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

    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, Vol. 46, 2014, p. 51-55.

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

  7. Published
  8. 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

  9. Published

    An integrated catalog of reference genes in the human gut microbiome. / Li, Junhua; Jia, Huijue; Cai, Xianghang; Zhong, Huanzi; Feng, Qiang; Sunagawa, Shinichi; Arumugam, Manimozhiyan; Kultima, Jens Roat; Prifti, Edi; Nielsen, Trine; Juncker, Agnieszka ; Nielsen, Henrik Bjørn; Brunak, Søren.

    In: Nature Biotechnology, Vol. 32, No. 8, 2014, p. 834-841.

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

  10. Published

    An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. / Brownstein, Catherine A ; Beggs, Alan H ; Homer, Nils ; Merriman, Barry ; Yu, Timothy W; Flannery, Katherine C ; DeChene, Elizabeth T ; Towne, Meghan C ; Savage, Sarah K ; Price, Emily N ; Dworzynski, Piotr.

    In: Genome Biology (Online Edition), Vol. 15, R53, 2014.

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

  11. Published

    Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics. / Lundby, Alicia; Rossin, Elizabeth J.; Steffensen, Annette B.; Acha, Moshe Ray; Newton-Cheh, Christopher; Pfeufer, Arne; Lyneh, Stacey N.; Olesen, Søren-Peter; Brunak, Søren; Ellinor, Patrick T.; Jukema, J. Wouter; Trompet, Stella; Ford, Ian; Macfarlane, Peter W.; Krijthe, Bouwe P.; Hofman, Albert; Uitterlinden, Andre G.; Stricker, Bruno H.; Nathoe, Hendrik M.; Spiering, Wilko; Daly, Mark J.; Asselbergs, Folkert W.; van der Harst, Pim; Milan, David J.; de Bakker, Paul I. W.; Lage, Kasper; Olsen, Jesper V.

    In: Nature Methods, Vol. 11, No. 8, 2014, p. 868-874.

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

  12. Published
  13. Published

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

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

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

  14. Published
  15. Published
  16. Published

    A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.. / Jiang, Li; Edwards, Stefan M.; Thomsen, Bo; Workman, Christopher; Guldbrandtsen, Bernt; Sørensen, Peter.

    In: BMC Bioinformatics, Vol. 15, No. 315, 2014.

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

  17. Published
  18. 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

  19. Published
  20. Published

    Biological insights from 108 schizophrenia-associated genetic loci. / Ripke, Stephan; Neale, Benjamin M.; Corvin, Aiden ; Walters, James T. R. ; Farh, Kai-How ; Holmans, Peter A. ; Lee, Phil ; Bulik-Sullivan, Brendan ; Collier, David A. ; Huang, Hailiang ; Pers, Tune Hannes; Agerbo, Esben ; Demontis, Ditte ; Hansen, Thomas; Hollegaard, Mads Vilhelm; Hougaard, David M.; Mors, Ole; Werge, Thomas.

    In: Nature, Vol. 511, 2014, p. 421-427.

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

  21. Published

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

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

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

  22. Published

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

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

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

  23. Published

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

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

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

  24. 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

  25. Published
  26. Published

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

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

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

  27. E-pub ahead of print
  28. 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

  29. Published

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

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

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

  30. 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

  31. 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

  32. 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

  33. 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

  34. Published

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

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

    Publication: ResearchPatent – Annual report year: 2014

  35. Published

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

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

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

  36. 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

  37. Published

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

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

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

  38. 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

  39. Published

    Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA. / Eriksson, Robert; Aagaard, Lise; Jensen, Lars Juhl; Borisova, Liza; Hørlück, Dorte; Brunak, Søren; Hansen, Ebba Holme.

    In: Pharmacology Research & Perspectives, Vol. 2, No. 3, e00038, 2014.

