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

    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

  10. Published
  11. Published
  12. Published
  13. 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

  14. Published
  15. 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

  16. 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

  17. 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

  18. 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

  19. Published
  20. 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

  21. E-pub ahead of print
  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. E-pub ahead of print
  37. 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

  38. 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

  39. 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

  40. 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

  41. Published
  42. 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

  43. 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

  44. 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

  45. Published
  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

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