC Isolates for Surveillance and Outbreak Detection. / Joensen, Katrine Grimstrup; Hasman, Henrik; Scheutz, F.; Nielsen, E. M.; Lund, Ole; Aarestrup, Frank Møller.

    10th International Meeting on Microbial Epidemiological Markers (IMMEM-10) - Abstract Book. Paris, France, 2013. p. 209.

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

  199. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. / Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Johnson, Philip L F; Fumagalli, Matteo; Vilstrup, Julia T; Raghavan, Maanasa; Korneliussen, Thorfinn Sand; Malaspinas, Anna Sapfo; Vogt, Josef Korbinian; Szklarczyk, Damian; Kelstrup, Christian; Vinther, Jakob; Dolocan, Andrei; Stenderup, Jesper; Velazquez, Amhed M. V.; Cahill, James; Rasmussen, Morten; Wang, Xiaoli; Min, Jiumeng; Zazula, Grant D; Seguin-Orlando, Andaine; Mortensen, Cecilie; Magnussen, Kim; Thompson, John F; Weinstock, Jacobo; Gregersen, Magnus Kristian; Røed, Knut H; Eisenmann, Véra; Rubin, Carl J; Miller, Donald C; Antczak, Douglas F; Bertelsen, Mads; Brunak, Søren; Al-Rasheid, Khaled A S; Ryder, Oliver; Andersson, Leif; Mundy, John; Krogh, Anders; Gilbert, Marcus Thomas Pius; Kjær, Kurt H.; Sicheritz-Pontén, Thomas; Jensen, Lars Juhl; Olsen, Jesper; Hofreiter, Michael; Nielsen, Rasmus; Shapiro, Beth; Wang, Jun; Willerslev, Eske.

    In: Nature, Vol. 499, 2013, p. 74-78.

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

  200. Published

    Reconstructing the highly virulent Classical Swine Fever Virus strain Koslov. / Fahnøe, Ulrik; Pedersen, Anders Gorm; Nielsen, Jens; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun.

    2013. Abstract from SMBE 2013 – Annual Meeting of the Society for Molecular Biology and Evolution, Chicago, IL, United States.

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

  201. Published

    Regulatory Coordination between Two Major Intracellular Homeostatic Systems : Heat shock response and autophagy. / Dokladny, Karol; Zuhl, Micah Nathaniel; Mandell, Michael; Bhattacharya, Dhruva; Schneider, Suzanne; Deretic, Vojo; Moseley, Pope.

    In: Journal of Biological Chemistry, Vol. 288, No. 21, 2013, p. 14959-14972.

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

  202. Published

    Reply to 'Mining electronic health records: an additional perspective'. / Jensen, Peter B.; Jensen, Lars J.; Brunak, Søren.

    In: Nature Reviews. Genetics, Vol. 14, No. 1, 2013, p. -.

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

  203. Published

    Richness of human gut microbiome correlates with metabolic markers.. / Le Chatelier, Emmanuelle; Nielsen, Trine; Qin, Junjie; Prifti, Edi; Hildebrand, Falk; Falony, Gwen; Almeida, Mathieu; Arumugam, Manimozhiyan; Batto, Jean-Michel; Kennedy, Sean; Leonard, Pierre; Li, Junhua; Burgdorf, Kristoffer; Grarup, Niels; Jørgensen, Torben; Brandslund, Ivan; Nielsen, Henrik Bjørn; Juncker, Agnieszka; dos Santos, Marcelo Bertalan Quintanilha; Levenez, Florence; Pons, Nicolas; Rasmussen, Simon; Sunagawa, Shinichi; Tap, Julien; Tims, Sebastian; Zoetendal, Erwin G; Brunak, Søren; Clément, Karine; Doré, Joël; Kleerebezem, Michiel; Kristiansen, Karsten; Renault, Pierre; Sicheritz-Pontén, Thomas; de Vos, Willem M.; Zucker, Jean-Daniel; Raes, Jeroen; Hansen, Torben; Bork, Peer; Wang, Jun; Ehrlich, S Dusko; Pedersen, Oluf.

    In: Nature, Vol. 500, No. 7464, 2013, p. 541-546.

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

  204. Published

    Scientific competency questions as the basis for semantically enriched open pharmacological space development. / Azzaoui, Kamal; Jacoby, Edgar; Senger, Stefan; Rodríguez, Emiliano Cuadrado; Loza, Mabel; Zdrazil, Barbara; Pinto, Marta; Williams, Antony J.; de la Torre, Victor; Mestres, Jordi; Pastor, Manuel; Taboureau, Olivier ; Rarey, Matthias; Chichester, Christine; Pettifer, Steve; Blomberg, Niklas; Harland, Lee; Williams-Jones, Bryn; Ecker, Gerhard F.

    In: Drug Discovery Today, Vol. 18, No. 17-18, 2013, p. 843-852.

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

  205. Published

    Sigma factors in a thousand E. coli genomes. / Cook, Helen Victoria; Ussery, David.

    In: Environmental Microbiology, Vol. 15, No. 12, 2013, p. 3121-3129.

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

  206. Published

    SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. / Jessen, Leon Ivar; Hoof, Ilka; Lund, Ole; Nielsen, Morten.

    In: Nucleic Acids Research, Vol. 41, No. W1, 2013, p. 20W286-W291.

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

  207. Published

    Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. / Andreatta, Massimo; Lund, Ole; Nielsen, Morten.

    In: Bioinformatics, Vol. 29, No. 1, 2013, p. 8-14.

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

  208. Published

    Structural analysis of B-cell epitopes in antibody:protein complexes. / Kringelum, Jens Vindahl; Nielsen, Morten; Padkjær, Søren Berg; Lund, Ole.

    In: Molecular Immunology, Vol. 53, No. 1-2, 2013, p. 24-34.

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

  209. Published

    Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs). / Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas; Panagiotou, Gianni.

    Systems Metabolic Engineering : Methods and Protocols. Springer, 2013. p. 409-428 (Methods in Molecular Biology, Vol. 985).

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

  210. Published

    Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4+ T cell depletion.. / Perez, Carina L. ; Milush, Jeffrey M. ; Buggert, Marcus; Eriksson, Emily M. ; Larsen, Mette Voldby; Liegler, Teri; Hartogensis, Wendy; Bacchetti, Peter; Lund, Ole; Hecht, Frederick M. ; Nixon, Douglas F. ; Karlsson, Annika C. .

    In: AIDS Research and Human Retroviruses, Vol. 29, No. 3, 2013, p. 602-612.

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

  211. Published

    Temporal variability in urinary phthalate metabolite excretion based on spot, morning, and 24-h urine samples: Considerations for epidemiological studies. / Frederiksen, Hanne; Kranich, Selma K.; Jørgensen, Niels; Taboureau, Olivier ; Petersen, Jørgen H.; Andersson, Anna-Maria.

    In: Environmental Science and Technology, Vol. 47, No. 2, 2013, p. 958-967.

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

  212. Published
  213. Published

    The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer.. / Szász, Attila Marcell; Li, Qiyuan; Eklund, Aron Charles; Sztupinszki, Zsófia; Rowan, Andrew; Tőkés, Anna-Mária; Székely, Borbála; Kiss, András; Szendrői, Miklós; Győrffy, Balázs; Szallasi, Zoltan Imre; Swanton, Charles; Kulka, Janina.

    In: PloS one., Vol. 8, No. 2, 2013, p. e56707.

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

  214. Published

    The effect of network biology on drug toxicology.. / Gautier, Laurent; Taboureau, Olivier ; Audouze, Karine Marie Laure.

    In: Expert Opinion on Drug Metabolism & Toxicology, Vol. 9, No. 11, 2013, p. 1409-1418.

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

  215. Published

    The piRNAs forge an immune system for the genome. / Muller, Sébastian; Pandey, R.R.; Pillai, R.S.

    In: Medecine Sciences, Vol. 29, No. 5, 2013, p. 487-494.

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

  216. Published

    The SH2 Domain Interaction Landscape. / Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin Lee; Sacco, Francesca; Olsen, Jesper; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M.; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J.; Castagnoli, Luisa; Cesareni, Gianni.

    In: Cell Reports, Vol. 3, No. 4, 2013, p. 1293-1305.

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

  217. Published

    Time dependent physiological characterization of yeast oxidative stress response and growth modulation of protein kinase/phosphatase mutants. / Altintas, Ali; Workman, Christopher.

    In: Yeast, Vol. 30, No. S1, 2013, p. 156-156.

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

  218. Published

    TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. / Hekmat, Omid; Munk, Stephanie; Fogh, Louise; Yadav, Rachita; Francavilla, Chiara; Horn, Heiko; Wurtz, Sidse Ornbjerg; Schrohl, Anne-Sofie; Damsgaard, Britt; Romer, Maria Unni; Belling, Kirstine C.; Jensen, Niels Frank; Gromova, Irina; Bekker-Jensen, Dorte B; Moreira, Jose Manuel Matos; Jensen, Lars Juhl; Gupta, Ramneek; Lademann, Ulrik; Brunner, Nils; Olsen, Jesper; Stenvang, Jan.

    In: Journal of Proteome Research, Vol. 12, No. 9, 2013, p. 4136–4151.

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

  219. Published

    TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression. / Bjerre, Christina; Vinther, Lena; Belling, Kirstine C.; Würtz, Sidse Ø.; Yadav, Rachita; Lademan, Ulrik; Rigina, Olga; Nguyen Do, Khoa; Ditzel, Henrik Jørn; Lykkesfeldt, Anne Elisabeth; Wang, Jun; Nielsen, Henrik Bjørn; Brünner, Nils; Gupta, Ramneek; Schrohl, Anne-Sofie; Stenvang, Jan.

    In: Tumor Biology, Vol. 34, 2013, p. 3839-3851.

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

  220. Published

    Transcriptome profiling of mice testes following low dose irradiation. / Belling, Kirstine C.; Tanaka, Masami; Dalgaard, Marlene Danner; Nielsen, John Erik; Nielsen, Henrik Bjørn; Brunak, Søren; Almstrup, Kristian; Leffers, Henrik.

    In: Reproductive Biology and Endocrinology, Vol. 11, No. 1, 2013.

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

  221. Published

    Transcriptome Responses to Combinations of Stresses in Arabidopsis. / Rasmussen, Simon; Barah, Pankaj; Suarez-Rodriguez, Maria Cristina; Bressendorff, Simon; Friis, Pia; Costantino, Paolo; Bones, Atle M.; Nielsen, Henrik Bjørn; Mundy, John.

    In: Plant Physiology, Vol. 161, No. 4, 2013, p. 1783-1794.

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

  222. Published

    Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations. / Birkbak, Nicolai Juul; Kochupurakkal, Bose; Gonzalez-Izarzugaza, Jose Maria; Eklund, Aron Charles; Li, Yang; Liu, Joyce; Szallasi, Zoltan Imre; Matulonis, Ursula A. ; Richardson, Andrea L. ; Iglehart, J. Dirk ; Wang, Zhigang C.

    In: P L o S One, Vol. 8, No. 11, e80023, 2013.

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

  223. Published

    VAR2CSA Epitope Identification - Finding All the Needles in All the Haystacks. / Jessen, L. E.; Ditlev, S. B.; Schafer-Nielsen, C.; Buus, S.; Salanti, A.; Lund, Ole.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 318-319.

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

  224. Published

    Veillonella, Firmicutes: Microbes disguised as Gram negatives. / Vesth, Tammi Camilla; Ozen, Asli; Andersen, Sandra Christine; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M.; Ussery, David.

    In: Standards in Genomic Sciences, Vol. 9, No. 2, 2013, p. 431-448.

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

  225. Published

    Whey protein reduces early life weight gain in mice fed a high-fat diet.. / Tranberg, Britt; Hellgren, Lars; Lykkesfeldt, Jens; Sejrsen, Kristen; Jeamet, Aymeric; Rune, Ida; Ellekilde, Merete; Nielsen, Dennis Sandris; Hansen, Axel Kornerup.

    In: PloS one., Vol. 8, No. 8, e71439, 2013.

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

  226. Published

    Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes. / Lohmueller, Kirk E. ; Sparsø, Thomas; Li, Qibin; Andersson, Ehm; Korneliussen, Thorfinn; Albrechtsen, Anders; Banasik, Karina; Grarup, Niels; Hallgrimsdottir, Ingileif; Kiil, Kristoffer; O. Kilpeläinen, Tuomas; T. Krarup, Nikolaj; Pers, Tune Hannes; Sanchez, Gaston; Hu, Youna; DeGiorgio, Michael; Jørgensen, Torben; Sandbæk, Annelli; Lauritzen, Torsten; Brunak, Søren; Kristiansen, Karsten; Li, Yingrui; Hansen, Torben; Wang, Jun; Nielsen, Rasmus; Pedersen, Oluf.

    In: American Journal of Human Genetics, Vol. 93, No. 6, 2013, p. 1072–1086.

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

  227. Published

    wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. / Gonzalez-Izarzugaza, Jose Maria; Vazquez, Miguel; del Pozo, Angela; Valencia, Alfonso.

    In: B M C Bioinformatics, Vol. 14, 345, 2013.

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

  228. 2012
  229. Published

    Absorption difference between diacylglycerol oil and butter blend containing diacylglycerol oil. / Kristensen, Janni Brogaard; Jørgensen, Henry; Mu, Huiling.

    In: European Journal of Lipid Science and Technology, Vol. 114, No. 2, 2012, p. 146-152.

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

  230. Published

    A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). / Hildebrand, Falk; Ebersbach, Tine; Nielsen, Henrik Bjørn; Li, Xiaoping; Sonne, Si Brask; dos Santos, Marcelo Bertalan Quintanilha; Dimitrov, Peter; Madsen, Lise; Qin, Junjie; Wang, Jun; Raes, Jeroen; Kristiansen, Karsten; Licht, Tine Rask.

    In: B M C Genomics, Vol. 13, No. 514, 2012.

