Center for Biological Sequence Analysis

  1. 2014
  2. Published
  3. Published

    Acute and perinatal-programming effects of a fat-rich diet on rat muscle mitochondrial function and hepatic lipid accumulation.. / Hellgren, Lars; Jensen, Runa I.; Waterstradt, Michelle S. G. ; Quistorff, Bjørn; Lauritzen, Lotte.

    In: Acta Obstetricia et Gynecologica Scandinavica, Vol. 93, 2014, p. 1170-1180.

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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Published
  9. 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

  10. 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

  11. 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

  12. 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

  13. Published
  14. 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

  15. Published

    Antibody structural modeling with prediction of immunoglobulin structure (PIGS).. / Marcatili, Paolo; Olimpieri, Pier Paolo; Chailyan, Anna; Tramontano, Anna.

    In: Nature Protocols, Vol. 9, No. 12, 2014, p. 2771-2783.

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

  16. Published
  17. Published
  18. 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

  19. Published

    A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations. / Clemente, Florian J. ; Cardona, Alexia; Inchley, Charlotte E. ; Peter, Benjamin M. ; Jacobs, Guy; Pagani, Luca ; Lawson, Daniel J. ; Antão, Tiago ; Vicente, Mário ; Mitt, Mario ; Rasmussen, Simon.

    In: American Journal of Human Genetics, Vol. 95, No. 5, 2014, p. 584–589.

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

  20. Published
  21. Published

    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, Vol. 18, 2014, p. 945-951.

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

  22. Published
  23. 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

  24. 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

  25. 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

  26. Published

    Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery.. / Hansen, Andreas M.; Rasmussen, Michael; Svitek, Nicholas; Harndahl, Mikkel; Golde, William T.; Barlow, John; Nene, Vishvanath; Buus, Søren; Nielsen, Morten.

    In: Immunogenetics, Vol. 66, No. 12, 2014, p. 705-718.

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

  27. 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

  28. 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

  29. Published
  30. 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

  31. E-pub ahead of print
  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. Published

    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution. / Fisher, Rosalie; Horswell, Stuart; Rowan, Andrew; Salm, Maximilian P.; de Bruin, Elza C.; Gulati, Sakshi; McGranahan, Nicholas; Stares, Mark; Gerlinger, Marco; Varela, Ignacio; Crockford, Andrew; Favero, Francesco; Quidville, Virginie; André, Fabrice; Navas, Carolina; Grönroos, Eva; Nicol, David; Hazell, Steve; Hrouda, David; O’Brien, Tim; Matthews, Nik; Phillimore, Ben; Begum, Sharmin; Rabinowitz, Adam; Biggs, Jennifer; Bates, Paul A.; McDonald, Neil Q.; Stamp, Gordon; Spencer-Dene, Bradley; Hsieh, James J.; Xu, Jianing; Pickering, Lisa; Gore, Martin; Larkin, James; Swanton, Charles.

    In: Genome Biology (Online Edition), Vol. 15, No. 8, 2014.

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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. E-pub ahead of print
  50. 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

  51. 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

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