Functional Genomics

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  1. 2014
  2. Published

    CRISPR adaptive immune systems of Archaea

    Vestergaard, G. A., Garrett, Roger Antony & Shah, S. A., 2014, In: R N A Biology. 11, 2, p. 157-168 12 p.

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

  3. 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

  4. Published

    Cell cycle regulation of homologous recombination in Saccharomyces cerevisiae

    Mathiasen, D. P. & Lisby, Michael, 2014, In: F E M S Microbiology Reviews. 38, 2, p. 172-184 13 p.

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

  5. 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

  6. Published

    DNA Methylation

    Marinus, M. G. & Løbner-Olesen, Anders, 2014, Synthesis and Processing of Macromolecules. Lovett, S. T. (ed.). ASM Press, (EcoSal Plus: Domain 4).

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

  7. Published

    DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    Sander, Adam F. , Lavstsen, Thomas, Rask, T. S., Lisby, Michael, Salanti, Ali, Fordyce, S. L., Jespersen, Jakob Schmidt, Carter, R., Deitsch, K. W., Theander, Thor Grundtvig, Pedersen, A. G. & Arnot, D. E., 2014, In: Nucleic Acids Research. 42, 4, p. 2270-81 12 p.

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

  8. Published

    First experimental evidence for the presence of a CRISPR toxin in Sulfolobus

    He, F., Chen, L. & Peng, Xu, 2014, In: Journal of Molecular Biology. 426, 22, p. 3683-3688 6 p.

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

  9. Published

    Flavour Compounds in Fungi: Flavour Analysis in Ascomycetes and the Contribution of the Ehrlich Pathway to Flavour Production in Saccharomyces cerevisiae and Ashbya gossypii

    Ravasio, D. A., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  10. 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

  11. Published

    Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis

    Sun, X., Liu, T., Peng, Xu & Chen, L., 2014, In: International Journal of Molecular Sciences (Online). 15, 12, p. 22539-22562 24 p.

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

  12. Published

    Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus

    Erdmann, S., Le Moine Bauer, S. & Garrett, Roger Antony, 2014, In: Molecular Microbiology. 91, 5, p. 900-917 18 p.

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

  13. Published

    Interplays between Sumoylation, SUMO-Targeted Ubiquitin Ligases, and the Ubiquitin-Adaptor Protein Ufd1 in Fission Yeast

    Køhler, J. B., 2014, Department of Biology, Faculty of Science, University of Copenhagen. 194 p.

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

  14. Published

    Length-dependent processing of telomeres in the absence of telomerase

    Fallet, E., Jolivet, P., Soudet, J., Lisby, Michael, Gilson, E. & Teixeira, M. T., 2014, In: Nucleic Acids Research. 42, 6, p. 3648-3665 18 p.

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

  15. Published

    Mechanisms and regulation of mitotic recombination in Saccharomyces cerevisiae

    Symington, L. S., Rothstein, R. & Lisby, Michael, 2014, In: Genetics (Print). 198, 3, p. 795-835 41 p.

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

  16. Published

    Meiosis and SUMO

    Holm, L. R., 2014, Department of Biology, Faculty of Science, University of Copenhagen. 170 p.

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

  17. Published

    Metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in Shanghai, China

    Jin, H., Li, B., Peng, Xu & Chen, L., 2014, In: Annals of Microbiology. 64, 2, p. 689-697 9 p.

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

  18. 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

  19. Published

    Nanobiomotors of archaeal DNA repair machineries: current research status and application potential

    Han, W., Shen, Y. & She, Q., 2014, In: Cell & Bioscience. 4, 32, 12 p.

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

  20. 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

  21. 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

  22. Published

    Regulation of Homologous Recombination by SUMOylation: SUMO, DNA Repair and New Insights into Telomere Maintenance

    Pinela da Silva, S. C., 2014, Department of Biology, Faculty of Science, University of Copenhagen. 211 p.

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

  23. Published

    Spd2 assists Spd1 in the modulation of ribonucleotide reductase architecture but does not regulate deoxynucleotide pools

    Vejrup-Hansen, R., Fleck, O., Landvad, K., Fahnøe, Ulrik, Broendum, S. S., Schreurs, A., Kragelund, Birthe Brandt, Carr, A. M., Holmberg, Christian & Nielsen, Olaf, 2014, In: Journal of Cell Science. 127, p. 2460-2470 11 p.

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

  24. Published

    Structure of Leptin Receptor Related with Obesity

    Toleikis, Z., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  25. Published

    Sulfolobus Replication Factor C stimulates the activity of DNA Polymerase B1

    Xing, X., Zhang, L., Guo, L., She, Q. & Huang, L., 2014, In: Journal of Bacteriology. 196, 13, p. 2367-2375 9 p.