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

  231. Published

    A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation.. / Dalgaard, Marlene D; Weinhold, Nils; Edsgard, Stefan Daniel; Silver, Jeremy D; Pers, Tune Hannes; Nielsen, John E.; Jørgensen, Niels; Juul, Anders; Gerds, Thomas A.; Giwercman, Aleksander; Giwercman, Yvonne L.; Cohn-Cedermark, Gabriella; Virtanen, Helena E.; Toppari, Jorma; Daugaard, Gedske; Jensen, Thomas Skøt; Brunak, Søren; Rajpert-De Meyts, Ewa; Skakkebæk, Niels E; Leffers, Henrik; Gupta, Ramneek.

    In: Journal of Medical Genetics, Vol. 49, No. 1, 2012, p. 58-65.

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

  232. Published

    Analysis of cytotoxic T cell epitopes in relation to cancer. / Stranzl, Thomas; Brunak, Søren (Main supervisor); Larsen, Mette Voldby (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 97 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  233. Published
  234. Published

    Androgen receptor signalling in peritubular myoid cells is essential for normal differentiation and function of adult Leydig cells. / Welsh, M.; Moffat, L.; Belling, Kirstine Christensen; de Franca, L. R.; Segatelli, T. M.; Saunders, P. T. K.; Sharpe, R. M.; Smith, L. B.

    In: International Journal of Andrology, Vol. 35, No. 1, 2012, p. 25-40.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  235. Published

    Applied systems biology - vanillin production in Saccharomyces cerevisiae. / Strucko, Tomas; Eriksen, Carsten; Nielsen, J.; Mortensen, Uffe Hasbro.

    In: The F E B S Journal (Online), Vol. 279, No. Supplement s1, 2012, p. 525-525.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2012

  236. Published

    Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures. / Krysiak-Baltyn, Konrad; Toppari, J.; Skakkebaek, N. E.; Jensen, Thomas Skøt; Virtanen, H. E.; Schramm, K.‐W.; Shen, Hao; Vartiainen, T.; Kiviranta, H.; Taboureau, Olivier ; Audouze, Karine Marie Laure; Brunak, S.; Main, K. M.

    In: International Journal of Andrology, Vol. 35, No. 3, 2012, p. 294-302.

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

  237. Published

    A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter. / Skovstrup, Soren; David, Laurent; Taboureau, Olivier; Jorgensen, Flemming Steen.

    In: P L o S One, Vol. 7, No. 6, 2012, p. -.

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

  238. Published

    Bacterial adaptive response to changing herbicide discharge rates in the streambed sediments impacted by a landfill. / Pazarbasi, Meric Batioglu; Bælum, Jacob; Pilloni, Giovanni; Larentis, Micheal; Jacobsen, Carsten S.; Lueders, Tillmann; Hansen, Lars H.; Aamand, Jens .

    2012. Poster session presented at 14th International Symposium on Microbial Ecology, Copenhagen, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2012

  239. Published

    Bayesian prediction of bacterial growth temperature range based on genome sequences. / Jensen, Dan Børge; Vesth, Tammi Camilla; Hallin, Peter Fischer; Pedersen, Anders Gorm; Ussery, David.

    Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology. Vol. 13 2012. (B M C Genomics).

    Publication: Research - peer-reviewArticle in proceedings – Annual report year: 2012

  240. Published

    BDDCS Class Prediction for New Molecular Entities. / Broccatelli, Fabio; Cruciani, Gabriele; Benet, Leslie Z.; Oprea, Tudor.

    In: Molecular Pharmaceutics, Vol. 9, No. 3, 2012, p. 570-580.

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

  241. Published

    Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. / Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D.; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W. G.; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H.; De Las Rivas, Javier; Holberg Blicher, Thomas; Jimenez, Rafael C.; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W.; Lopez, Rodrigo; Attwood, Teresa K.; Brooksbank, Catherine.

    In: Briefings in Bioinformatics, Vol. 13, No. 3, 2012, p. 383-389.

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

  242. Published

    Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets. / Ali, Amjad; Soares, Siomar C.; Santos, Anderson R.; Guimarães, Luis C.; Barbosa, Eudes; Almeida, Sintia S.; Abreu, Vinícius A.C.; Carneiro, Adriana R.; Ramos, Rommel T.J.; Bakhtiar, Syeda Marriam; Hassan, Syed S.; Ussery, David W.; On, Stephen; Silva, Artur; Schneider, Maria P.; Lage, Andrey P.; Miyoshi, Anderson; Azevedo, Vasco.

    In: Gene, Vol. 508, No. 2, 2012, p. 145-156.

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

  243. Published

    Cells, shared memory and breaking the PTM code.. / Creixell, Pau; Linding, Rune.

    In: Molecular Systems Biology, Vol. 8, 2012.

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

  244. Published

    Ceramide profile in hypohidrotic ectodermal dysplasia. / Jungersted, J. M.; Høgh, Julie Kaae; Hellgren, Lars; Agnert, T.; Jemec, G. B. E.

    In: Clinical and Experimental Dermatology, Vol. 37, No. 2, 2012, p. 153-155.

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

  245. Published

    CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid‐specific cancer cell death through autophagy induction. / Lee, Alvin J. X.; Roylance, Rebecca; Sander, Jil; Gorman, Patricia; Endesfelder, David; Kschischo, Maik; Jones, Neil P.; East, Philip; Nicke, Barbara; Spassieva, Stefka; Obeid, Lina M.; Birkbak, Nicolai Juul; Szallasi, Zoltan; McKnight, Nicole C.; Rowan, Andrew J.; Speirs, Valerie; Hanby, Andrew M.; Downward, Julian; Tooze, Sharon A.; Swanton, Charles.

    In: Journal of Pathology, Vol. 226, No. 3, 2012, p. 482-494.

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

  246. Published

    Characterization of HIV-Specific CD4+T Cell Responses against Peptides Selected with Broad Population and Pathogen Coverage. / Buggert, Marcus; Norstrom, Melissa M.; Czarnecki, Chris; Tupin, Emmanuel; Luo, Ma; Gyllensten, Katarina; Sonnerborg, Anders; Lundegaard, Claus; Lund, Ole; Nielsen, Morten; Karlsson, Annika C.

    In: P L o S One, Vol. 7, No. 7, 2012.

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

  247. Published

    Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign. / Andreatta, Massimo; Nielsen, Morten.

    In: Immunology, Vol. 136, No. 3, 2012, p. 306-311.

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

  248. Published

    Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo. / Jørgensen, Jesper Roland; Fransson, Anette; Fjord-Larsen, Lone; Thompson, Lachlan H.; Houchins, Jeffrey P.; Andrade, Nuno; Torp, Malene; Kalkkinen, Nisse; Andersson, Elisabet; Lindvall, Olle; Ulfendahl, Mats; Brunak, Søren; Johansen, Teit E.; Wahlberg, Lars U.

    In: Experimental Neurology, Vol. 233, No. 1, 2012, p. 172-181.

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

  249. Published

    Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae. / Udatha, D. B. R. K. Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth.

    In: P L o S One, Vol. 7, No. 6, 2012, p. e39473.

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

  250. Published

    Comparative genomics of bifidobacterium, lactobacillus and related probiotic genera.. / Lukjancenko, Oksana; Ussery, David; Wassenaar, Trudy M.

    In: Microbial Ecology, Vol. 63, No. 3, 2012, p. 651-673.

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

  251. Published

    Computational Methods for Conformational Sampling of Biomolecules. / Bottaro, Sandro; Ferkinghoff-Borg, Jesper (Main supervisor); Lindorff-Larsen, Kresten (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 147 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  252. Published

    Concepts in Mechanism Based Modeling. / Lund, Ole; Laugesen, Jakob Lund; Mosekilde, Erik.

    Biosimulation in Biomedical Research, Health Care and Drug Development. Springer, 2012. p. 19-41.

    Publication: Research - peer-reviewBook chapter – Annual report year: 2012

  253. Published

    Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.. / Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne; Rochat, Tatiana; Leduc, Aurélie; Pigeonneau, Nathalie; Bidnenko, Elena; Marchadier, Elodie; Hoebeke, Mark; Aymerich, Stéphane; Becher, Dörte; Bisicchia, Paola; Botella, Eric; Delumeau, Olivier; Doherty, Geoff; Denham, Emma L; Fogg, Mark J; Fromion, Vincent; Goelzer, Anne; Hansen, Annette; Härtig, Elisabeth; Harwood, Colin R; Homuth, Georg; Jarmer, Hanne; Jules, Matthieu; Klipp, Edda; Le Chat, Ludovic; Lecointe, François; Lewis, Peter; Liebermeister, Wolfram; March, Anika; Mars, Ruben A T; Nannapaneni, Priyanka; Noone, David; Pohl, Susanne; Rinn, Bernd; Rügheimer, Frank; Sappa, Praveen K; Samson, Franck; Schaffer, Marc; Schwikowski, Benno; Steil, Leif; Stülke, Jörg; Wiegert, Thomas; Devine, Kevin M; Wilkinson, Anthony J; van Dijl, Jan Maarten; Hecker, Michael; Völker, Uwe; Bessières, Philippe; Noirot, Philippe.

    In: Science, Vol. 335, No. 6072, 2012, p. 1103-1106.

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

  254. Published

    Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes.. / Russell, Meaghan K; Longoni, Mauro; Wells, Julie; Maalouf, Faouzi I; Tracy, Adam A; Loscertales, Maria; Ackerman, Kate G; Pober, Barbara R; Hansen, Kasper Lage; Bult, Carol J; Donahoe, Patricia K.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 8, 2012, p. 2978-2983.

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

  255. Published

    Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks. / Longoni, Mauro; Hansen, Kasper Lage; Russell, Meaghan K.; Loscertales, Maria; Abdul‐Rahman, Omar A.; Baynam, Gareth; Bleyl, Steven B.; Brady, Paul D.; Breckpot, Jeroen; Chen, Chih P.; Devriendt, Koenraad; Gillessen‐Kaesbach, Gabriele; Grix, Arthur W.; Rope, Alan F.; Shimokawa, Osamu; Strauss, Bernarda; Wieczorek, Dagmar; Zackai, Elaine H.; Coletti, Caroline M.; Maalouf, Faouzi I.; Noonan, Kristin M.; Park, Ji H.; Tracy, Adam A.; Lee, Charles; Donahoe, Patricia K.; Pober, Barbara R.

    In: American Journal of Medical Genetics. Part A, Vol. 158A, No. 12, 2012, p. 3148-3158.

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

  256. Published

    Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?. / Özen, Asli Ismihan; Ussery, David.

    In: Microbial Ecology in Health & Disease, Vol. 63, No. 2, 2012, p. 239-248.

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

  257. Published

    Describing the Peptide Binding Specificity of HLA-C. / Rasmussen, Michael; Harndahl, Mikkel Nors; Nielsen, Morten; Buus, Soren; Stryhn, Anette.

    2012. Abstract from 99th Annual Meeting of the American-Association-of-Immunologists, Boston MA, .

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2012

  258. Published

    Designing bovine T cell vaccines via reverse immunology. / Nene, Vishvanath; Svitek, Nicholas; Toye, Philip; Golde, William T.; Barlow, John; Harndahl, Mikkel Nors; Buus, Soren; Nielsen, Morten.

    In: Ticks and Tick-borne Diseases, Vol. 3, No. 3, 2012, p. 188-192.

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

  259. Published

    Differential Protein Pathways in 1,25-Dihydroxyvitamin D-3 and Dexamethasone Modulated Tolerogenic Human Dendritic Cells. / Ferreira, Gabriela Bomfim; Kleijwegt, Fleur S.; Waelkens, Etienne; Hansen, Kasper Lage; Nikolic, Tatjana; Hansen, Daniel Aaen; Workman, Christopher; Roep, Bart O.; Overbergh, Lut; Mathieu, Chantal.

    In: Journal of Proteome Research, Vol. 11, No. 2, 2012, p. 941-971.

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

  260. Published

    Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. / Teppa, Elin; Wilkins, Angela D.; Nielsen, Morten; Marino Buslje, Cristina.

    In: B M C Bioinformatics, Vol. 13, 2012, p. -.

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

  261. Published
  262. Published

    Drug Repurposing: Far Beyond New Targets for Old Drugs. / Oprea, Tudor; Mestres, J.

    In: A A P S Journal, Vol. 14, No. 4, 2012, p. 759-763.

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

  263. Published

    Effects of Butter and Phytanic acid intake on metabolic parameters and T-cell polarization. / Drachmann, Tue; Hellgren, Lars (Main supervisor); Pedersen, Susanne Brix (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 173 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  264. Published

    Enantioselective determination of methylphenidate and ritalinic acid in whole blood from forensic cases using automated solid-phase extraction and liquid chromatography-tandem mass spectrometry.. / Thomsen, Ragnar; B. Rasmussen, Henrik; Linnet, Kristian; Brunak, Søren; Taboureau, Olivier .

    In: Journal of Analytical Toxicology, Vol. 36, 2012, p. 560-568.

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

  265. Published

    Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era. / Taboureau, Olivier; Baell, Jonathan B.; Fernández-Recio, Juan; Villoutreix, Bruno O.

    In: Chemistry & Biology, Vol. 19, No. 1, 2012, p. 29-41.

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

  266. Published
  267. Published
  268. Published

    Evolution and diversification of Pseudomonas aeruginosa in the paranasal sinuses of cystic fibrosis children have implications for chronic lung infection. / Hansen, Susse Kirkelund; Rau, Martin Holm; Johansen, Helle Krogh; Ciofu, Oana; Jelsbak, Lars; Yang, Lei; Folkesson, Anders; Jarmer, Hanne Østergaard; Aanæs, Kasper; von Buchwald, Christian; Høiby, Niels; Molin, Søren.

    In: I S M E Journal, Vol. 6, No. 1, 2012, p. 31.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  269. Published

    Expanding user’s query with tag-neighbors for effective medical information retrieval. / Durao, Frederico; Bayyapu, Karunakar Reddy; Xu, Guandong; Dolog, Peter; Lage, Ricardo.

