Functional Genomics

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  1. 2015
  2. Published

    Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system

    Fusco, S., Liguori, R., Limauro, D., Bartolucci, S., She, Q. & Contursi, P., 2015, In: Biochimie. 118, p. 322-332 11 p.

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

  3. Published

    Unravelling the role of the F55 regulator in the transition from lysogeny to UV induction of sulfolobus spindle-shaped virus 1

    Fusco, S., She, Q., Fiorentino, G., Bartolucci, S. & Contursi, P., 2015, In: Journal of Virology. 89, 12, p. 6453-6461 9 p.

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

  4. Published

    Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control

    Gallina, I., S.Colding-Christensen, Camilla, Henriksen, P., Beli, P., Nakamura, K., Offman, J., Barfred, D. P., Pinela da Silva, S. C., Hoffmann, E., Groth, Anja, Choudhary, C. & Lisby, Michael, 2015, In: Nature Communications. 6, 16 p., 6533.

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

  5. Published

    CRISPR-Cas adaptive immune systems of the sulfolobales: unravelling their complexity and diversity

    Garrett, Roger Antony, Shah, S. A., Erdmann, S., Guannan, L., Mousaei, M., León Sobrino, C., Peng, W., Islin, S. R., Deng, Ling, Vestergaard, G., Peng, Xu & She, Q., 2015, In: Life. 5, 1, p. 783-817 35 p.

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

  6. Published

    Studying Extrachromosomal Genetic Elements in Sulfolobus

    Guannan, L., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 85 p.

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

  7. Published

    Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    Guo, Y., Kragelund, Birthe Brandt, White, M. F. & Peng, Xu, 2015, In: Journal of Molecular Biology. 427, 12, p. 2179-2191 13 p.

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

  8. Published

    Recombinational DNA repair is regulated by compartmentalization of DNA lesions at the nuclear pore complex

    Géli, V. & Lisby, Michael, 2015, In: BioEssays. 37, 12, p. 1287-1292 6 p.

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

  9. Published

    Crystallization of two operator complexes from the Vibrio cholerae HigBA2 toxin-antitoxin module

    Hadzi, S., Garcia-Pino, A., Gerdes, K., Lah, J. & Loris, R., 2015, In: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications Online. 71, 2, p. 226-233 8 p.

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

  10. Published

    Studies on DNA Damage Response in Sulfolobus islandicus

    Han, W., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 139 p.

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

  11. Published

    Adenylylation of gyrase and topo IV by FicT toxins disrupts bacterial DNA topology

    Harms, A., Stanger, F. V., Scheu, P. D., de Jong, I. G., Goepfert, A., Glatter, T., Gerdes, K., Schirmer, T. & Dehio, C., 2015, In: Cell Reports. 12, 9, p. 1497-1507 11 p.

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

  12. Published

    Regulation of the Anti-Viral Immune System CRISPR in Sulfolobus and Development of a Genetic Tool for the Linear Sulfolobus Rudivirus SIRV2

    He, F., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 101 p.

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

  13. Published

    Efficient 5 '-3 ' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus

    Huang, Q., Liu, L., Liu, J., Ni, J., She, Q. & Shen, Y., 2015, In: B M C Molecular Biology. 16, 14 p., 2.

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

  14. Published

    Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus

    Huang, Q., Li, Y., Zeng, C., Song, T., Yan, Z., Ni, J., She, Q. & Shen, Y., 2015, In: Extremophiles. 19, 2, p. 505-514 10 p.

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

  15. Published

    Transcriptome and genome size analysis of the venus flytrap

    Jensen, M. K., Vogt, J. K., Bressendorff, Simon, Seguin-Orlando, A., Petersen, Morten, Sicheritz-Pontén, T. & Mundy, J., 2015, In: P L o S One. 10, 4, 13 p., e0123887.

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

  16. Published

    Cell growth of wall-free L-form bacteria is limited by oxidative damage

    Kawai, Y., Mercier, R., Wu, L. J., Dominguez Cuevas, P., Oshima, T. & Errington, J., 2015, In: Current Biology. 25, 12, p. 1613-1618 6 p.

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

  17. Published

    An IPTG-inducible derivative of the fission yeast nmt promoter

    Kjærulff, S. & Nielsen, Olaf, 2015, In: Yeast. 32, p. 469-478 10 p.

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

  18. Published

    Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

    Køhler, J. B., Tammsalu, T., Jørgensen, M. L. M., Steen, N., Hay, R. T. & Thon, Genevieve, 2015, In: Nature Communications. 6, 14 p., 8827.

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

  19. Published

    STSV2 as a Model Crenarchaeal Virus for Studying Virus-Host Interactions and CRISPR-Cas Adaptive Immunity

    León Sobrino, C., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 159 p.

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

  20. Published

    Heterologous expression of mannanase and developing a new Reporter gene system in Lactobacillus casei and Escherichia coli

    Lin, J., Zou, Y., Ma, C., She, Q., Liang, Y., Chen, Z. & Ge, X., 2015, In: PLOS ONE. 10, 11, 16 p., e0142886.

