Functional Genomics

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  1. 2013
  2. Published

    Genome Sequence of a Novel Archaeal Rudivirus Recovered from a Mexican Hot Spring

    Servín-Garcidueñas, L., Peng, Xu, Garrett, Roger Antony & Martínez-Romero, E., 2013, In: Genome Announcements. 1, 1, p. 1-2 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02

    Servín-Garcidueñas, L. E., Garrett, Roger Antony, Amils, R. & Martínez-Romero, E., 2013, In: Genome Announcements. 1, 1, p. 1-2 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress

    Barah, P., Jayavelu, N. D., Mundy, J. & Bones, A. M., 2013, In: Frontiers in Plant Science. 4, 10 p., 532.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    Barah, P., Jayavelu, N. D., Rasmussen, Simon, Nielsen, H. B., Mundy, J. & Bones, A. M., 2013, In: B M C Genomics. 14, 16 p., 722 .

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon

    Jaubert, C., Danioux, C., Oberto, J., Cortez, D., Bize, A., Krupovic, M., She, Q., Forterre, P., Prangishvili, D. & Sezonov, G., 2013, In: Open Biology. 3, 4, 19 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

    Bagger, F. O., Rapin, N. P. J., Theilgaard-Mønch, Kim, Kaczkowski, B., Thorén, L. A. M., Jendholm, L. J., Winther, Ole & Porse, Bo Torben, 2013, In: Nucleic Acids Research. 41, Database issue, p. D1034-D1039 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Knockouts of RecA-Like proteins RadC1 and RadC2 have distinct responses to DNA damage agents in Sulfolobus islandicus

    Liang, P., Han, W., Huang, Q., Li, Y., Ni, J., She, Q. & Shen, Y., 2013, In: Journal of Genetics and Genomics. 40, 10, p. 533-542 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    MRX protects fork integrity at protein-DNA barriers, and its absence causes checkpoint activation dependent on chromatin context

    Bentsen, I. B., Nielsen, I., Lisby, Michael, Nielsen, H. B., Sen Gupta, S., Mundbjerg, K., Andersen, A. H. & Bjergbaek, L., 2013, In: Nucleic Acids Research. 41, 5, p. 3173-3189 17 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Molecular cloning and antimicrobial activity of enterolysin A and helveticin J of bacteriolysins from metagenome of Chinese traditional fermented foods

    Zhang, T., Pan, Y., Li, B., Ou, J., Zhang, J., Chen, Y., Peng, Xu & Chen, L., 2013, In: Food Control. 31, 2, p. 499-507 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Molecular cloning of a novel bioH gene from an environmental metagenome encoding a carboxylesterase with exceptional tolerance to organic solvents

    Shi, Y., Pan, Y., Li, B., He, W., She, Q. & Chen, L., 2013, In: B M C Biotechnology. 13, 11 p., 13.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    New aspects of protein stability and turnover in the regulation of genome integrity: the role of Cmr1 and Rad56

    Gallina, I., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 195 p.

    Research output: Book/Report › Ph.D. thesis › Research

  13. Published

    Novel insights into gene regulation of the rudivirus SIRV2 infecting Sulfolobus cells

    Okutan, E., Deng, Ling, Mirlashari, S., Uldahl, K., Halim, M., Liu, C., Garrett, Roger Antony, She, Q. & Peng, Xu, 2013, In: R N A Biology. 10, 5, p. 1-11 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Protein dielectric constants determined from NMR chemical shift perturbations

    Kukic, P., Farrell, D., McIntosh, L. P., García-Moreno E., B., Jensen, K. S., Toleikis, Z., Teilum, Kaare & Nielsen, J. E., 2013, In: Journal of the American Chemical Society. 135, 45, p. 16968–16976 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2013, In: PLoS ONE. 8, 12, 10 p., e84123.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Protospacer recognition motifs: Mixed identities and functional diversity

    Shah, S. A., Erdmann, S., Mojica, F. J. M. & Garrett, Roger Antony, 2013, In: R N A Biology. 10, 5, p. 1-9 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    RNAi screening for characterisation of ER-associated degradation pathways in mammalian cells

    Månsson, M. D. J., 2013, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  18. Published

    RPA coordinates DNA end resection and prevents formation of DNA hairpins

    Chen, H., Lisby, Michael & Symington, L. S., 2013, In: Molecular Cell. 50, 4, p. 589-600 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2

    Erdmann, S., Shah, S. A. & Garrett, Roger Antony, 2013, In: Biochemical Society Transactions. 41, 6, p. 1449-1458 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