    In: Multimedia Tools and Applications, 2012.

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

  270. Published

    Fish intake, erythrocyte n-3 fatty acid status and metabolic health in Danish adolescent girls and boys. / Lauritzen, Lotte; Harsløf, Laurine B. S.; Hellgren, Lars; Pedersen, Maiken Højgaard; Mølgaard, Christian; Michaelsen, Kim F.

    In: British Journal of Nutrition, Vol. 107, 2012, p. 697-704.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  271. Published

    Fitting the complexity of GPCRs modulation into simple hypotheses of ligand design. / Custodi, Chiara; Nuti, Roberto; Oprea, Tudor; Macchiarulo, Antonio.

    In: Journal of Molecular Graphics and Modelling, Vol. 38, 2012, p. 70-81.

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

  272. Published

    Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion. / Parisio, Giulia; Sperotto, Maria Maddalena; Ferrarini, Alberta.

    In: American Chemical Society. Journal, Vol. 134, No. 29, 2012, p. 12198-12208.

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

  273. Published

    From Genome Sequence to Taxonomy - A Skeptic’s View. / Özen, Asli Ismihan; Vesth, Tammi Camilla; Ussery, David.

    The Prokaryotes. ed. / Rosenberg E.2012 : Springer, 2012.

    Publication: Research - peer-reviewBook chapter – Annual report year: 2012

  274. Published

    From genomic variation to personalized medicine. / Wesolowska, Agata; Gupta, Ramneek (Supervisor); Brunak, Søren (Supervisor); Schmiegelow, Kjeld .

    Department of Systems Biology, DTU, 2012. 151 p.

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

  275. Published

    From Viral genome to specific peptide epitopes - Methods for identifying porcine T cell epitopes based on in silico predictions, in vitro identification and ex vivo verification. / Pedersen, Lasse Eggers; Rasmussen, Michael ; Harndahl, Mikkel ; Nielsen, Morten; Buus, Søren; Jungersen, Gregers.

    2012. Abstract from 4th European Veterinary Immunology Workshop (EVIW), Edinburgh, United Kingdom.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2012

  276. Published

    Functional and phenotypic profiling of innate immunity during Salmonella infection. / Sørensen, Rikke Brandt; Pedersen, Susanne Brix.

    Kgs. Lyngby : Technical University of Denmark, 2012. 128 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  277. Published

    Gene expression dynamics in the oxidative stress response of fission yeast. / Papadakis, Emmanouil; Workman, Christopher (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark (DTU), 2012. 221 p.

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

  278. Published

    Gene prioritization for livestock diseases by data integration. / Jiang, Li; Sørensen, Peter; Thomsen, Bo Stjerne; Edwards, Stefan McKinnon; Skarman, Axel; Røntved, Christine Maria; Lund, Mogens Sandø; Workman, Christopher T.

    In: Physiological Genomics, Vol. 44, No. 5, 2012, p. 305-317.

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

  279. Published

    Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. / Hansen, Kasper Lage; Greenway, Steven C.; Rosenfeld, Jill A.; Wakimoto, Hiroko; Gorham, Joshua M.; Segrè, Ayellet V.; Roberts, Amy E.; Smoot, Leslie B.; Pu, William T.; C. Pereira, Alexandre; Mesquita, Sonia M.; Tommerup, Niels; Brunak, Søren; Ballif, Blake C.; Shaffer, Lisa G.; Donahoe, Patricia K.; Daly, Mark J.; Seidman, Jonathan G.; Seidman, Christine E.; Larsen, Lars.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 35, 2012, p. 14035-14040.

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

  280. Published

    Genome‐wide analysis of cytogenetic aberrations in ETV6/RUNX1‐positive childhood acute lymphoblastic leukaemia. / Borst, Louise; Wesolowska, Agata; Joshi, Tejal; Borup, Rehannah; Nielsen, Finn; Andersen, Mette K.; Jonsson, Olafur G.; Wehner, Peder Skov; Wesenberg, Finn; Frost, Britt‐Marie; Gupta, Ramneek; Schmiegelow, Kjeld.

    In: British Journal of Haematology, Vol. 157, No. 4, 2012, p. 476-482.

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

  281. Published
  282. Published

    Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.. / Buescher, Joerg Martin; Liebermeister, Wolfram; Jules, Matthieu; Uhr, Markus; Muntel, Jan; Botella, Eric; Hessling, Bernd; Kleijn, Roelco Jacobus; Le Chat, Ludovic; Lecointe, François; Mäder, Ulrike; Nicolas, Pierre; Piersma, Sjouke; Rügheimer, Frank; Becher, Dörte; Bessieres, Philippe; Bidnenko, Elena; Denham, Emma L; Dervyn, Etienne; Devine, Kevin M; Doherty, Geoff; Drulhe, Samuel; Felicori, Liza; Fogg, Mark J; Goelzer, Anne; Hansen, Annette; Harwood, Colin R; Hecker, Michael; Hubner, Sebastian; Hultschig, Claus; Jarmer, Hanne; Klipp, Edda; Leduc, Aurélie; Lewis, Peter; Molina, Frank; Noirot, Philippe; Peres, Sabine; Pigeonneau, Nathalie; Pohl, Susanne; Rasmussen, Simon; Rinn, Bernd; Schaffer, Marc; Schnidder, Julian; Schwikowski, Benno; Van Dijl, Jan Maarten; Veiga, Patrick; Walsh, Sean; Wilkinson, Anthony J; Stelling, Jörg; Aymerich, Stéphane; Sauer, Uwe.

    In: Science, Vol. 335, No. 6072, 2012, p. 1099-1103.

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

  283. Published

    Group a Pfemp1 functional domains bind icam1 and induce cross-reactive and adhesion inhibitory antibodies during malaria infections. / Bengtsson, A.; Jørgensen, L.; Rask, Thomas Salhøj; Olsen, R. W.; Andersen, M. A.; Turner, L.; Theander, T. G. ; Higins, M. K.; Craig, A.; Brown, A.; Christoffersen, S.; Jensen, A. T. R.

    Joint Spring Symposium 2012 - Double burden of disease – how parasites interact with each other, their host and the society: Danish Society for Parasitology and Danish Society for Tropical Medicine & International Health. Danish Society for Parasitology, 2012. p. 9.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2012

  284. Published

    How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. / Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni.

    In: Scientific Reports, Vol. 2, 2012.

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

  285. Published

    Hyperactivity of the Ero1α Oxidase Elicits Endoplasmic Reticulum Stress but No Broad Antioxidant Response. / Hansen, Henning Gram; Schmidt, Jonas Damgard; Soltoft, Cecilie Lutzen; Ramming, Thomas; Geertz-Hansen, Henrik Marcus; Christensen, Brian; Sorensen, Esben Skipper; Juncker, Agnieszka; Appenzeller-Herzog, Christian; Ellgaard, Lars.

    In: Journal of Biological Chemistry, Vol. 287, No. 47, 2012, p. 39513-39523.

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

  286. Published
  287. Published

    Identification of a Novel UTY‐Encoded Minor Histocompatibility Antigen. / Mortensen, B. K.; Rasmussen, A. H.; Larsen, Malene Erup; Larsen, Mette Voldby; Lund, Ole; Braendstrup, P.; Harndahl, Mikkel Nors; Rasmussen, M.; Buus, S.; Stryhn, A.; Vindeløv, Lars.

    In: Scandinavian Journal of Immunology, Vol. 76, No. 2, 2012, p. 141-150.

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

  288. Published
  289. Published

    Immune epitope database analysis resource. / Kim, Yohan; Ponomarenko, Julia; Zhu, Zhanyang; Tamang, Dorjee; Wang, Peng; Greenbaum, Jason; Lundegaard, Claus; Sette, Alessandro; Lund, Ole; Bourne, Philip E.; Nielsen, Morten; Peters, Bjoern.

    In: Nucleic Acids Research, Vol. 40, No. W1, 2012, p. W525-W530.

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

  290. Published

    Immune Recognition of Latency-insitigating Pathogens by Human Dendritic Cells. / Søndergaard, Jonas Nørskov; Pedersen, Susanne Brix (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 106 p.

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

  291. Published

    Immunogenicity of Mycobacterium avium subsp. paratuberculosis specific peptides for inclusion in a subunit vaccine against paratuberculosis. / Mikkelsen, Heidi; Tollefsen, S.; Olsen, I.; Aagaard, C.; Lundegaard, Claus; Jungersen, Gregers.

    2012. Abstract from 4th European Veterinary Immunology Workshop (EVIW), Edinburgh, United Kingdom.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2012

  292. Published

    Improving the prediction of the brain disposition for orally administered drugs using BDDCS. / Broccatelli, Fabio; Larregieu, Caroline A.; Cruciani, Gabriele; Oprea, Tudor; Benet, Leslie Z.

    In: Advanced Drug Delivery Reviews, Vol. 64, No. 1, 2012, p. 95-109.

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

  293. Published

    Integrative data analysis of male reproductive disorders. / Edsgard, Stefan Daniel; Brunak, Søren (Main supervisor); Jensen, Thomas Skøt (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 186 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  294. Published

    Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. / Gerlinger, Marco; Rowan, Andrew J.; Horswell, Stuart; Larkin, James; Endesfelder, David; Gronroos, Eva; Martinez, Pierre; Matthews, Nicholas; Stewart, Aengus; Tarpey, Patrick; Varela, Ignacio; Phillimore, Benjamin; Begum, Sharmin; McDonald, Neil Q.; Butler, Adam; Jones, David; Raine, Keiran; Latimer, Calli; Santos, Claudio R.; Nohadani, Mahrokh; Eklund, Aron Charles; Spencer-Dene, Bradley; Clark, Graham; Pickering, Lisa; Stamp, Gordon; Gore, Martin; Szallasi, Zoltan Imre; Downward, Julian; Futreal, P. Andrew; Swanton, Charles.

    In: New England Journal of Medicine, Vol. 366, No. 10, 2012, p. 883-892.

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

  295. Published

    Isolation of IL-12p70-competent human monocyte-derived dendritic cells. / Søndergaard, Jonas Nørskov; Pedersen, Susanne Brix.

    In: Journal of Immunological Methods, Vol. 386, No. 1-2, 2012, p. 112-116.

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

  296. Published

    Is the pan-genome also a pan-selectome?. / Ussery, David; Rodriguez-Valera, Francisco.

    In: F1000Research, Vol. 1, No. 16, 2012.

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

  297. Published

    Knowledge engineering for health: A new discipline required to bridge the “ICT gap” between research and healthcare. / Beck, Tim; Gollapudi, Sirisha; Brunak, Søren; Graf, Norbert; Lemke, Heinz U.; Dash, Debasis; Buchan, Iain; Díaz, Carlos; Sanz, Ferran; Brookes, Anthony J.

    In: Human Mutation, Vol. 33, No. 5, 2012, p. 797-802.

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

  298. Published

    LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. / Dillon, Shane C.; Espinosa, Elena; Hokamp, Karsten; Ussery, David; Casadesús, Josep; Dorman, Charles J.

    In: Molecular Microbiology, Vol. 85, No. 6, 2012, p. 1072-1089.

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

  299. Published

    LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. / Will, Sebastian; Joshi, Tejal; Hofacker, Ivo L.; Stadler, Peter F.; Backofen, Rolf.

    In: R N A, Vol. 18, No. 5, 2012, p. 900-914.

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

  300. Published
  301. Published

    Maternal high-fat/high-sucrose diet during lactation results in increased adipose tissue mass, and altered hepatic fatty acid metabolism at weaning. / Ingvorsen, Camilla; Hellgren, Lars.

    2012. Abstract from Symposium for Biotech Research at DTU - Systems Biology, Lyngby, Denmark.

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

  302. Published

    Maternal high-fat/high-sucrose diet during lactation results in increased adipose tissue mass, and altered hepatic fatty acid metabolism at weaning. / Ingvorsen, Camilla; Hellgren, Lars.

    2012. Abstract from Benzon Symposium No. 58 Adipose Tissue in Health and Disease, Copenhagen, Denmark.

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

  303. Published

    Mechanisms of G Protein-Coupled Estrogen Receptor-Mediated Spinal Nociception. / Deliu, Elena; Brailoiu, G. Cristina; Arterburn, Jeffrey B.; Oprea, Tudor I.; Benamar, Khalid; Dun, Nae J.; Brailoiu, Eugen.

    In: Journal of Pain, Vol. 13, No. 8, 2012, p. 742-754.

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

  304. Published

    MicroRNA expression profiling of carcinoma in situ cells of the testis. / Novotny, Guy Wayne; Belling, Kirstine Christensen; Bramsen, Jesper Bertram; Nielsen, John E; Bork-Jensen, Jette; Almstrup, Kristian; Sonne, Si Brask; Kjems, Jørgen; Rajpert-De Meyts, Ewa; Leffers, Henrik.

    In: Endocrine - Related Cancer, Vol. 19, No. 3, 2012, p. 365-379.

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

  305. Published

    Mining electronic health records: towards better research applications and clinical care.. / Jensen, Peter B; Jensen, Lars Juhl; Brunak, Søren.

    In: Nature Reviews. Genetics, Vol. 13, No. 6, 2012, p. 395-405.

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

  306. Published

    Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene. / Bælum, Jacob; Prestat, Emmanuel; David, Maude M.; Strobel, Bjarne W.; Jacobsen, Carsten Suhr.

    In: Applied and Environmental Microbiology, Vol. 78, No. 15, 2012, p. 5305-5312.

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

  307. Published

    Motion gør dig mere sund end et vægttab. / Hoffmann, Thomas Jøhnk; Nordby, Pernille.

    In: Videnskab.dk, 2012.

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

  308. Published
  309. Published

    Muscle ceramide content is similar after 3 weeks’ consumption of fat or carbohydrate diet in a crossover design in patients with type 2 diabetes. / Helge, J. W.; Tobin, L.; Drachmann, Tue; Hellgren, Lars; Dela, F.; Galbo, H.

    In: European Journal of Applied Physiology, Vol. 112, No. 3, 2012, p. 911-918.