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

  21. Published

    Cell biology of mitotic recombination

    Lisby, Michael & Rothstein, R., 2015, In: Cold Spring Harbor Perspectives in Biology. 7, 3, 23 p., a016535.

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

  22. Published

    Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

    Liu, T., Li, Y., Wang, X., Ye, Q., Li, H., Liang, Y., She, Q. & Peng, N., 30 Jan 2015, In: Nucleic Acids Research. 43, 2, p. 1044-1055 12 p.

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

  23. Published

    Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p

    Madsen, C. T., Sylvestersen, K. B., Young, C., Buch-Larsen, Sara Charlotte, Poulsen, J. W., Andersen, M. A., Palmqvist, E. A., Hey-Mogensen, M., Jensen, P. B., Treebak, Jonas Thue, Lisby, Michael & Nielsen, Michael Lund, 2015, In: Nature Communications. 6, 12 p., 7726.

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

  24. Published

    An updated evolutionary classification of CRISPR-Cas systems

    Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M. F., Yakunin, A. F., Garrett, R. A., van der Oost, J., Backofen, R. & 1 others, Koonin, E. V., 2015, In: Nature Reviews. Microbiology. 13, 11, p. 722-736 15 p.

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

  25. Published

    Single site suppressors of a fission yeast temperature-sensitive mutant in cdc48 identified by whole genome sequencing

    Marinova, I. N., Engelbrecht, J., Ewald, A., Langholm, L. L., Holmberg, Christian, Kragelund, Birthe Brandt, Gordon, C., Nielsen, Olaf & Hartmann-Petersen, Rasmus, 2015, In: P L o S One. 10, 2, 15 p., e0117779.

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

  26. Published

    The pearl millet mitogen-activated protein kinase PgMPK4 is involved in responses to downy mildew infection and in jasmonic- and salicylic acid-mediated defense

    Melvin, P., Prabhu, S. A., Veena, M., Shailasree, S., Petersen, Morten, Mundy, J., Shetty, S. H. & Kini, K. R., 2015, In: Plant Molecular Biology. 87, 3, p. 287-302 16 p.

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

  27. Published

    Comparative metagenomics of eight geographically remote terrestrial hot springs

    Menzel, P., Islin, S. R., Rike, A. G., Lin, L., Zhang, Q., Contursi, P., Moracci, M., Kristjansson, J. K., Bolduc, B., Gavrilov, S., Ravin, N., Mardanov, A., Bonch-Osmolovskaya, E., Young, M., Krogh, Anders & Peng, Xu, 2015, In: Microbial Ecology. 70, 2, p. 411-424 14 p.

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

  28. Published

    Compartment-specific aggregases direct distinct nuclear and cytoplasmic aggregate deposition

    Miller, S. B., Ho, C., Winkler, J., Khokhrina, M., Neuner, A., Mohamed, M. Y., Guilbride, D. L., Richter, K., Lisby, Michael, Schiebel, E., Mogk, A. & Bukau, B., 2015, In: E M B O Journal. 34, 6, p. 778-797 20 p.

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

  29. Published

    Coupled positive and negative feedbacks produce diverse gene expression patterns in colonies

    Mitarai, Namiko, Jensen, Mogens Høgh & Semsey, S., 7 Apr 2015, In: mBio (Print). 6, 2, e00059-15 .

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

  30. Published

    Retromer contributes to immunity-associated cell death in Arabidopsis

    Munch, D., Teh, O., Malinovsky, F. G., Liu, Q., Vetukuri, R. R., El Kasmi, F., Brodersen, Peter, Hara-Nishimura, I., Dangl, J. L., Petersen, Morten, Mundy, J. & Hofius, D., 2015, In: Plant Cell. 27, 2, p. 463-479 17 p.

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

  31. Published

    Top2 and Sgs1-Top3 act redundantly to ensure rDNA replication termination

    Mundbjerg, K., Jørgensen, S. W., Fredsøe, J. C., Nielsen, I., Pedersen, J. M., Bentsen, I. B., Lisby, Michael, Bjergbaek, L. & Andersen, A. H., 2015, In: P L o S Genetics. 11, 12, 24 p., e1005697.

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

  32. Published

    Immunogenic and protective efficacy of recombinant protein GtxA-N against Gallibacterium anatis challenge in chickens

    Pedersen, I. J., Pors, S. E., Skjerning, R. B., Nielsen, Søren Saxmose & Bojesen, Anders Miki, Oct 2015, In: Avian pathology : journal of the W.V.P.A. 44, 5, p. 386-391 6 p.

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

  33. Published

    The Functional Role of TopBP1 in DNA Maintenance at Mitosis

    Pedersen, R. T., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 167 p.

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

  34. Published

    TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells

    Pedersen, R. T., Kruse, Thomas, Nilsson, Jakob, Østergaard, Vibe Hallundbæk & Lisby, Michael, 2015, In: Journal of Cell Biology. 210, 4, p. 565-582 18 p.

