Center for Biological Sequence Analysis

  1. 2015
  2. E-pub ahead of print

    Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways.. / Ninel Hansen, Stine; Westergaard, David ; Borg Houlberg Thomsen, Mathilde; Vistesen, Mette; Nguyen Do, Khoa; Fogh, Louise; Belling, Kirstine C.; Wang, Jun; Yang, Huanming; Gupta, Ramneek; Ditzel, Henrik Jørn; Moreira, José ; Brünner, Nils; Stenvang, Jan; Schrohl, Anne-Sofie.

    In: Tumor Biology, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  3. Accepted

    Acylcarnitine plasma levels suggest incomplete mitochondrial fatty acid oxidation in young, healthy men with low birth weight. / Ribel-Madsen, Amalie; Ribel-Madsen, Rasmus; Brøns, Charlotte; B. Newgard, Christopher; Vaag, Allan; Hellgren, Lars.

    2015. Abstract from 28th Nordic Lipid Symposium, Reykjavik, Iceland.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  4. Published

    Airway Mucosal Immune-suppression in Neonates of Mothers Receiving A(H1N1)pnd09 Vaccination During Pregnancy. / Pedersen, Susanne Brix; Bischoff, Anne L.; Folsgaard, Nilofar V.; Vissing, Nadja H.; Birch, Sune; Bisgaard, Hans .

    In: Pediatric Infectious Disease Journal, Vol. 34, No. 1, 2015, p. 84-90.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  5. Published

    Archival Bone Marrow Samples: Suitable for Multiple Biomarker Analysis?. / Lund, Bendik; Najmi, A. Laeya; Wesolowska, Agata; Landsem, Veslemoy M.; Rasmussen, Kirsten K.; Borst, Louise; Gupta, Ramneek; Schmiegelow, Kjeld; Klungland, Helge.

    In: Applied Immunohistochemistry & Molecular Morphology, Vol. 23, No. 1, 2015, p. 71-77.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  6. Published

    Bioinformatics prediction of swine MHC class I epitopes from Porcine Reproductive and Respiratory Syndrome Virus. / Welner, Simon; Nielsen, Morten; Lund, Ole; Jungersen, Gregers; Larsen, Lars Erik.

    2015. Abstract from Keystone Symposia on Molecular and Cellular Biology: Accelerating life science discovery, Keystone, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  7. Published
  8. Published

    Gene expression analysis identifies global gene dosage sensitivity in cancer. / Fehrmann, Rudolf S. N.; Karjalainen, Juha M.; Krajewska, Malgorzata; Westra, Harm-Jan; Maloney, David; Simeonov, Anton; Pers, Tune Hannes; Hirschhorn, Joel N.; Jansen, Ritsert C.; Schultes, Erik A.; van Haagenl, Herman H. H. B. M.; de Vries, Elisabeth G. E.; Meerman, Gerard J. te; Wijmenga, Cisca; van Vugt, Marcel A. T. M.; Franke, Lude.

    In: Nature Genetics, Vol. 47, No. 2, 2015, p. 115-125.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  9. Published

    Genomic Dissection of Travel-Associated Extended-Spectrum-Beta-Lactamase-Producing Salmonella enterica Serovar Typhi Isolates Originating from the Philippines: a One-Off Occurrence or a Threat to Effective Treatment of Typhoid Fever?. / Hendriksen, Rene S.; Leekitcharoenphon, Pimlapas; Mikoleit, Matthew; Jensen, Jacob Dyring; Kaas, Rolf Sommer; Roer, Louise; Joshi, Heena B.; Pornruangmong, Srirat; Pulsrikarn, Chaiwat; Gonzalez-Aviles, Gladys D.; Reuland, E. Ascelijn; Al Naiemi, Nashwan; Wester, Astrid Louise; Aarestrup, Frank Møller; Hasman, Henrik.