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

  310. Published

    Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues. / Creixell, Pau; Schoof, Erwin M.; Tan, Chris Soon Heng; Linding, Rune.

    In: Royal Society of London. Philosophical Transactions B. Biological Sciences, Vol. 367, No. 1602, 2012, p. 2584-2593.

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

  311. Published

    Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal. / Bobosha, Kidist; Tang, Sheila Tuyet; van der Ploeg-van Schip, Jolien J.; Bekele, Yonas; Martins, Marcia V. S. B.; Lund, Ole; Franken, Kees L. M. C.; Khadge, Saraswoti; de Andrade Pontes, Maria Araci; Goncalves, Heitor de Sa; Hussien, Jemal; Thapa, Pratibha; Kunwar, Chhatra B.; Hagge, Deanna A.; Aseffa, Abraham; Vidal Pessolani, Maria Cristina; Pereira, Geraldo M. B.; Ottenhoff, Tom H. M.; Geluk, Annemieke.

    In: Instituto Oswaldo Cruz, Rio de Janeiro. Memorias, Vol. 107, 2012, p. 112-123.

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

  312. Published

    Nature of bacterial colonization influences transcription of mucin genes in mice during the first week of life. / Bergström, Anders; Kristensen, Matilde Bylov; Bahl, Martin Iain; Metzdorff, Stine B.; Fink, Lisbeth Nielsen; Frøkiær, Hanne; Licht, Tine Rask.

    In: B M C Research Notes, Vol. 5, No. 1, 2012, p. 402.

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

  313. Published

    Navigating cancer network attractors for tumor-specific therapy.. / Creixell, Pau; Schoof, Erwin; Erler, Janine Terra; Linding, Rune.

    In: Nature Biotechnology, Vol. 30, No. 9, 2012, p. 842-848.

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

  314. Published

    Neonatal Cytokine Profile in the Airway Mucosal Lining Fluid Is Skewed by Maternal Atopy. / Folsgaard, Nilofar V.; Chawes, Bo L.; Rasmussen, Morten A.; Bischoff, Anne L.; Carson, Charlotte G.; Stokholm, Jakob; Pedersen, Louise; Hansel, Trevor T.; Bonnelykke, Klaus; Pedersen, Susanne Brix; Bisgaard, Hans.

    In: American Journal of Respiratory and Critical Care Medicine, Vol. 185, No. 3, 2012, p. 275-280.

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

  315. Published

    NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. / Karosiene, Edita; Lundegaard, Claus; Lund, Ole; Nielsen, Morten.

    In: Immunogenetics, Vol. 64, No. 3, 2012, p. 177-186.

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

  316. Published

    Network Medicine Strikes a Blow against Breast Cancer. / Erler, Janine Terra; Linding, Rune.

    In: Cell, Vol. 149, No. 4, 2012, p. 731-733.

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

  317. Published

    Non-O1 Vibrio cholerae unlinked to cholera in Haiti. / Mekalanos, John J.; Robins, William; Ussery, David; Davis, Brigid M.; Schadt, Eric; Waldor, Matthew K.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 47, 2012, p. E3206.

    Publication: Research - peer-reviewLetter – Annual report year: 2012

  318. Published

    Of possible cheminformatics futures. / Oprea, Tudor I.; Taboureau, Olivier; Bologa, Cristian G.

    In: Journal of Computer - Aided Molecular Design, Vol. 26, No. 1, 2012, p. 107-112.

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

  319. Published

    Partial migration in fishes: definitions, methodologies and taxonomic distribution.. / Chapman, B B; Skov, C; Hulthén, K; Brodersen, Jacob; Nilsson, P A; Hansson, L-A; Brönmark, C.

    In: Journal of Fish Biology, Vol. 81, No. 2, 2012, p. 479-499.

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

  320. Published

    Peptide‐MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. / Harndahl, Mikkel Nors; Rasmussen, Michael; Roder, Gustav; Dalgaard Pedersen, Ida; Sørensen, Mikael; Nielsen, Morten; Buus, Søren.

    In: European Journal of Immunology, Vol. 42, No. 6, 2012, p. 1405-1416.

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

  321. Published

    Peptide-MHC class I stability is a stronger predictor of CTL immunogenicity than peptide affinity. / Harndahl, Mikkel Nors; Rasmussen, Michael; Nielsen, Morten; Buus, Soren.

    Molecular Immunology. Vol. 51 Elsevier, 2012. p. 11.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2012

  322. Published

    Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children. / Lavstsen, Thomas; Turner, Louise; Saguti, Fredy; Magistrado, Pamela Almeida; Rask, Thomas Salhøj; Jespersen, Jakob S.; Wang, Christian W.; Berger, Sanne Schou; Baraka, Vito; Marquard, Andrea M.; Seguin-Orlando, Andaine; Willerslev, Eske; Gilbert, Marcus Thomas Pius; Lusingu, John Peter Andrea; Theander, Thor Grundtvig.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 26, 2012, p. E1791-E1800.

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

  323. Published

    Polyclonality of Concurrent Natural Populations of Alteromonas macleodii. / Gonzaga, Aitor; Martin-Cuadrado, Ana-Belen; López-Pérez, Mario; Megumi Mizuno, Carolina; García-Heredia, Inmaculada; Kimes, Nikole E.; Lopez-García, Purificación; Moreira, David; Ussery, David; Zaballos, Mila; Ghai, Rohit; Rodriguez-Valera, Francisco.

    In: Genome Biology and Evolution, Vol. 4, No. 12, 2012, p. 201360-1374.

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

  324. Published
  325. Published

    Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?. / Lundegaard, Claus; Lund, Ole; Nielsen, Morten.

    In: Expert Review of Vaccines, Vol. 11, No. 1, 2012, p. 43.

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

  326. Published

    Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome. / Wang, Zhigang C.; Birkbak, Nicolai Juul; Culhane, Aedín C.; Drapkin, Ronny; Fatima, Aquila; Tian, Ruiyang; Schwede, Matthew; Alsop, Kathryn; Daniels, Kathryn E.; Piao, Huiying; Liu, Joyce; Etemadmoghadam, Dariush; Miron, Alexander; Salvesen, Helga B.; Mitchell, Gillian; DeFazio, Anna; Quackenbush, John; Berkowitz, Ross S.; Iglehart, J. Dirk; Bowtell, David D.L.; Matulonis, Ursula A.

    In: Clinical Cancer Research, Vol. 18, No. 20, 2012, p. 5806-5815.

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

  327. Published
  328. Published

    Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). / Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R., III; Rodriguez, Henry.

    In: Proteomics, Vol. 12, No. 1, 2012, p. 11-20.

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

  329. Published

    Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). / Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R., III; Rodriguez, Henry.

    In: Journal of Proteome Research, Vol. 11, No. 2, 2012, p. 1412-1419.

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

  330. Published

    Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. / Bohlin, Jon; van Passel, Mark W. J.; Snipen, Lars; Kristoffersen, Anja B.; Ussery, David; Hardy, Simon P.

    In: B M C Genomics, Vol. 13, No. 66, 2012.

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

  331. Published

    Reliable B cell epitope predictions: impacts of method development and improved benchmarking.. / Kringelum, Jens Vindahl; Lundegaard, Claus; Lund, Ole; Nielsen, Morten.

    In: P L o S Computational Biology, Vol. 8, No. 12, 2012, p. e1002829.

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

  332. Published

    Scale-free behaviour of amino acid pair interactions in folded proteins. / Petersen, Steffen B. ; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J. ; Henriksen, Svend B. ; Geertz-Hansen, Henrik Marcus.

    In: P L o S One, Vol. 7, No. 7, 2012, p. e41322-e41322.

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

  333. Published
  334. Published

    Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries. / Talkowski, Michael E.; Rosenfeld, Jill A.; Blumenthal, Ian; Pillalamarri, Vamsee; Chiang, Colby; Heilbut, Adrian; Ernst, Carl; Hanscom, Carrie; Rossin, Elizabeth; Lindgren, Amelia M.; Pereira, Shahrin; Ruderfer, Douglas; Kirby, Andrew; Ripke, Stephan; Harris, David J.; Lee, Ji-Hyun; Ha, Kyungsoo; Kim, Hyung-Goo; Solomon, Benjamin D.; Gropman, Andrea L.; Lucente, Diane; Sims, Katherine; Ohsumi, Toshiro K.; Borowsky, Mark L.; Loranger, Stephanie; Quade, Bradley; Hansen, Kasper Lage; Miles, Judith; Wu, Bai-Lin; Shen, Yiping; Neale, Benjamin; Shaffer, Lisa G.; Daly, Mark J.; Morton, Cynthia C.; Gusella, James F.

    In: Cell, Vol. 149, No. 3, 2012, p. 525-537.

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

  335. Published

    Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.. / Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki.

    In: Methods in Molecular Biology, Vol. 856, 2012, p. 513-527.

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

  336. Published
  337. Published

    System chemical biology studies of endocrine disruptors. / Taboureau, Olivier; Oprea, Tudor I.

    2012. Abstract from 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2012

  338. Published

    Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents. / Birkbak, Nicolai J.; Wang, Zhigang C.; Kim, Ji-Young; Eklund, Aron C.; Li, Qiyuan; Tian, Ruiyang; Bowman-Colin, Christian; Li, Yang; Greene-Colozzi, April; Iglehart, J. Dirk; Tung, Nadine; Ryan, Paula D.; Garber, Judy E.; Silver, Daniel P.; Szallasi, Zoltan; Richardson, Andrea L.

    In: Cancer Drug Discovery and Development, Vol. 2, No. 4, 2012, p. 366-375.

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

  339. Published
  340. Published

    The Duffy-Binding-Like β domain (DBLβ) of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variant, PFD1235w, binds ICAM1. / Andersen, M. A.; Bengtsson, A.; Rask, Thomas Salhøj; Jørgensen, L.; Jensen, A. T. R.

    Joint Spring Symposium 2012 - Double burden of disease – how parasites interact with each other, their host and the society: Danish Society for Parasitology and Danish Society for Tropical Medicine & International Health. Danish Society for Parasitology, 2012. p. 10.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2012

  341. Published

    The impact of network biology in pharmacology and toxicology. / Panagiotou, Gianni; Taboureau, Olivier .

    In: S A R and Q S A R in Environmental Research, Vol. 23, No. 3-4, Sp. Iss. SI, 2012, p. 221-235.

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

  342. Published

    The role of miRNA regulation in cancer progression and drug resistance. / Joshi, Tejal; Workman, Christopher (Main supervisor).

    Technical University of Denmark (DTU), 2012. 106 p.

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

  343. Published

    The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. / Kröger, Carsten; Dillon, Shane C.; Cameron, Andrew D. S.; Papenfort, Kai; Sivasankaran, Sathesh K.; Hokamp, Karsten; Chao, Yanjie; Sittka, Alexandra; Hébrard, Magali; Händler, Kristian; Colgan, Aoife; Leekitcharoenphon, Pimlapas; Langridge, Gemma C.; Lohan, Amanda J.; Loftus, Brendan; Lucchini, Sacha; Ussery, David; Dorman, Charles J.; Thomson, Nicholas R.; Vogel, Jörg; Hinton, Jay C. D.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 20, 2012, p. E1277-E1286.

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

  344. Published

    TLR2 Controls Intestinal Carcinogen Detoxication by CYP1A1.. / Do, Khoa; Fink, Lisbeth Nielsen; Jensen, Thomas Elbenhardt; Gautier, Laurent; Parlesak, Alexandr.

    In: P L o S One, Vol. 7, No. 3, 2012, p. e32309.

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

  345. Published

    Toxicogenomics Investigation Under the eTOX Project. / Taboureau, Olivier ; Hersey, Anne; Audouze, Karine Marie Laure; Gautier, Laurent; Jacobsen, Ulrik Plesner; Akhtar, Ruth; Atkinson, Francis; Overington, John P.; Brunak, Søren.

    In: Journal of Pharmacogenomics & Pharmacoproteomics, 2012.

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

  346. Published

    Transcriptome Dynamics of Pseudomonas putida KT2440 under Water Stress. / Gülez, Gamze; Dechesne, Arnaud; Workman, Christopher; Smets, Barth F.

    In: Applied and Environmental Microbiology, Vol. 78, No. 3, 2012, p. 676-683.

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

  347. Published

    Two novel methods for using genome sequences to infer taxonomy. / Ussery, David; Gordon, Stephen V.

    In: Microbiology, Vol. 158, No. Pt 6, 2012, p. 1414.

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

  348. Published

    Uncovering the Molecular Machinery of the Human Spindle-An Integration of Wet and Dry Systems Biology. / Rojas, Ana M.; Santamaria, Anna; Malik, Rainer; Jensen, Thomas Skot; Korner, Roman; Morilla, Ian; de Juan, David; Krallinger, Martin; Hansen, Daniel Aaen; Hoffmann, Robert Daniel; Lees, Jonathan; Reid, Adam; Yeats, Corin; Wehner, Anja; Elowe, Sabine; Clegg, Andrew B.; Brunak, Soren; Nigg, Erich A.; Orengo, Christine; Valencia, Alfonso; Ranea, Juan A. G.

    In: P L o S One, Vol. 7, No. 3, 2012, p. e31813.

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

  349. Published

    Upregulation of TGF-beta 1 in neonates of mothers receiving Influenza A (H1N1) vaccination during pregnancy. / Bischoff, Anne Louise; Folsgaard, N.; Bisgaard, H.; Rasmussen, M.; Pedersen, Susanne Brix.

    In: Allergy, Vol. 67, No. s96, 2012, p. 475.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2012

  350. Published

    Wide Distribution of Closely Related, Antibiotic-Producing Arthrobacter Strains throughout the Arctic Ocean. / Wietz, Matthias; Månsson, Maria; Bowman, Jeff S.; Blom, Nikolaj; Ng, Yin; Gram, Lone.

    In: Applied and Environmental Microbiology, Vol. 78, No. 6, 2012, p. 2039-2042.