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

  40. 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

  41. 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

  42. Published

    Early immune response patterns to pathogenic bacteria are associated to increased risk of lower respiratory infections in children. / Vissing, N. H.; Larsen, Jeppe Madura; Rasmussen, Mette Annelie; Thysen, Anna Hammerich; Chawes, B. L.; Bønnelykke, K.; Pedersen, Susanne Brix; Bisgaard, Hans Flinker.

    In: ALLERGY, Vol. 69, No. Supplement s99, 84, 2014, p. 37-37.

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

  43. 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

  44. E-pub ahead of print
  45. 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

  46. Published

    Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?. / Shi, Leming; Haibe-Kains, Benjamin; Birkbak, Nicolai Juul; Bedard, Philippe L.; Hatzis, Christos; Stern, David F.; Clarke, Robert; Quackenbush, John; Beck, Andrew H.; Aerts, Hugo J. W. L.

    In: Cancer Research, Vol. 74, No. 15, 2014, p. 4016-4023.

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

  47. Published

    Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts. / Boomsma, Wouter; Tian, Pengfei; Frellsen, J.; Ferkinghoff-Borg, Jesper; Hamelryck, T.; Lindorff-Larsen, K.; Vendruscolo, M.

    In: Proceedings of the National Academy of Sciences, Vol. 111, No. 38, 2014, p. 13852-13857.

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

  48. 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

  49. 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

  50. Published
  51. 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, Vol. 71, No. 2, 2014, p. 905-929.

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

  52. Published

    Experimental and computational tools for analysis of signaling networks in primary cells. / Schoof, Erwin M; Linding, Rune.

    In: Current Protocols in Immunology, Vol. 104, 2014.

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

  53. Published

    Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. / Westergaard, David; Li, Jun; Jensen, Kasper; Kouskoumvekaki, Irene; Panagiotou, Gianni.

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

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

  54. Published

    Genome-wide association analyses identify variants in developmental genes associated with hypospadias. / Geller, Frank; Feenstra, Bjarke; Carstensen, Lisbeth; Pers, Tune H.; van Rooij, Iris A. L. M.; Korberg, Izabella Baranowska; Choudhry, Shweta; Karjalainen, Juha M.; Schnack, Tine H.; Hollegaard, Mads V.; Feitz, Wout F. J.; Roeleveld, Nel; Hougaard, David M.; Hirschhorn, Joel N.; Franke, Lude; Baskin, Laurence S.; Nordenskjold, Agneta; van der Zanden, Loes F. M.; Melbye, Mads.

    In: Nature Genetics, Vol. 46, No. 9, 2014, p. 957-967.

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

  55. Published
  56. E-pub ahead of print

    Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients. / Wesolowska, Agata; Borst, L.; Dalgaard, Marlene Danner; Yadav, Rachita; Rasmussen, K. K. ; Wehner, Peder Skov; Rasmussen, M.; Ørntoft, T.F.; Nordentoft, I.; Koehler, R.; Sicheritz-Pontén, Thomas; Gautier, Laurent; Brunak, Søren; Gupta, Ramneek.

    In: Leukemia, 2014.

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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. Published

    Improving biotech education through gamified laboratory simulations. / Bonde, Mads; Makransky, Guido; Wandall, Jakob; Larsen, Mette Voldby; Morsing, Mikkel; Jarmer, Hanne Østergaard; Sommer, Morten.

    In: Nature Biotechnology, Vol. 32, No. 7, 2014, p. 694-697.

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

  65. Published

    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, Vol. 30, No. 19, 2014, p. 2733-2740.

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

  66. 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

  67. Published

    In silico prediction of Gallibacterium anatis pan-immunogens. / Bager, Ragnhild J.; Kudirkiene, Egle; da Piedade, Isabelle; Seemann, Torsten; Nielsen, Tine K.; Pors, Susanne E.; Mattsson, Andreas Holm; Boyce, John D.; Adler, Ben; Bojesen, Anders M.

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

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

  68. 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

  69. Published
  70. 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

  71. Published

    Library sequencing strategies for comparative analysis of stress resistance mechanisms in Escherichia coli strains. / Lennen, Rebecca; Bonde, Ida; Koza, Anna; Herrgard, Markus.