    In: Journal of Clinical Microbiology, Vol. 53, No. 2, 2015, p. 20677-680.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  10. Published

    Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012.. / Hendriksen, Rene S.; Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Lukwesa-Musyani, Chileshe; Tambatamba, Bushimbwa; Mwaba, John; Kalonda, Annie; Nakazwe, Ruth; Kwenda, Geoffrey; Jensen, Jacob Dyring; Svendsen, Christina Aaby; Dittmann, Karen K.; Kaas, Rolf Sommer; Cavaco, Lina; Aarestrup, Frank Møller; Hasman, Henrik; Mwansa, James C. L.

    In: Journal of Clinical Microbiology, Vol. 53, No. 1, 2015, p. 262-272.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  11. Published

    Gliadin affects glucose homeostasis and intestinal metagenome in C57BL6 mice fed a high-fat diet. / Zhang, Li; Hansen, Axel Kornerup; Bahl, Martin Iain; Hansen, Camilla Hartmann Friis; Andersen, Daniel; Pedersen, Susanne Brix; Hellgren, Lars; Licht, Tine Rask.

    2015. Abstract from Keystone Symposia - Gut Microbiota Modulation of Host Physiology: The Search for Mechanism, Keystone, Colorado, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  12. Accepted

    Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macroevolution of a double minute chromosome.. / Favero, Francesco; McGranahan, Nicholas; Salm, Maximilian P.; Birkbak, Nicolai Juul; Sanborn, J. Zachary ; Benz, Stephen C. ; Becq, Jennifer; Peden, John F. ; Kingsbury, Zoya ; Grocok, Russell J. ; Eklund, Aron Charles.

    In: Annals of Oncology, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  13. Published

    Identification of novel immune and barrier genes in atopic dermatitis by means of laser capture microdissection. / Esaki, Hitokazu; Ewald, David Adrian; Ungar, Benjamin; Rozenblit, Mariya; Zheng, Xiuzhong; Xu, Hui; Estrada, Yeriel D.; Peng, Xiangyu; Mitsui, Hiroshi; Litman, Thomas; Suarez-Farinas, Mayte; Krueger, James G.; Guttman-Yassky, Emma.

    In: Journal of Allergy and Clinical Immunology, Vol. 135, No. 1, 2015, p. 153-163.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  14. Published

    Lactococcus lactis Thioredoxin Reductase Is Sensitive to Light Inactivation. / Björnberg, Olof; Viennet, Thibault; Skjoldager, Nicklas; Curovic, Aida; Nielsen, Kristian Fog; Svensson, Birte; Hagglund, P.

    In: Biochemistry, Vol. 54, No. 8, 2015, p. 1628-1637.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  15. Published

    Metagenomic heterogeneity explains dual immune effects of endotoxins. / Pedersen, Susanne Brix; Eriksen, Carsten; Larsen, Jeppe Madura; Bisgaard, Hans Flinker.

    In: Journal of Allergy and Clinical Immunology, Vol. 135, No. 1, 2015, p. 277-280.

    Publication: Research - peer-reviewComment/debate – Annual report year: 2015

  16. Published

    Microbial Biofilm as a Smart Material. / Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper; Sams, Thomas.

    In: Sensors, Vol. 15, No. 2, 2015, p. 4229-4241.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  17. Published

    Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. / Besenbacher, Søren; Liu, Siyang; Gonzalez-Izarzugaza, Jose Maria; Grove, Jakob; Belling, Kirstine C.; Bork-Jensen, Jette; Huang, Shujia; Dam-Als, Thomas; Li, Shengting; Yadav, Rachita; Yadav, Rachita; Rubio García, Arcadio; Lescai, Francesco; Demontis, Ditte ; Rao, Junhua ; Ye, Weijian ; Mailund, Thomas; Friborg, Rune M. ; Pedersen, Christian N. S.; Xu, Ruiqi; Sun, Jihua; Liu, Hao ; Wang, Ou ; Cheng, Xiaofang ; Flores Santa Cruz, David; Rydza, Emil Karol; Rapacki, Kristoffer; Sørensen, John Damm; Chmura, Piotr Jaroslaw; Westergaard, David; Dworzynski, Piotr; Sørensen, Thorkild I. A.; Lund, Ole; Hansen, Torben; Xu, Xun; Li, Ning; Bolund, Lars; Pedersen, Oluf; Eiberg, Hans; Krogh, Anders; Børglum, Anders D.; Brunak, Søren; Kristiansen, Karsten; Schierup, Mikkel H; Jun, Wang; Gupta, Ramneek; Villesen, Palle ; Rasmussen, Simon.

    In: Nature Communications, Vol. 6, 5969, 2015.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  18. In press
  19. Published

    Renal impairment and late toxicity in germ-cell cancer survivors.. / Lauritsen, J.; Mortensen, M. S.; Kier, M. G. G.; Christensen, I. J.; Agerbaek, M.; Gupta, Ramneek; Daugaard, G.

    In: Annals of Oncology, Vol. 26, No. 1, 2015, p. 173-178.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  20. Published
  21. Published

    SNPsnap: a Web-based tool for identification and annotation of matched SNPs. / Pers, Tune Hannes; Timshel, Pascal; Hirschhorn, Joel N.

    In: Bioinformatics, Vol. 31, No. 3, 2015, p. 418-420.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  22. Published

    Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria. / Lau, Clinton K.Y.; Turner, Louise; Jespersen, Jakob S.; Lowe, Edward D. ; Petersen, Bent; Wang, Christian W.; Petersen, Jens E.V.; Lusingu, John; Theander, Thor G.; Lavstsen, Thomas; Higgins, Matthew K.

    In: Cell Host & Microbe, Vol. 17, 2015, p. 118-129.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  23. Published

    Tabhu: tools for antibody humanization.. / Olimpieri, Pier Paolo; Marcatili, Paolo; Tramontano, Anna.

    In: Bioinformatics, Vol. 31, No. 3, 2015, p. 20434-20435.

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

  24. Published

    Traces of ATCV-1 associated with laboratory component contamination. / Kjartansdóttir, Kristín Rós ; Friis-Nielsen, Jens; Asplund, Maria ; Mollerup, Sarah ; Mourier, Tobias ; Holm Jensen, Randi ; Arn Hansen, Thomas; Rey-Iglesia, Alba ; Raith Richter, Stine ; Alquezar-Planas, David E. ; Olsen, Pernille V. S. ; Vinner, Lasse ; Fridholm, Helena ; Sicheritz-Pontén, Thomas; Nielsen, Lars Peter; Brunak, Søren; Willerslev, Eske; Gonzalez-Izarzugaza, Jose Maria; Hansen, Anders Johannes .

    In: National Academy of Sciences. Proceedings, 2015, p. E925–E926.

    Publication: Research - peer-reviewLetter – Annual report year: 2015

  25. Published

    Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism. / Hao, Qin; Yadav, Rachita; Basse, Astrid L.; Petersen, Sidsel ; Sonne, Si B.; Rasmussen, Simon; Zhu, Qianhua; Lu, Zhike; Wang, Jun; Audouze, Karine Marie Laure; Gupta, Ramneek; Madsen, Lise; Kristiansen, Karsten; Hansen, Jacob B.

    In: Endocrinology and Metabolism, Vol. 308, No. 5, 2015, p. E380-E392.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

  26. Published

    Two Lactococcus lactis thioredoxin paralogues play different roles in responses to arsenate and oxidative stress. / Efler, Petr; Kilstrup, Mogens; Johnsen, Stig; Svensson, Birte; Hägglund, Per.

    In: Microbiology, Vol. 161, No. Pt 3, 2015, p. 528-538.

    Publication: Research - peer-reviewJournal article – Annual report year: 2015

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