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

  351. 2011
  352. Published

    Integrative Systems Biology: Elucidating Complex Traits. / Pers, Tune Hannes; Brunak, Søren (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2011. 161 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2011

  353. Published

    Prediction of protein structural features by use of artificial neural networks. / Petersen, Bent; Lundegaard, Claus (Supervisor); Petersen, Thomas Nordahl (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2011. 122 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2011

  354. Published

    Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer. / Roylance, Rebecca; Endesfelder, David; Gorman, Patricia; Sander, Jil; Tomlinson, Ian; M. Hanby, Andrew; Speirs, Valerie; L. Richardson, Andrea; Birkbak, Nicolai Juul; Eklund, Aron Charles; Downward, Julian; Kschischo, Maik; Szallasi, Zoltan Imre; Swanton, Charles.

    In: Cancer Epidemiology, Biomarkers & Prevention, 22.07.2011, p. 2184-2197.

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

  355. Published

    Using Compound-Protein Interactions and Systems Biology to Study Environmental Effects on diseases development. / Weinhold, Nils; Brunak, Søren (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2011.

    Publication: ResearchPh.D. thesis – Annual report year: 2011

  356. Published

    Protein Interactions and Phenotype Association for Disease Finding. / Roque, francisco jose sousa simôes almeida; Brunak, Søren (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2011.

    Publication: ResearchPh.D. thesis – Annual report year: 2011

  357. Published

    A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables.. / Endesfelder, David; McGranahan, Nicholas; Birkbak, Nicolai Juul; Szallasi, Zoltan Imre; Kschischo, Maik; A. Graham, Trevor; Swanton, Charles.

    In: OncoTarget, 2011.

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

  358. Published

    A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut. / Karlsson, Fredrik H.; Ussery, David; Nielsen, Jens; Nookaew, Intawat.

    In: Microbial Ecology, Vol. 61, No. 3, 2011, p. 473-485.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  359. Published

    An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. / Rasmussen, Morten; Guo, Xiaosen; Wang, Yong; Lohmueller, Kirk E.; Rasmussen, Simon; Albrechtsen, Anders; Skotte, Line; Lindgreen, Stinus; Metspalu, Mait; Jombart, Thibaut; Kivisild, Toomas; Zhai, Weiwei; Eriksson, Anders; Manica, Andrea; Orlando, Ludovic; De La Vega, Francisco M.; Tridico, Silvana; Metspalu, Ene; Nielsen, Kasper; Ávila-Arcos, María C.; Moreno-Mayar, J. Víctor; Muller, Craig; Dortch, Joe; Gilbert, M. Thomas P.; Lund, Ole; Wesolowska, Agata; Karmin, Monika; Weinert, Lucy A.; Wang, Bo; Li, Jun; Tai, Shuaishuai; Xiao, Fei; Hanihara, Tsunehiko; van Driem, George; Jha, Aashish R.; Ricaut, François-Xavier; de Knijff, Peter; Migliano, Andrea B; Gallego Romero, Irene; Kristiansen, Karsten; Lambert, David M.; Brunak, Søren; Forster, Peter; Brinkmann, Bernd; Nehlich, Olaf; Bunce, Michael; Richards, Michael; Gupta, Ramneek; Bustamante, Carlos D.; Krogh, Anders; Foley, Robert A.; Lahr, Marta M.; Balloux, Francois; Sicheritz-Pontén, Thomas; Villems, Richard; Nielsen, Rasmus; Wang, Jun; Willerslev, Eske.

    In: Science, Vol. 334, No. 6052, 2011, p. 94-98.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  360. Published

    Application of computational systems biology to explore environmental toxicity hazards.. / Audouze, Karine Marie Laure; Grandjean, Philippe.

    In: Environmental Health Perspectives, Vol. 119, No. 12, 2011, p. 1754-1759.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  361. Published

    A randomized controlled intervention with fish oil versus sunflower oil from 9 to 18 months of age : exploring changes in growth and skinfold thicknesses. / Andersen, Anders D; Michaelsen, Kim F; Hellgren, Lars; Trolle, Ellen; Lauritzen, Lotte.

    In: Pediatric Research, Vol. 70, No. 4, 2011, p. 368-374.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  362. Published

    Are NOD2 polymorphisms linked to a specific disease endophenotype of Crohn's disease?. / Jensen, Stina Rikke; Nielsen, Ole Haagen; Pedersen, Susanne Brix.

    In: Inflammatory Bowel Diseases, Vol. 17, No. 11, 2011, p. 2392-2401.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  363. Published

    Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing. / Oprea, Tudor; Nielsen, Sonny Kim; Ursu, Oleg; Yang, Jeremy J.; Taboureau, Olivier; Mathias, Stephen L.; Kouskoumvekaki, Irene; Sklar, Larry A.; Bologa, Cristian G.

    In: Molecular Informatics, Vol. 30, No. 2-3, 2011, p. 100-111.

    Publication: Research - peer-reviewConference article – Annual report year: 2011

  364. Published

    A Systematic Study of Site-specific GalNAc-type O-Glycosylation Modulating Proprotein Convertase Processing. / Schjoldager, Katrine Ter-Borch Gram; Vester-Christensen, Malene B.; Goth, Christoffer K.; Petersen, Thomas Nordahl; Brunak, Søren; Bennett, Eric P.; Levery, Steven B.; Clausen, Henrik.

    In: Journal of Biological Chemistry, Vol. 286, No. 46, 2011, p. 40122-40132.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  365. Published

    A systems biology approach to identify potential health risk from chemical exposure. / Audouze, Karine Marie Laure.

    In: Miljø og Sundhed, Vol. 17, No. 1, 2011, p. 19-25.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  366. Published

    Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine. / Polur, Honey; Joshi, Tejal; Workman, Christopher; Lavekar, Gandhidas; Kouskoumvekaki, Irene.

    In: Molecular Informatics, Vol. 30, No. 2-3, 2011, p. 181-187.

    Publication: Research - peer-reviewConference article – Annual report year: 2011

  367. Published

    BDDCS Applied to Over 900 Drugs. / Benet, Leslie Z.; Broccatelli, Fabio; Oprea, Tudor.

    In: The A A P S Journal. Annual Meeting Abstracts, Vol. 13, No. 4, 2011, p. 519-547.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  368. Published

    Bioinformatics-Driven Identification and Examination of Candidate Genes for Non-Alcoholic Fatty Liver Disease. / Banasik, Karina; Justesen, Johanne M.; Hornbak, Malene; Krarup, Nikolaj T.; Gjesing, Anette P.; Sandholt, Camilla H.; Jensen, Thomas Skøt; Grarup, Niels; Andersson, Åsa; Jørgensen, Torben; Witte, Daniel R.; Sandbaek, Annelli; Lauritzen, Torsten; Thorens, Bernard; Brunak, Søren; Sørensen, Thorkild I. A.; Pedersen, Oluf; Hansen, Torben.

    In: P L o S One, Vol. 6, No. 1, 2011, p. e16542.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  369. Published

    Bistability in autoimmune diseases. / Rapin, Nicolas; Mosekilde, Erik; Lund, Ole.

    In: Autoimmunity, Vol. 44, No. 4, 2011, p. 256-260.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  370. Published

    Bovine colostrum is superior to enriched formulas in stimulating intestinal function and necrotising enterocolitis resistance in preterm pigs. / Møller, Hanne Kristine; Thymann, Thomas; Fink, Lisbeth Nielsen; Frokiaer, Hanne; Kvistgaard, Anne S.; Sangild, Per T.

    In: British Journal of Nutrition, Vol. 105, No. 1, 2011, p. 44-53.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  371. Published

    Cancer stem cell overexpression of nicotinamide N-methyltransferase enhances cellular radiation resistance. / D’Andrea, Filippo P.; Safwat, Akmal; Kassem, Moustapha; Gautier, Laurent; Overgaard, Jens; Horsman, Michael R.

    In: Radiotherapy & Oncology, Vol. 99, No. 3, 2011, p. 373-378.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  372. Published
  373. Published
  374. Published

    Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant. / Brede, Dag Anders; Snipen, Lars Gustav; Ussery, David; Nederbragt, Alexander J.; Nes, Ingolf F.

    In: Journal of Bacteriology, Vol. 193, No. 9, 2011, p. 2377-2378.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  375. Published

    Computational methods in epitope discovery : Abstract. / Lundegaard, Claus.

    In: INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, Vol. 28, No. Supplement 1, 2011, p. S54.

    Publication: Research - peer-reviewConference article – Annual report year: 2011

  376. Published

    Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. / Li, Qiyuan; Eklund, Aron Charles; Birkbak, Nicolai Juul; Desmedt, Christine; Haibe-Kains, Benjamin; Sotiriou, Christos; Symmans, W. Fraser; Pusztai, Lajos; Brunak, Søren; Richardson, Andrea L; Szallasi, Zoltan Imre.

    In: B M C Bioinformatics, Vol. 12, No. 1, 2011, p. 310.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  377. Published

    Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. / Wesolowska, Agata; Dalgaard, M. D.; Borst, L.; Gautier, Laurent; Bak, M.; Weinhold, Nils; Nielsen, B. F.; Helt, L. R.; Audouze, Karine Marie Laure; Nersting, J; Tommerup, N.; Brunak, Søren; Sicheritz-Pontén, Thomas; Leffers, H.; Schmiegelow, K.; Gupta, Ramneek.

    In: Leukemia, Vol. 25, 2011, p. 1001-1006.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  378. Published
  379. Published

    DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. / Shaknovich, Rita; Cerchietti, Leandro; Tsikitas, Lucas; Kormaksson, Matthias; De, Subhajyoti; Figueroa, Maria E.; Ballon, Gianna; Yang, Shao Ning; Weinhold, Nils; Reimers, Mark; Clozel, Thomas; Luttrop, Karin; Ekstrom, Tomas J.; Frank, Jared; Vasanthakumar, Aparna; Godley, Lucy A.; Michor, Franziska; Elemento, Olivier; Melnick, Ari.

    In: Blood, Vol. 118, No. 13, 2011, p. 3559-3569.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  380. Published

    Drug repurposing from an academic perspective. / Oprea, Tudor; Bauman, Julie E.; Bologa, Cristian G.; Buranda, Tione; Chigaev, Alexandre; Edwards, Bruce S.; Jarvik, Jonathan W.; Gresham, Hattie D.; Haynes, Mark K.; Hjelle, Brian; Hromas, Robert; Hudson, Laurie; Mackenzie, Debra A.; Muller, Carolyn Y.; Reed, John C.; Simons, Peter C.; Smagley, Yelena; Strouse, Juan; Surviladze, Zurab; Thompson, Todd; Ursu, Oleg; Waller, Anna; Wandinger-Ness, Angela; Winter, Stuart S.; Wu, Yang; Young, Susan M.; Larson, Richard S.; Willman, Cheryl; Sklar, Larry A.

    In: Drug Discovery Today: Therapeutic Strategies, Vol. 8, No. 3-4, 2011, p. 61-69.

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

  381. Published

    Effect of dairy fat on plasma phytanic acid in healthy volunteers - a randomized controlled study. / Werner, Louise B.; Hellgren, Lars; Raff, Marianne; Jensen, Søren K.; Petersen, Rikke A.; Drachmann, Tue; Tholstrup, Tine.

    In: Lipids in Health and Disease, Vol. 10, No. 1, 2011, p. 95.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  382. Published

    Effect of industrially produced trans fat on markers of systemic inflammation: evidence from a randomized trial in women. / Bendsen, Nathalie T.; Stender, Steen; Szecsi, Pal B.; Pedersen, Steen B.; Basu, Samar; Hellgren, Lars; Newman, John W.; Larsen, Thomas M.; Haugaard, Steen B.; Astrup, Arne.

    In: Journal of Lipid Research, Vol. 52, No. 10, 2011, p. 1821-1828.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  383. Published

    Effects of Topical Corticosteroid and Tacrolimus on Ceramides and Irritancy to Sodium Lauryl Sulphate in Healthy Skin. / Jungersted, Jakob Mutanu; Høgh, Julie Kaae; Hellgren, Lars; Jemec, Gregor B.E.; Agner, Tove.

    In: Acta Dermato Venereologica, Vol. 91, No. 3, 2011, p. 290-294.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  384. Published

    Enterotypes of the human gut microbiome. / Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric; Le Paslier, Denis; Yamada, Takuji; Mende, Daniel R.; Fernandes, Gabriel R.; Tap, Julien; Bruls, Thomas; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Borruel, Natalia; Casellas, Francesc; Fernandez, Leyden; Gautier, Laurent; Hansen, Torben; Hattori, Masahira; Hayashi, Tetsuya; Kleerebezem, Michiel; Kurokawa, Ken; Leclerc, Marion; Levenez, Florence; Manichanh, Chaysavanh; Nielsen, Henrik Bjørn; Nielsen, Trine; Pons, Nicolas; Poulain, Julie; Qin, Junjie; Sicheritz-Pontén, Thomas; Tims, Sebastian; Torrents, David; Ugarte, Edgardo; Zoetendal, Erwin G.; Wang, Jun; Guarner, Francisco; Pedersen, Oluf; de Vos, Willem M.; Brunak, Søren; Doré, Joel; Antolín, María; Artiguenave, François; Blottiere, Hervé M.; Almeida, Mathieu; Brechot, Christian; Cara, Carlos; Chervaux, Christian; Cultrone, Antonella; Delorme, Christine; Denariaz, Gérard; Dervyn, Rozenn; Foerstner, Konrad U.; Friss, Carsten; van de Guchte, Maarten; Guedon, Eric; Haimet, Florence; Huber, Wolfgang; van Hylckama-Vlieg, Johan; Jamet, Alexandre; Juste, Catherine; Kaci, Ghalia; Knol, Jan; Lakhdari, Omar; Layec, Severine; Le Roux, Karine; Maguin, Emmanuelle; Mérieux, Alexandre; Melo Minardi, Raquel; M'rini, Christine; Muller, Jean; Oozeer, Raish; Parkhill, Julian; Renault, Pierre; Rescigno, Maria; Sanchez, Nicolas; Sunagawa, Shinichi; Torrejon, Antonio; Turner, Keith; Vandemeulebrouck, Gaetana; Varela, Encarna; Winogradsky, Yohanan; Zeller, Georg; Weissenbach, Jean; Ehrlich, S. Dusko; Bork, Peer.