    In: New Biotechnology, Vol. 31, 2014, p. S86.

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

  72. Published

    Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells.. / Re, Angela; Workman, Christopher T.; Waldron, Levi; Quattrone, Alessandro; Brunak, Søren.

    In: Stem Cell Research, Vol. 13, No. 2, 2014, p. 316-328.

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

  73. 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

  74. 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

  75. Published

    Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. / Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio; Robbins-Pianka, Adam; Bælum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J.; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C.; Fortney, Julian L.; Jurelevicius, Diogo; Stringfellow, William T.; Alvarez-Cohen, Lisa; Hazen, Terry C.; Knight, Rob; Gilbert, Jack A.; Jansson, Janet K.

    In: I S M E Journal, Vol. 8, No. 7, 2014, p. 1464-1475.

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

  76. Published

    Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase. / Schoof, Erwin M.; Linding, Rune; de Medina-Redondo, Maria; Toprak, Umut H.; Meraldi, Patrick; Herzog, Franz; Maiolica, Alessio; Novy, Karel; Hauri, Simon; Gatti, Marco; Penengo, Lorenza; Villa, Fabrizio; Chaikuad, Apirat; Knapp, Stefan; Lou, Hua Jane; Turk, Benjamin E.; Jeganathan, Siva; Aebersold, Ruedi.

    In: Molecular and Cellular Proteomics, Vol. 13, No. 7, 2014, p. 1724-1740.

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

  77. Published

    MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage.. / Gold, Marielle C.; McLaren, James E.; Reistetter, Joseph A.; Smyk-Pearson, Sue; Ladell, Kristin; Swarbrick, Gwendolyn M.; Yu, Yik Y. L.; Hansen, Ted H.; Lund, Ole; Nielsen, Morten; Gerritsen, Bram; Kesmir, Can; Miles, John J.; Lewinsohn, Deborah A.; Price, David A.; Lewinsohn, David M.

    In: Journal of Experimental Medicine, Vol. 211, No. 8, 2014, p. 1601-1610.

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

  78. 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

  79. 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

  80. Published

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

    In: Immunogenetics, Vol. 66, No. 7-8, 2014, p. 449-456.

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

  81. Accepted

    NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. / Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene.

    In: Nucleic Acids Research, 2014.

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

  82. Published
  83. 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

  84. Published

    Probabilistic Determination of Native State Ensembles of Proteins. / Olsson, Simon; Vögeli, Beat Rolf; Cavalli, Andrea; Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten; Hamelryck, Thomas.

    In: Journal of Chemical Theory and Computation, Vol. 10, No. 8, 2014, p. 3484-3491.

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

  85. 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

  86. 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

  87. Published
  88. Published
  89. Published
  90. 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

  91. Published
  92. 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

  93. 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

  94. 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

  95. 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

  96. E-pub ahead of print
  97. 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

  98. Published

    Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms. / Kaas, Rolf Sommer; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller; Lund, Ole.

    In: PLOS ONE, Vol. 9, No. 8, e104984, 2014.

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

  99. 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

  100. Published

    Synthetic Promoter Library for Modulation of Actinorhodin Production in Streptomyces coelicolor A3(2). / Sohoni, Sujata Vijay; Fazio, Alessandro; Workman, Christopher; Mijakovic, Ivan; Eliasson Lantz, Anna.

    In: PLOS ONE, Vol. 9, No. 6, e99701, 2014.

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

  101. Published

    T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+T Cells in HIV Infection. / Buggert, Marcus; Tauriainen, Johanna; Yamamoto, Takuya; Frederiksen, Juliet Wairimu; Ivarsson, Martin A.; Michaelsson, Jakob; Lund, Ole; Hejdeman, Bo; Jansson, Marianne; Sonnerborg, Anders; Koup, Richard A.; Betts, Michael R.; Karlsson, Annika C.

    In: P L o S Pathogens, Vol. 10, No. 7, e1004251, 2014.

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

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