    Kenchappa, C., Heiðarsson, P. O., Kragelund, Birthe Brandt, Garrett, Roger Antony & Poulsen, F., 2013, In: Nucleic Acids Research. 41, 5, p. 3424-3435 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Spd1 accumulation causes genome instability independently of ribonucleotide reductase activity but functions to protect the genome when deoxynucleotide pools are elevated

    Fleck, O., Vejrup-Hansen, R., Watson, A., Carr, A. M., Nielsen, Olaf & Holmberg, Christian, 2013, In: Journal of Cell Science. 126, p. 4985-4994 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Specificity and function of Archaeal DNA replication initiator proteins

    Samson, R., Xu, Y., Gadelha, C., Stone, T., Faqiri, J., Li, D., Qin, N., Pu, F., Liang, Y., She, Q. & Bell, S., 2013, In: Cell Reports. 3, 2, p. 485-496 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Structure, function and networks of transcription factors involved in abiotic stress responses

    Lindemose, Søren, O'Shea, Charlotte, Jensen, M. K. & Skriver, Karen, 2013, In: International Journal of Molecular Sciences (Online). 14, 3, p. 5842-78 37 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Studies of archaeal virus-host systems in thermal environments

    Erdmann, S., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 147 p.

    Research output: Book/Report › Ph.D. thesis › Research

  25. Published

    Subnuclear relocalization and silencing of a chromosomal region by an ectopic ribosomal DNA repeat

    Jakociunas, T., Domange Jordö, M. E., Mebarek, M. A., Bünner, C. M., Hansen, J. V., Oddershede, L. B. & Thon, Genevieve, 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 47, p. E4465-E4473 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    Tlys, a newly identified Sulfolobus spindle-shaped virus 1 transcript expressed in the lysogenic state, encodes a DNA-binding protein interacting at the promoters of the early genes

    Fusco, S., She, Q., Bartolucci, S. & Contursi, P., 2013, In: Journal of Virology. 87, 10, p. 5926-5936 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Published

    The PCNA interaction protein box sequence in Rad54 is an integral part of its ATPase domain and is required for efficient DNA repair and recombination

    Burgess, R. C., Sebesta, M., Sisakova, A., Marini, V. P., Lisby, Michael, Damborsky, J., Klein, H., Rothstein, R. & Krejci, L., 2013, In: PLoS ONE. 8, 12, p. e82630 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    The alkaloid compound harmane increases the lifespan of Caenorhabditis elegans during bacterial infection, by modulating the nematode's innate immune response

    Jakobsen, H., Bojer, Martin Saxtorph, Marinus, M. G., Xu, T., Struve, C., Krogfelt, K. A. & Løbner-Olesen, Anders, 2013, In: P L o S One. 8, 3, 8 p., e60519.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    The role of C/EBPa in PD-1+ CD4+ T cells & modulation of RNR activity prolongs survival of mice with AML

    Norrie, I. C., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 118 p.

    Research output: Book/Report › Ph.D. thesis › Research

  30. Published

    Transcriptome responses to combinations of stresses in Arabidopsis

    Rasmussen, S., Barah, P., Suarez Rodriguez, M. C., Bressendorff, Simon, Friis, P., Costantino, P., Bones, A. M., Nielsen, H. B. & Mundy, J., 2013, In: Plant Physiology. 161, 4, p. 1783-1794 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi

    Ren, Y., She, Q. & Huang, L., 2013, In: Virology. 441, 2, p. 126-134 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    Two portable recombination enhancers direct donor choice in fission yeast heterochromatin

    Jakociunas, T., Holm, L. R., Hansen, J. V., Trusina, Ala & Thon, Genevieve, 2013, In: P L o S Genetics. 9, 10, 14 p., e1003762.

    Research output: Contribution to journal › Journal article › Research › peer-review

  33. Published

    Volume of Hsp90 ligand binding and the unfolding phase diagram as a function of pressure and temperature

    Petrauskas, V., Gylyte, J., Toleikis, Z., Cimmperman, P. & Matulis, D., 2013, In: European Biophysics Journal. 42, 5, p. 355-362 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. 2012
  35. Published

    A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus

    Peng, N., Deng, Ling, Mei, Y., Jiang, D., Hu, Y., Awayez, M., Liang, Y. & She, Q., 2012, In: Applied and Environmental Microbiology. 78, 16, p. 5630-5637 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. Published

    An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease

    Hu, Y., Peng, N., Han, W., Mei, Y., Chen, Z., Feng, X., Liang, Y. X. & She, Q., 2012, In: Bioscience Reports. 32, p. 609-618 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Archaeal viruses-novel, diverse and enigmatic

    Peng, Xu, Garrett, Roger Antony & She, Q., 2012, In: Science China Life Sciences. 55, 5, p. 422-433 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. Published