    In: Nature, Vol. 473, No. 7346, 2011, p. 174-180.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  385. Published
  386. Published

    Experience with the use of online lectures, video Modules, and wiki-websites in engineering education. / Pedersen, Anders Gorm; Wernersson, Rasmus.

    7th International CDIO Conference 2011. Technical University of Denmark, 2011.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2011

  387. Published

    Ex vivo intestinal adhesion of Escherichia coli LF82 in Crohn’s disease. / Jensen, Stina Rikke; Fink, Lisbeth Nielsen; Nielsen, Ole Haagen; Brynskov, Jørn; Pedersen, Susanne Brix.

    In: Microbial Pathogenesis, Vol. 51, No. 6, 2011, p. 426-431.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  388. Published

    FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data. / Manijak, Mieszko P.; Nielsen, Henrik Bjørn.

    In: B M C Research Notes, Vol. 4, No. 1, 2011, p. 181.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  389. Published

    Fish oil combined with SCFA synergistically prevent tissue accumulation of NEFA during weight loss in obese mice. / Pedersen, Maiken Højgaard; Lauritzen, Lotte; Hellgren, Lars.

    In: British Journal of Nutrition, Vol. 106, No. 10, 2011, p. 1449-1456.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  390. Published

    Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities. / Southwood, Scott; Solomon, Christopher; Hoof, Ilka; Rudersdorf, Richard; Sidney, John; Peters, Bjoern; Wahl, Angela; Hawkins, Oriana; Hildebrand, William; Mothé, Bianca R.; Sette, Alessandro.

    In: Immunogenetics, Vol. 63, No. 5, 2011, p. 275-290.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  391. Published

    Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis. / Tang, Sheila Tuyet; van Meijgaarden, Krista E.; Caccamo, Nadia; Guggino, Giuliana; Klein, Michel R.; van Weeren, Pascale; Kazi, Fatima; Stryhn, Anette; Zaigler, Alexander; Sahin, Ugur; Buus, Søren; Dieli, Francesco; Lund, Ole; Ottenhoff, Tom H. M.

    In: Journal of Immunology, Vol. 186, No. 2, 2011, p. 1068-1080.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  392. Published

    Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. / Takamiya, Monica; Özen, Asli Ismihan; Rasmussen, Morten; Alter, Thomas; Gilbert, Tom; Ussery, David; Knøchel, Susanne.

    In: Standards in Genomic Sciences, Vol. 4, No. 2, 2011, p. 113-122.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  393. Published

    Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099.. / Takamiya, Monica; Özen, Asli Ismihan; Rasmussen, Morten; Alter, Thomas; Gilbert, Tom; Ussery, David; Knøchel, S.

    In: Journal of Bacteriology, Vol. 193, No. 19, 2011, p. 5546-5547.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  394. Published

    ”Good teaching practice” at DTU Systems Biology - sustaining quality in teaching and learning. / Kilstrup, Mogens; Hellgren, Lars; Andersson, Pernille Hammar.

    7th International CDIO Conference 2011. Technical University of Denmark, 2011.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2011

  395. Published

    Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information. / Edsgard, Stefan Daniel; Scheel, M.; Hansen, Niclas Tue; Ralfkiaer, U.; Jensen, Thomas Skøt; Skakkebæk, N. E.; Brunak, Søren; Gupta, Ramneek; Rajpert‐De Meyts, E.; Ottesen, A. M.

    In: International Journal of Andrology, Vol. 34, No. 4pt2, 2011, p. e122-e132.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  396. Published

    HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. / Larsen, Malene Erup; Kloverpris, H.; Stryhn, A.; Koofhethile, C.K.; Sims, S.; Ndung'u, T.; Goulder, P.; Buus, S.; Nielsen, Morten.

    In: Immunogenetics, Vol. 63, No. 1, 2011, p. 43-55.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  397. Published

    Human Leukocyte Antigen (HLA) Class I Restricted Epitope Discovery in Yellow Fewer and Dengue Viruses: Importance of HLA Binding Strength.. / Lund, Ole; Nascimento, Eduardo J. M.; Maciel, Milton, Jr; Nielsen, Morten; Larsen, Mette Voldby; Lundegaard, Claus; Harndahl, Mikkel; Lamberth, Kasper; Buus, Søren; Salmon, Jérôme; August, Thomas J.; Marques, Ernesto T A, Jr.

    In: P L o S One, Vol. 6, No. 10, 2011, p. e26494.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  398. Published

    Identification of MHC class II restricted T‐cell‐mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides. / Wang, Mingjun; Tang, Sheila Tuyet; Stryhn, Anette; Justesen, Sune; Larsen, Mette Voldby; Dziegiel, Morten H.; Lewinsohn, David M.; Buus, Søren; Lund, Ole; Claesson, Mogens H.

    In: Immunology, Vol. 132, No. 4, 2011, p. 482-491.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  399. Published

    Ileal adhesion of virulent E. coli LF82 is not enhanced in Crohn's disease.. / Jensen, Rikke S.; Fink, Lisbeth Nielsen; Pedersen, Susanne Brix; Brynskov, J.; Nielsen, Haagen O.

    In: Inflammatory Bowel Diseases, Vol. 17, No. 1, 2011, p. S16-S17.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2011

  400. Published

    Ileal adhesion of virulent E. coli LF82 is not enhanced in Crohn’s disease. / Jensen, Rikke S.; Fink, Lisbeth Nielsen; Pedersen, Susanne Brix; Brynskov, J.; Nielsen, Haagen O.

    Inflammatory Bowel Diseases. Vol. 17, S1 2011. p. P-017.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2011

  401. Published

    Immune system simulation online. / Rapin, Nicolas; Lund, Ole; Castiglione, Filippo.

    In: Bioinformatics, Vol. 27, No. 14, 2011, p. 2013-2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  402. Published

    Immunogenic CTL Epitopes Tend to be Stably Bound to MHC Class I Molecules: Implications for 'Holes in the Stably Bound MHC-I Repertoire'. / Harndahl, M.; Rasmussen, M.; Roder, G.; Pedersen, I. D.; Sørensen, Mikael; Nielsen, Morten; Buus, S.

    In: Scandinavian Journal of Immunology, Vol. 73, No. 4, 2011, p. 353-353.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2011

  403. Published

    Improved glucose tolerance after intensive life style intervention occurs without changes in muscle ceramide or triacylglycerol in morbidly obese subjects. / Helge, J. W.; Stallknecht, B.; Drachmann, Tue; Hellgren, Lars; Jimenez-Jimenez, R.; Andersen, J. L.; Richelsen, B.; Bruun, J. M.

    In: Acta Physiologica (Print), Vol. 201, No. 3, 2011, p. 357-364.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  404. Published

    Induction of Foot-and-Mouth Disease Virus-Specific Cytotoxic T Cell Killing by Vaccination. / Patch, J.R.; Pedersen, Lasse Eggers; Toka, F.N.; Moreas, M.; Grubman, M.J.; Nielsen, Morten; Jungersen, Gregers; Buus, S.; Golde, W.T.

    In: Clinical and Vaccine Immunology, Vol. 18, No. 2, 2011, p. 280-288.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  405. Published
  406. Published

    Integrating phenotypic data from electronic patient records with molecular level systems biology : Abstract of invited lecture. / Brunak, Søren (Invited author).

    In: FEBS JOURNAL, Vol. 278, No. Suppl. s1, 2011, p. 27.

    Publication: Research - peer-reviewConference article – Annual report year: 2011

  407. Published

    Interdisciplinary Evaluation of Broadly-Reactive HLA Class II Restricted Epitopes Eliciting HIV-Specific CD4+T Cell Responses : Abstract of poster presentation. / Buggert, M.; Norström, M.; Lundegaard, Claus; Lund, Ole; Nielsen, Morten; Karlsson, A. C.

    In: AIDS RESEARCH AND HUMAN RETROVIRUSES, Vol. 27, No. 10, 2011, p. A88-A88.

    Publication: Research - peer-reviewConference article – Annual report year: 2011

  408. Published

    Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. / Kristensen, David Møbjerg; Hass, Ulla; Lesné, Laurianne; Lottrup, Grete; Jacobsen, Pernille Rosenskjold; Desdoits-Lethimonier, Christele; Boberg, Julie; Petersen, Jørgen Holm; Toppari, Jorma; Jensen, Tina Kold; Brunak, Søren; Skakkebæk, Niels E.; Nellemann, Christine Lydia; Main, Katharina M.; Jégou, Bernard; Leffers, Henrik.

    In: Human Reproduction, Vol. 26, No. 1, 2011, p. 235-244.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  409. Published

    Jetset: selecting the optimal microarray probe set to represent a gene. / Li, Qiyuan; Birkbak, Nicolai Juul; Gyorffy, Balazs; Szallasi, Zoltan Imre; Eklund, Aron Charles.

    In: B M C Bioinformatics, Vol. 12, No. 1, 2011, p. 474.

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

  410. Published

    Leptin levels in the young offspring from dams fed hypercaloric diets during gestation are decoupled from body-weight, regardless of maternal post-natal diets. / Ingvorsen, Camilla; Hellgren, Lars.

    2011. Poster session presented at Scientific meeting in Centre for Fetal Programming, Statens Serum Institut, Copenhagen, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2011

  411. Published

    Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers. / Madsen, Karina Marie; Udatha, Gupta D. B. R. K.; Semba, Saori; Otero, Jose M.; Koetter, Peter; Nielsen, Jens; Ebizuka, Yutaka; Kushiro, Tetsuo; Panagiotou, Gianni.

    In: P L o S One, Vol. 6, No. 3, 2011, p. e14763.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  412. Published

    Machine learning competition in immunology – Prediction of HLA class I binding peptides. / Zhang, Guang Lan; Ansari, Hifzur Rahman; Bradley, Phil; Cawley, Gavin C.; Hertz, Tomer; Hu, Xihao; Jojic, Nebojsa; Kim, Yohan; Kohlbacher, Oliver; Lund, Ole; Lundegaard, Claus; Magaret, Craig A.; Nielsen, Morten; Papadopoulos, Harris; Raghava, G.P.S.; Tal, Vider-Shalit; Xue, Li C.; Yanover, Chen; Zhu, Shanfeng; Rock, Michael T.; Crowe, James E.; Panayiotou, Christos; Polycarpou, Marios M.; Duch, Włodzisław; Brusic, Vladimir.

    In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 1-4.

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

  413. Published

    Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis. / Kristensen, David M.; Skalkam, Maria L.; Audouze, Karine Marie Laure; Lesné, Laurianne; Desdoits-Lethimonier, Christele; Frederiksen, Hanne; Brunak, Søren; Skakkebæk, Niels E.; Jégou, Bernard; Hansen, Jacob B.; Junker, Steffen; Leffers, Henrik.

    In: Environmental Health Perspectives, Vol. 119, No. 4, 2011, p. 534-541.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  414. Published

    Maternal energy intake during lactation and gestation has an effect on leptin levels in the young and adult pups. / Ingvorsen, Camilla; Hellgren, Lars.

    2011. Abstract from Symposium for Biotech Research at DTU - Systems Biology, Lyngby, Denmark.

    Publication: ResearchConference abstract for conference – Annual report year: 2011

  415. Published

    Meta-Analysis of Heterogeneous Data Sources for Genome-Scale Identification of Risk Genes in Complex Phenotypes. / Pers, Tune Hannes; Hansen, Niclas Tue; Hansen, Kasper Lage; Koefoed, Pernille; Dworzynski, Piotr; Miller, Martin Lee; Flint, Tracey J.; Mellerup, Erling; Dam, Henrik; Andreassen, Ole A.; Djurovic, Srdjan; Melle, Ingrid; Børglum, Anders D.; Werge, Thomas; Purcell, Shaun; Ferreira, Manuel A.; Kouskoumvekaki, Irene; Workman, Christopher; Hansen, Torben; Mors, Ole; Brunak, Søren.

    In: Genetic Epidemiology, Vol. 35, No. 5, 2011, p. 318-332.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  416. Published

    Metatranscriptomics of the human gut microbiome. / Sicheritz-Pontén, Thomas (Invited author).

    In: Genome Biology (Online Edition), Vol. 12 Suppl 1, 2011, p. I15.

    Publication: ResearchConference abstract in journal – Annual report year: 2011

  417. Published

    Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.. / Bowman, Jeff S.; Rasmussen, Simon; Blom, Nikolaj; Deming, Jody W; Rysgaard, Søren; Sicheritz-Pontén, Thomas.

    In: I S M E Journal, 2011, p. 1-10.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  418. Published

    MicroRNA-130a–mediated down-regulation of Smad4 contributes to reduced sensitivity to TGF-β1 stimulation in granulocytic precursors. / Häger, Mattias; Pedersen, Corinna Cavan; Larsen, Maria Torp; Andersen, Mette Klarskov; Hother, Christoffer; Grønbæk, Kirsten; Jarmer, Hanne Østergaard; Borregaard, Niels; Cowland, Jack Bernard.

    In: Blood, Vol. 118, No. 25, 2011, p. 6649-6659.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  419. Published

    Mir-130a-Mediated Downregulation of SMAD4 Contributes to Reduced Sensitivity to TGE beta Stimulation in Promyelocytic Cells. / Hager, Mattias; Pedersen, Corinna Cavan; Larsen, Maria Torp; Andersen, Mette Klarskov; Hother, Christoffer; Gronbaek, Kirsten; Jarmer, Hanne; Borregaard, Niels; Cowland, Jack B.