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

  35. Published

    An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference

    Peng, W., Feng, M., Feng, X., Liang, Y. X. & She, Q., 2015, In: Nucleic Acids Research. 43, 1, p. 406-417 12 p.

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

  36. Published

    Genetic Studies on CRISPR-Cas Functions in Invader Defense in Sulfolobus islandicus

    Peng, W., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  37. Published

    Identification and Investigation of Native Chromosomal Fragile Sites in the Avian Cell Line DT40: Chromosomal Fragile Sites and Genome Integrity

    Pentzold, C., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 150 p.

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

  38. Published

    MAP Kinase 4 Substrates and Plant Innate Immunity

    Rasmussen, M. W., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  39. Published

    The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2

    Roux, M. E., Rasmussen, M. W., Palma, K., Lolle, S., Regué, À. M., Bethke, G., Glazebrook, J., Zhang, W., Sieburth, L., Larsen, M. R., Mundy, J. & Petersen, Morten, 2015, In: E M B O Journal. 34, 5, p. 593-608 16 p.

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

  40. Published

    Hyperthermophilic Archaeal Viruses as Novel Nanoplatforms

    Uldahl, K. B., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  41. Published

    Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

    Vischer, N. O. E., Verheul, J., Postma, M., van Saparoea, B. V. D. B., Galli, E., Natale, P., Gerdes, K., Luirink, J., Vollmer, W., Vicente, M. & den Blaauwen, T., 2015, In: Frontiers in Microbiology. 6, 18 p., 586.

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

  42. Published

    Archaeal extrachromosomal genetic elements

    Wang, H., Peng, N., Shah, S. A., Huang, L. & She, Q., 2015, In: Microbiology and Molecular Biology Reviews. 79, 1, p. 117-152 36 p.

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

  43. 2014
  44. Published

    CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

    Alkhnbashi, O. S., Costa, F., Shah, S. A., Garrett, Roger Antony, Saunders, S. J. & Backofen, R., 2014, In: Bioinformatics. 30, 17, p. i489-i496 8 p.

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

  45. Published

    Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

    Andersen, K. S., Bojsen, R. K., Sørensen, L. G. R., Weiss Nielsen, M., Lisby, Michael, Folkesson, A. & Regenberg, Birgitte, 2014, In: G3: Genes, Genomes, Genetics (Bethesda). 4, 9, p. 1671-1680 10 p.

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

  46. Published

    Correction: 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 (PLoS ONE (2013) 8, 12 (e82630) DOI: 10.1371/journal.pone.0082630)

    Burgess, R. C., Sebesta, M., Sisakova, A., Marini, V. P. & Lisby, Michael, 24 Jun 2014, In: PLoS ONE. 9, 6, e101095.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  47. Published

    Oxidative DNA damage is instrumental in hyperreplication stress-induced inviability of Escherichia coli

    Charbon, Godefroid, Bjørn, L., Mendoza-Chamizo, B., Frimodt-Møller, Jakob & Løbner-Olesen, Anders, 2014, In: Nucleic Acids Research. 42, 21, p. 13228-13241 14 p.

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

  48. Published

    Characterization of pMC11, a plasmid with dual origins of replication isolated from Lactobacillus casei MCJ and construction of shuttle vectors with each replicon

    Chen, Z., Lin, J., Ma, C., Zhao, S., She, Q. & Liang, Y., 2014, In: Applied Microbiology and Biotechnology. 98, 13, p. 5977-5989 13 p.

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

  49. Published

    Molecular biology of fuselloviruses and their satellites

    Contursi, P., Fusco, S., Cannio, R. & She, Q., 2014, In: Extremophiles. 18, 3, p. 473-489 17 p.

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

  50. Published

    Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry

    Deng, Ling, He, F., Bhoobalan, Yuvaraj, Martinez Alvarez, Laura, Guo, Y. & Peng, Xu, 2014, In: Journal of Virology. 88, 17, p. 10264-10268 5 p.

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

  51. Published

    Origins and emergent evolution of life: the colloid microsphere hypothesis revisited

    Egel, Richard, 2014, In: Origins of Life and Evolution of Biospheres. 44, 2, p. 87-110 24 p.

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

  52. Published

    Upregulated baseline plasma CCL19 and CCR7 cell-surface expression on monocytes in early rheumatoid arthritis normalized during treatment and CCL19 correlated with radiographic progression

    Ellingsen, T., Hansen, I., Thorsen, J., Møller, B. K., Tarp, U., Lottenburger, T., Andersen, L. S., Skjødt, H., Pedersen, J. K., Lauridsen, U. B., Svendsen, A., Lindegaard, H., Jacobsen, S., Østergaard, M., Vestergaard, A., Jurik, A. G., Junker, P., Christensen, A. F., Hetland, M. L., Hørslev-Petersen, K. & 1 others, Stengaard-Pedersen, K., 2014, In: Scandinavian Journal of Rheumatology. 43, 2, p. 91-100 10 p.

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

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