    CRISPR/Cas and CRISPR/Cmr immune systems of archaea

    Shah, S. A., Vestergaard, G. A. & Garrett, Roger Antony, 2012, Regulatory RNAs in prokaryotes. Springer, p. 163-181 19 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  39. Published

    Crystal structure of ATVORF273, a new fold for a thermo- and acido-stable protein from the Acidianus two-tailed virus

    Felisberto-Rodrigues, C., Blangy, S., Goulet, A., Vestergaard, G. A., Cambillau, C., Garrett, Roger Antony & Ortiz-Lombardía, M., 2012, In: P L o S One. 7, 10, 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  40. Published

    Cyclin-dependent kinase suppression by WEE1 kinase protects the genome through control of replication initiation and nucleotide consumption

    Beck, H., Nähse-Kumpf, V., Larsen, Marie Sofie Yoo, O'Hanlon, K. A., Patzke, S., Holmberg, Christian, Mejlvang, J., Groth, Anja, Nielsen, Olaf, Syljuåsen, R. G. & Sørensen, Claus Storgaard, 2012, In: Molecular and Cellular Biology. 32, 20, p. 4226-4236 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. Published

    Development of a Simvastatin Selection Marker for a Hyperthermophilic Acidophile, Sulfolobus islandicus

    Zheng, T., Huang, Q., Zhang, C., Ni, J., She, Q. & Shen, Y., 2012, In: Applied and Environmental Microbiology. 78, 2, p. 568-574 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  42. Published

    Dissection of the functional domains of an archaeal holliday junction helicase

    Hong, Y., Chu, M., Li, Y., Ni, J., Sheng, D., Hou, G., She, Q. & Shen, Y., 2012, In: D N A Repair. 11, 2, p. 102-111 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Ekstremernes herrer

    Uldahl, K. B. & Peng, Xu, 2012, In: Aktuel Naturvidenskab. 2012, 05, p. 28-29 2 p.

    Research output: Contribution to journal › Journal article › Research

  44. Published

    Exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host

    Mei, Y., Peng, N., Zhao, S., Hu, Y., Wang, H., Liang, Y. & She, Q., 2012, In: Applied Microbiology and Biotechnology. 93, 5, p. 1965-1974 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Guidelines for the use and interpretation of assays for monitoring autophagy

    Klionsky, D. J., Abdalla, F. C., Abeliovich, H., Farkas, T., Frankel, Lisa, Høyer-Hansen, M., Jäätteä, M., Lund, Anders H., Olsson, S. & Petersen, Morten, 2012, In: Autophagy. 8, 4, p. 445-544 100 p.

    Research output: Contribution to journal › Review › Research › peer-review

  46. Published

    Histone H3 lysine 56 acetylation and the response to DNA replication fork damage

    Wurtele, H., Kaiser, G. S., Bacal, J., St-Hilaire, E., Lee, E., Tsao, S., Dorn, J., Maddox, P., Lisby, Michael, Pasero, P. & Verreault, A., 2012, In: Molecular and Cellular Biology. 32, 1, p. 154-172 19 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Published

    Immunity in the moss Physcomitrella patens

    Bressendorff, Simon, 2012, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  48. Published

    Lack of the RNA chaperone Hfq attenuates pathogenicity of several Escherichia coli pathotypes towards Caenorhabditis elegans

    Bojer, M. S., Jakobsen, H., Struve, C., Krogfelt, K. A. & Løbner-Olesen, Anders, 2012, In: Microbes and Infection. 14, 12, p. 1034-1039 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Published

    Live cell microscopy of DNA damage response in Saccharomyces cerevisiae

    Pinela da Silva, S. C., Gallina, I., Eckert-Boulet, N. V. & Lisby, Michael, 2012, DNA repair protocols. Springer Science+Business Media, p. 433-443 11 p. (Methods in Molecular Biology, Vol. 920).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  50. Published

    MAP kinase cascades in Arabidopsis innate immunity

    Rasmussen, M. W., Roux, M. E., Petersen, Morten & Mundy, J., 2012, In: Frontiers in Plant Science. 3, 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  51. Published

    MRN1 implicates chromatin remodeling complexes and architectural factors in mRNA maturation.

    Düring, L., Thorsen, M., Petersen, D., Køster, B., Jensen, T. H. & Holmberg, Steen, 2012, In: P L o S One. 7, 9, 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    Mediator regulates non-coding RNA transcription at fission yeast centromeres

    Thorsen, M., Hansen, H., Venturi, M., Holmberg, Steen & Thon, Genevieve, 2012, In: Epigenetics & Chromatin. 5, p. 1-10 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

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