    In: Blood, Vol. 118, No. 21, 2011, p. 1450-1451.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2012

  420. Published

    MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. / Zhang, Guang Lan; DeLuca, David S.; Keskin, Derin B.; Chitkushev, Lou; Zlateva, Tanya; Lund, Ole; Reinherz, Ellis L.; Brusic, Vladimir.

    In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 53-61.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  421. Published

    Mycobacterial species as case-study of comparative genome analysis. / Zakham, F.; Belayachi, L.; Ussery, David; Akrim, M.; Benjouad, A.; El Aouad, R.; Ennaji, M. M.

    In: Cellular and Molecular Biology, Vol. 57, 2011, p. 1462-1469.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  422. Published

    Natural genetic engineering: intelligence & design in evolution?. / Ussery, David.

    In: Microbial Informatics and Experimentation, Vol. 1, No. 11, 2011.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  423. Published

    Next-generation QSAR. / Oprea, Tudor.

    In: Molecular Informatics, Vol. 30, No. 2-3, 2011, p. 89.

    Publication: Research - peer-reviewEditorial – Annual report year: 2011

  424. Published

    NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data. / Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten.

    In: P L o S One, Vol. 6, No. 11, 2011, p. e26781.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  425. Published

    OpenFreezer: a reagent information management software system.. / Olhovsky, Marina; Williton, Kelly; Dai, Anna Yue; Pasculescu, Adrian; Lee, John Paul; Goudreault, Marilyn; Wells, Clark D; Park, Jin Gyoon; Gingras, Anne-Claude; Linding, Rune; Pawson, Tony; Colwill, Karen.

    In: Nature Methods, Vol. 8, No. 8, 2011, p. 612-613.

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

  426. Published

    Paradoxical Relationship between Chromosomal Instability and Survival Outcome in Cancer. / Birkbak, Nicolai Juul; Eklund, Aron Charles; Li, Qiyuan; McClelland, Sarah E.; Endesfelder, David; Tan, Patrick; Tan, Iain B.; Richardson, Andrea L.; Szallasi, Zoltan Imre; Swanton, Charles.

    In: Cancer Research, Vol. 71, No. 10, 2011, p. 3447-3452.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  427. Published
  428. Published

    Pervasive Sharing of Genetic Effects in Autoimmune Disease. / Cotsapas, Chris; Voight, Benjamin F.; Rossin, Elizabeth; Hansen, Kasper Lage; Neale, Benjamin M.; Wallace, Chris; Abecasis, Goncalo R.; Barrett, Jeffrey C.; Behrens, Timothy; Cho, Judy; De Jager, Philip L.; Elder, James T.; Graham, Robert R.; Gregersen, Peter; Klareskog, Lars; Siminovitch, Katherine A.; van Heel, David A.; Wijmenga, Cisca; Worthington, Jane; Todd, John A.; Hafler, David A.; Rich, Stephen S.; Daly, Mark J.

    In: P L o S Genetics, Vol. 7, No. 8, 2011.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  429. Published

    Pharmacophore-driven identification of PPARγ agonists from natural sources. / Petersen, R. K.; Christensen, Kathrine Bisgaard; Assimopoulou, A. N.; Fretté, X.; Papageorgiou, V. P.; Kristiansen, K.; Kouskoumvekaki, Irene.

    In: Journal of Computer - Aided Molecular Design, Vol. 25, No. 2, 2011, p. 107-116.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  430. E-pub ahead of print

    PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. / Olsen, Lars Rønn; Hansen, Niels Bjørn; Bonde, Mads; Genee, Hans Jasper; Holm, Dorte Marie Koefoed; Carlsen, Simon; Hansen, Bjarne Gram; Patil, Kiran Raosaheb; Mortensen, Uffe Hasbro; Wernersson, Rasmus.

    In: Nucleic Acids Research, Vol. 39, No. Web Server issue, 2011, p. W61-W67.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  431. E-pub ahead of print

    PINTA: a web server for network-based gene prioritization from expression data. / Nitsch, Daniela; Tranchevent, Léon-Charles; Goncalves, Joana P.; Vogt, Josef Korbinian; Madeira, Sara C.; Moreau, Yves.

    In: Nucleic Acids Research, Vol. 39, No. Web Server issue, 2011, p. W334-W338.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  432. Published

    Plug ‘n’ Play with DNA. / Lund, Anne Mathilde; Andreasen, Elisa W.; Korgaard, Jaide V.; Rank, Julie; Knudsen, Maja Skovbjerg.

    2011. Poster session presented at iGEM 2011 European Final, Amsterdam, Netherlands.

    Publication: Research - peer-reviewPoster – Annual report year: 2011

  433. Published

    Plug ‘n’ Play with DNA. / Lund, Anne Mathilde; Andreasen, Elisa W.; Korgaard, Jaide V.; Rank, Julie; Knudsen, Maja Skovbjerg.

    2011. Poster session presented at SBR 2011, Kgs. Lyngby, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2011

  434. Published

    Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. / Pedersen, Lasse Eggers; Harndahl, Mikkel; Rasmussen, Michael; Lamberth, Kasper; Golde, William T.; Lund, Ole; Nielsen, Morten; Buus, Soren.

    In: Immunogenetics, Vol. 63, No. 12, 2011, p. 821-834.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  435. Published

    Prediction of epitopes using neural network based methods. / Lundegaard, Claus; Lund, Ole; Nielsen, Morten.

    In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 26-34.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  436. Published

    Probiotika. / Pedersen, Susanne Brix; Nielsen, Ole Haagen; Kjeldsen, Hans Christian ; Johannessen, Terje ; Løge, Ingard.

    Lægehåndbogen. 2011.

    Publication: Research - peer-reviewBook chapter – Annual report year: 2011

  437. Published

    Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease. / Jensen, Majken Karoline; Pers, Tune Hannes; Dworzynski, Piotr; Girman, Cynthia J.; Brunak, Søren; Rimm, Eric B.

    In: Circulation: Cardiovascular Genetics, Vol. 4, No. 5, 2011, p. 549-U159.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  438. Published

    Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology. / Rossin, Elizabeth J.; Hansen, Kasper Lage; Raychaudhuri, Soumya; Xavier, Ramnik J.; Tatar, Diana; Benita, Yair; Cotsapas, Chris; Daly, Mark J.

    In: P L o S Genetics, Vol. 7, No. 1, 2011, p. e1001273.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  439. Published

    PSICQUIC and PSISCORE: accessing and scoring molecular interactions. / Aranda, Bruno; Blankenburg, Hagen; Kerrien, Samuel; Brinkman, Fiona S. L.; Ceol, Arnaud; Chautard, Emilie; Dana, Jose M.; De Las Rivas, Javier; Dumousseau, Marine; Galeota, Eugenia; Gaulton, Anna; Goll, Johannes; Hancock, Robert E. W.; Isserlin, Ruth; Jimenez, Rafael C.; Kerssemakers, Jules; Khadake, Jyoti; Lynn, David J.; Michaut, Magali; O'Kelly, Gavin; Ono, Keiichiro; Orchard, Sandra; Prieto, Carlos; Razick, Sabry; Rigina, Olga; Salwinski, Lukasz; Simonovic, Milan; Velankar, Sameer; Winter, Andrew; Wu, Guanming; Bader, Gary D.; Cesareni, Gianni; Donaldson, Ian M.; Eisenberg, David; Kleywegt, Gerard J.; Overington, John; Ricard-Blum, Sylvie; Tyers, Mike; Albrecht, Mario; Hermjakob, Henning.

    In: Nature Methods, Vol. 8, No. 7, 2011, p. 528-529.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  440. Published

    Quantification of specific E. coli in gut mucosa from Crohn's disease patients. / Jensen, Stina Rikke; Fink, Lisbeth Nielsen; Struve, Carsten; Sternberg, Claus; Andersen, Jens Bo; Brynskov, Jørn; Nielsen, Ole Haagen; Pedersen, Susanne Brix.

    In: Journal of Microbiological Methods, Vol. 86, No. 1, 2011, p. 111-114.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  441. Published

    Rational Discovery of T Helper Epitopes Specific for Bovine Infections with Mycobacterium avium ssp paratuberculosis. / Lundegaard, Claus; Aagaard, C.; Ussery, David; Andersen, P. L.; Jungersen, Gregers.

    In: Scandinavian Journal of Immunology, Vol. 73, No. 4, 2011, p. 392-393.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2011

  442. Published

    Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). / Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R., III; Rodriguez, Henry.

    In: Molecular and Cellular Proteomics, Vol. 10, No. 12, 2011, p. O111.015446.

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

  443. Published

    Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). / Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R., III; Rodriguez, Henry.

    In: Proteomics - Clinical Applications, Vol. 5, No. 11-12, 2011, p. 580-589.

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

  444. Published

    Response to Comment on "Positive Selection of Tyrosine Loss in Metazoan Evolution". / Tan, Chris Soon Heng; Schoof, Erwin; Creixell, Pau; Pasculescu, Adrian; Lim, Wendell A.; Pawson, Tony; Bader, Gary D.; Linding, Rune.

    In: Science, Vol. 332, No. 6032, 2011, p. 917.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  445. Published
  446. Published

    Role of Natural Killer and Dendritic Cell Crosstalk in Immunomodulation by Commensal Bacteria Probiotics. / Rizzello, Valeria; Bonaccorsi, Irene; Dongarra, Maria Luisa; Fink, Lisbeth Nielsen; Ferlazzo, Guido.

    In: Journal of Biomedicine and Biotechnology, Vol. 2011, 473097, 2011.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  447. Published

    SignalP 4.0: discriminating signal peptides from transmembrane regions. / Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar; Nielsen, Henrik.

    In: Nature Methods, Vol. 8, No. 10, 2011, p. 785-786.

    Publication: Research - peer-reviewLetter – Annual report year: 2011

  448. Published

    Temperature influences the expression profiling of immune response genes in rainbow trout following DNA vaccination and VHS virus infection. / Einer-Jensen, Katja; Gautier, Laurent; Rasmussen, Jesper Skou; Lorenzen, Ellen; Christensen, Mikkel Black; Villanueva, Sara A.; Martin, Samuel; Evensen, Øystein; Schyth, Brian Dall; Lorenzen, Niels.

    2011. Abstract from Joint Western Fish Disease Workshop & AFS fish Health Section meeting, Nanaimo, British Columbia, Canada, .

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2011

  449. Published
  450. Published

    The Genomic Standards Consortium. / Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy; Cole, James R.; Dawyndt, Peter; Garrity, George M.; Gilbert, Jack; Glöckner, Frank Oliver; Hirschman, Lynette; Karsch-Mizrachi, Ilene; Klenk, Hans-Peter; Knight, Rob; Kottmann, Renzo; Kyrpides, Nikos; Meyer, Folker; San Gil, Inigo; Sansone, Susanna-Assunta; Schriml, Lynn M.; Sterk, Peter; Tatusova, Tatiana; Ussery, David; White, Owen; Wooley, John.

    In: P L o S Biology, Vol. 9, No. 6, 2011, p. e1001088.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  451. Published

    The impact of ultraviolet therapy on stratum corneum ceramides and barrier function. / Jungersted, Jakob Mutanu; Høgh, Julie Kaae; Hellgren, Lars; Jemec, Gregor B. E.; Agner, Tove.

    In: Photodermatology, Photoimmunology & Photomedicine, Vol. 27, 2011, p. 331-333.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  452. Published
  453. Published

    The pathogenicity of S. Typhimurium SL1344 is coupled to invasiveness and not the ensuing immune response. / Brandt, R.; Petersen, A.; Pedersen, Susanne Brix; Licht, Tine Rask; Frøkiær, H.

    2011. Abstract from 15th International Congress of Mucosal Immunology, Paris, France.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2011

  454. Published

    The pathogenicity of S. Typhimurium SL1344 is coupled to invasiveness and not the ensuing immune response. / Brandt, R.; Petersen, A.; Pedersen, Susanne Brix; Licht, Tine Rask; Frøkiær, H.

    2011. Poster session presented at 15th International Congress of Mucosal Immunology, Paris, France.

    Publication: Research - peer-reviewPoster – Annual report year: 2011

  455. Published

    The Salmonella enterica Pan-genome. / Jacobsen, Annika; Hendriksen, Rene S.; Aarestrup, Frank Møller; Ussery, David; Friis, Carsten.

    In: Microbial Ecology, Vol. 62, No. 3, 2011, p. 487-504.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  456. Published

    The strength of intron donor splice sites in human genes displays a bell-shaped pattern. / Wang, Kai; Wernersson, Rasmus; Brunak, Søren.

    In: Bioinformatics, Vol. 27, No. 22, 2011, p. 3079-3084.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  457. Published
  458. Published

    Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. / Roque, Francisco S.; Jensen, Peter B.; Schmock, Henriette; Dalgaard, Marlene; Andreatta, Massimo; Hansen, Thomas; Søeby, Karen; Bredkjaer, Søren; Juul, Anders; Werge, Thomas; Jensen, Lars J.; Brunak, Søren.

    In: P L o S Computational Biology, Vol. 7, No. 8, 2011.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  459. Published

    Verification of systems biology research in the age of collaborative competition.. / Meyer, Pablo; Alexopoulos, Leonidas G; Bonk, Thomas; Califano, Andrea; Cho, Carolyn R.; de la Fuente, Alberto; de Graaf, David; Hartemink, Alexander J.; Hoeng, Julia; Ivanov, Nikolai V.; Koeppl, Heinz; Linding, Rune; Marbach, Daniel; Norel, Raquel; Peitsch, Manuel C.; Rice, J Jeremy; Royyuru, Ajay; Schacherer, Frank; Sprengel, Joerg; Stolle, Katrin; Vitkup, Dennis; Stolovitzky, Gustavo.

    In: Nature Biotechnology, Vol. 29, No. 9, 2011, p. 811-815.

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

  460. 2010
  461. Published

    Systems Biology of Saccharomyces cerevisiae Physiology and its DNA Damage Response. / Fazio, Alessandro; Workman, Christopher (Supervisor); Nielsen, Jens (Supervisor); Heierhorst, Jörg (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  462. Published

    Functional Analysis of the Bacillus Subtilis Phosphoproteome. / Soufi, Boumediene; Workman, Christopher (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  463. Published

    Milk Bioactives to Prevent Gut Inflammation. / Møller, Hanne Kristine; Frøkiær, Hanne (Supervisor); Hellgren, Lars (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  464. Published

    Protein Function Prediction in Bacteria. / Kiil, Kristoffer; Ussery, David (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  465. Published

    Systems Biology in Industrial Biotechnology and Disease. / Rasmussen, Simon; Brunak, Søren (Supervisor); Nielsen, Henrik Bjørn (Supervisor); Jarmer, Hanne Østergaard (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  466. Published

    Computational tools and Interoperability in Comparative Genomics. / Hallin, Peter Fischer; Ussery, David (Supervisor).

    Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2010.

    Publication: ResearchPh.D. thesis – Annual report year: 2010

  467. Published

    A focused, PCR based gene expression signature to refine grade in breast cancer. / Szasz, A.; Tokes, A. M.; Szittya, L.; Baranyak, Z. S.; Szekely, B.; Eklund, Aron Charles; Li, Qiyuan; Swanton, C.; Szallasi, Zoltan Imre; Kulka, J.

    In: EJC SUPPLEMENTS, Vol. 8, No. 3, 2010, p. 226-226.

    Publication: ResearchConference abstract in journal – Annual report year: 2010

  468. Published

    A human gut microbial gene catalogue established by metagenomic sequencing. / dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn; Brunak, Søren; Qin, Junjie; Li, Ruiqiang; Raes, Jeroen; Arumugam, Manimozhiyan; Burgdorf, Kristoffer Solvsten; Manichanh, Chaysavanh; Nielsen, Trine; Pons, Nicolas; Levenez, Florence; Yamada, Takuji; Mende, Daniel R.; Li, Junhua; Xu, Junming; Li, Shaochuan; Li, Dongfang; Cao, Jianjun; Wang, Bo; Liang, Huiqing; Zheng, Huisong; Xie, Yinlong; Tap, Julien; Lepage, Patricia; Batto, Jean-Michel; Hansen, Torben; Paslier, Denis Le; Linneberg, Allan; Pelletier, Eric; Renault, Pierre; Turner, Keith; Zhu, Hongmei; Yu, Chang; Li, Shengting; Jian, Min; Zhou, Yan; Li, Yingrui; Zhang, Xiuqing; Li, Songgang; Qin, Nan; Yang, Huanming; Wang, Jian; Dore, Joel; Guarner, Francisco; Kristiansen, Karsten; Pedersen, Oluf; Parkhil, Julian; Weissenbach, Jean; Bork, Peer; Ehrlich, S. Dusko; Wang, Jun.

    In: Nature, Vol. 464, No. 7285, 2010, p. 59.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  469. Published

    A kit for the investigation of live Escherichia coli cell adhesion to glycosylated surfaces. / Hartmann, M.; Horst, A. K.; Klemm, Per; Lindhorst, T. K.

    In: Chemical Communications, Vol. 46, No. 2, 2010, p. 330-332.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  470. Published

    Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. / Szallasi, Zoltan Imre; Li, Yang; Zou, Lihua; Li, Qiyuan; Haibe-Kains, Benjamin; Tian, Ruiyang; Li, Yan; Desmedt, Christine; Sotiriou, Christos; Iglehart, J Dirk; Richardson, Andrea L; Wang, Zhigang Charles.

    In: Nature Medicine, Vol. 16, No. 2, 2010, p. 214-218.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  471. Published

    Analysis of intra-genomic GC content homogeneity within prokaryotes. / Bohlin, J; Snipen, L; Hardy, S.P.; Kristoffersen, A.B.; Lagesen, Karin; Donsvik, T.; Skjerve, E.; Ussery, David.

    In: B M C Genomics, Vol. 11, 2010, p. 464.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  472. Published

    Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo. / Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus; Pedersen, Jacob Skov; Albrechtsen, Anders; Moltke, Ida; Metspalu, Mait; Metspalu, Ene; Kivisild, Toomas; Gupta, Ramneek; dos Santos, Marcelo Bertalan Quintanilha; Nielsen, Kasper; Gilbert, MTP; Wang, Y; Raghavan, M; Campos, PF; Kamp, HM; Wilson, AS; Gledhill, A; Tridico, S; Bunce, M; Lorenzen, ED; Binladen, J; Guo, X; Zhao, J; Zhang, X; Zhang, H; Li, Z; Chen, M; Orlando, L; Kristiansen, K; Bak, M; Tommerup, N; Bendixen, C; Pierre, TL; Grønnow, B; Meldgaard, M; Andreasen, C; Fedorova, SA; Osipova, LP; Higham, TFG; Ramsey, CB; Hansen, TV; Nielsen, FC; Crawford, MH; Brunak, Søren; Sicheritz-Pontén, Thomas; Villems, R; Nielsen, R; Krogh, A; Wang, J; Willerslev, E.

    In: Nature, Vol. 463, No. 7282, 2010, p. 757-762.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  473. Published

    An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators. / Gautier, Laurent.

    In: B M C Bioinformatics, Vol. 11, No. Suppl. 12, 2010, p. 11.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  474. Published

    An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. / Györffy, B; Lanczky, A; Eklund, Aron Charles; Denkert, Carsten; Budczies, J; Li, Qiyuan; Szallasi, Zoltan Imre.

    In: Breast Cancer Research and Treatment, Vol. 123, No. 3, 2010, p. 725-731.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  475. Published
  476. Published

    Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials. / Juul, Nicolai Stefan; Szallasi, Zoltan Imre; Eklund, Aron Charles; Li, Qiyuan; Burrell, RA; Gerlinger, M; Valero, V; Andreopoulou, E; Esteva, FJ; Symmans, WF; Desmedt, C; Haibe-Kains, B; Sotiriou, C; Pusztai, L; Swanton, C.

    In: Lancet Oncology, Vol. 11, No. 4, 2010, p. 358-365.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  477. Published

    Autoimmunity in Arabidopsis acd11 Is Mediated by Epigenetic Regulation of an Immune Receptor. / Palma, K.; Thorgrimsen, S.; Malinovsky, F.G.; Fiil, B.K.; Nielsen, Henrik Bjørn; Brodersen, P.; Hofius, D.; Petersen, M.; Mundy, John.

    In: P L o S Pathogens, Vol. 6, No. 10, 2010, p. e1001137.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  478. Published
  479. Published

    Bioinformatics Training: A Review of Challenges, Actions and Support Requirements. / Schneider, M.V.; Watson, J.; Attwood, T.; Rother, K.; Budd, A.; McDowall, J.; Via, A.; Fernandes, P.; Nyronen, T.; Holberg Blicher, Thomas; Jones, P.; Blatter, M.C.; De Las Rivas, J.; Judge, D.P.; vaan der Gool, W.; Brooksbank, C.

    In: Briefings in Bioinformatics, 2010.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  480. Published

    BioXSD: the common data-exchange format for everyday bioinformatics web services. / Kalas, M.; Puntervoll, P.; Joseph, A.; Bartaseviciute, Edita; Topfer, A.; Venkataraman, P.; Pettifer, S.; Bryne, J.C.; Ison, J.; Blanchet, C.; Rapacki, Kristoffer; Jonassen, I.

    In: Bioinformatics, Vol. 26, No. 18, 2010, p. i540-i546.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  481. Published
  482. Published
  483. Published

    Ceramides and barrier function in healthy skin. / Jungerstedt, J; Hellgren, Lars; Drachmann, Tue; Høgh, Julie Kaae; Jemec, GBE; Agner, T.

    In: Acta Dermatovenereologica, Vol. 90, No. 4, 2010, p. 350-353.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  484. Published

    Changes in skin barrier during treatment with systemic alitretinoin: focus on skin susceptibility and stratum corneum ceramides. / Jungersted, J.M.; Høgh, Julie Kaae; Hellgren, Lars; Jemec, G.B.; Agner, T.

    In: Archives of Dermatological Research, Vol. 302, No. 9, 2010, p. 653-656.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  485. Published

    Chemoinformatics-assisted development of new anti-biofilm compounds. / Dürig, Anna; Kouskoumvekaki, Irene; Vejborg, Rebecca Munk; Klemm, P.

    In: Applied Microbiology and Biotechnology, Vol. 87, No. 1, 2010, p. 309-317.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  486. Published

    Chronic exposure of adults and embryos of Pandalus borealis to oil causes PAH accumulation, initiation of biomarker responses and an increase in larval mortality. / Bechmann, R.K.; Larsen, Bodil Katrine; Taban, I.C.; Hellgren, Lars; Møller, Per; Sanni, S.

    In: Marine Pollution Bulletin, Vol. 60, No. 11, 2010, p. 2087-2098.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  487. Published
  488. Published

    Comparative Genomics of Green Sulfur Bacteria. / Ussery, David; Davenport, C; Tümmler, B.

    In: Photosynthesis Research, Vol. 104, No. 2-3, 2010, p. 137-152.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  489. Published

    Comparison of 61 Sequenced Escherichia coli Genomes. / Lukjancenko, Oksana; Wassenaar, T. M.; Ussery, David.

    In: Microbial Ecology, Vol. 60, No. 4, 2010, p. 708-720.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  490. Published

    Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System. / Rapin, N.; Lund, Ole; Bernaschi, M.; Castiglione, F.

    In: P L o S One, Vol. 5, No. 4, 2010.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  491. Published

    Country-specific chemical signatures of persistent environmental compounds in breast milk. / Krysiak-Baltyn, Konrad; Toppari, J.; Skakkebaek, N.E.; Jensen, Thomas Skøt; Virtanen, H.E.; Schramm, K.W.; Shen, H.; Vartiainen, T.; Kiviranta, H.; Taboureau, Olivier; Brunak, Søren; Main, K.M.

    In: International Journal of Andrology, Vol. 33, No. 2, 2010, p. 270-278.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  492. Published

    CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. / Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl.

    In: Nucleic Acids Research, Vol. 38, 2010, p. W576-W581.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  493. Published

    CTL epitopes of FMDV determined by NetMHCpan-driven predictions of SLA/peptide binding, confirmed by tetramer complex formation and staining. / Pedersen, Lasse Eggers; Nielsen, Morten; Patch, Jared R.; Jungersen, Gregers; Buus, Søren; Golde, William T.

    2010. Poster session presented at 9th International Veterinary Immunology Symposium, Tokyo, Japan.

    Publication: ResearchPoster – Annual report year: 2010

  494. Published
  495. Published
  496. Published
  497. Published

    Design of an Enterobacteriaceae Pan-genome Microarray Chip. / Lukjancenko, Oksana; Ussery, David.

    CSBio 2010. Vol. 115 Springer, 2010. p. 174-189.

    Publication: Research - peer-reviewArticle in proceedings – Annual report year: 2010

  498. Published

    Dietary fibers as immunoregulatory compounds in health and disease. / Wismar, René; Pedersen, Susanne Brix; Frøkiær, Hanne; Lærke, H. N.

    Foods For Health in the 21st Century: a Road Map For the Future. Oxford : Blackwell Publishing Ltd, 2010. p. 70-85 (New York Academy of Sciences. Annals, Vol. 1190).

    Publication: Research - peer-reviewArticle in proceedings – Annual report year: 2010

  499. Published

    Dietary plant components ellagic acid and tannic acid inhibit Escherichia coli biofilm formation. / Hancock, Viktoria; Dahl, M.; Vejborg, Rebecca Munk; Klemm, Per.

    In: Journal of Medical Microbiology, Vol. 59, No. 4, 2010, p. 496-498.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  500. Published

    Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis. / Binnewies, Tim Terence; Ussery, David; Lavín, JL; Pisabarro, AG; García-Lobo, JM; Oguiza, JA.

    In: Veterinary Microbiology, Vol. 144, No. 3-4, 2010, p. 478-483.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  501. Published

    Differential sensitivity of melanoma cell lines with BRAFV600E mutation to the specific raf inhibitor PLX4032. / Søndergaard, Jonas Nørskov; Nazarian, R.; Wang, Q.; Guo, D.; Hsueh, T.; Mok, S.; Sazegar, H.; Macconail, L. E.; Barretina, J. G.; Kehoe, S.M.; Attar, N.; von Euw, E.; Zuckerman, J.E.; Chmielowski, B.; Comin-Anduix, B.; Koya, R. C.; Mischel, P. S.; Lo, R. S.; Ribas, A. J.

    In: Journal of Translational Medicine, Vol. 8, 2010.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  502. Published

    Dissecting spatio-temporal protein networks driving human heart development and related disorders. / Hansen, Kasper Lage; Mølgård, Kjeld; Greenway, Steven; Wakimoto, Hiroko; Gorham, Joshua M.; Workman, Christopher; Bendsen, Eske; Hansen, Niclas Tue; Rigina, Olga; Roque, Francisco José Sousa Simões Almeida; Wiese, Cornelia; Christoffels, Vincent M.; Roberts, Amy E.; Smoot, Leslie B.; Pu, William T.; Donahoe, Patricia K.; Tommerup, Niels; Brunak, Søren; Seidman, Christine E.; Seidman, Jonathan G.; Larsen, Lars A.

    In: Molecular Systems Biology, Vol. 6, 2010, p. 381.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  503. Published
  504. Published

    E Durans Strain M4-5 Isolated From Human Colonic Flora Attenuates Intestinal Inflammation. / Avram-Hananel, L.; Stock, J.; Parlesak, Alexandr; Bode, C.; Schwartz, B.

    In: Diseases of the Colon and Rectum, Vol. 53, No. 12, 2010, p. 1676-1686.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

  505. Published

    Effects of Fish Oil Supplementation on Markers of the Metabolic Syndrome. / Pedersen, Maiken Højgaard; Mølgaard, C.; Hellgren, Lars; Lauritzen, L.

    In: Journal of Pediatrics, Vol. 157, No. 3, 2010, p. 395-U72.

    Publication: Research - peer-reviewJournal article – Annual report year: 2010

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