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

  26. Published

    Suppressing autoimmunity in Arabidopsis thaliana with dominant negative immune receptors

    Greeff, M. C., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  27. Published

    The Role of the CRL4Cdt2 Target Spd1 in Chromosome Segregation in Fission Yeast

    Landvad, K., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  28. Published

    The genetic and biochemical basis of FANCD2 Monoubiquitination

    Rajendra, E., Østergaard, Vibe Hallundbæk, Langevin, F., Wang, M., Dornan, G. L., Patel, K. J. & Passmore, L. A., 2014, In: Molecular Cell. 54, 5, p. 858-869 12 p.

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

  29. Published

    The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Kristensen, T. P., Cherian, R. M., Gray, F. C. & Macneill, S. A., 2014, In: Frontiers in Microbiology. 5, 13 p., 123.

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

  30. Published

    The influence of pressure on the intrinsic dissolution rate of amorphous indomethacin

    Löbmann, Korbinian, Flouda, K., Qiu, D., Tsolakou, T., Wang, W. & Rades, Thomas, 2014, In: Pharmaceutics. 6, 3, p. 481-93 13 p.

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

  31. Published

    TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability

    Germann, S. M., Schramke, V., Pedersen, R. T., Gallina, I., Eckert-Boulet, N., Østergaard, Vibe Hallundbæk & Lisby, Michael, 2014, In: Journal of Cell Biology. 204, 1, p. 45-59 15 p.

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

  32. 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

  33. 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

  34. Published

    relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

    Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., Teilum, Kaare, Gagne, S., Marion, D., Griesinger, C., Blackledge, M. & d’Auvergne, E. J., 2014, In: Bioinformatics. 30, 15, p. 2219-2220 2 p.

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

  35. 2013
  36. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

    Orlando, L. A. A., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, T. S., Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J. & 36 others, Dolocan, A., Stenderup, Jesper Tandberg, Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Røed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. A. S., Ryder, O., Andersson, L., Mundy, J., Krogh, Anders, Gilbert, M Thomas P, Kjær, Kurt H., Sicheritz-Pontén, T., Jensen, Lars Juhl, Olsen, Jesper Velgaard, Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J. & Willerslev, Eske, 4 Jul 2013, In: Nature. 499, 7456, p. 74-78 5 p.

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

  37. Published

    Physical mapping and cloning of RAD56

    Mathiasen, D. P., Gallina, I., Germann, S. M., Hamou, W., Eléouët, M., Thodberg, S., Eckert-Boulet, N., Game, J. & Lisby, Michael, 25 Apr 2013, In: Gene. 519, 1, p. 182-186 5 p.

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

  38. Published

    Rapid selection of Plasmodium falciparum chloroquine resistance transporter gene and multidrug resistance gene-1 haplotypes associated with past chloroquine and present artemether-lumefantrine use in Inhambane District, southern Mozambique

    Thomsen, T. T., Madsen, L. B., Hansson, Helle Smedegaard, Tomás, E. V. E., Charlwood, D., Bygbjerg, Ib Christian & Alifrangis, Michael, Mar 2013, In: American Journal of Tropical Medicine and Hygiene. 88, 3, p. 536-41 6 p.

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

  39. Published

    A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates

    Li, Y., Pan, Y., She, Q. & Chen, L., 2013, In: B M C Biotechnology. 13, 13 p., 89.

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

  40. Published

    A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus

    Deng, Ling, Garrett, Roger Antony, Shah, S. A., Peng, Xu & She, Q., 2013, In: Molecular Microbiology. 87, 5, p. 1088-1099 12 p.

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

  41. Published

    ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana

    Jensen, M. K., Lindemose, Søren, Masi, F. D., Reimer, J. J., Nielsen, M., Perera, V., Workman, C. T., Turck, F., Grant, M. R., Mundy, J., Petersen, Morten & Skriver, Karen, 2013, In: FEBS Open Bio. 3, p. 321-327 7 p.

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

  42. Published

    Archaeal type II toxin-antitoxins

    Shah, S. A. & Garrett, Roger Antony, 2013, Prokaryotic toxin-antitoxins. Gerdes, K. (ed.). Springer, p. 225-238 14 p.

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

  43. Published

    Biology, biodiversity and application potential of thermophilic viruses

    Uldahl, K. B. & Peng, Xu, 2013, Thermophilic Microbes in Environmental and Industrial Biotechnology: Biotechnology of Thermophiles. Satyanarayana, T., Littlechild, J. & Kawarabayasi, Y. (eds.). Springer, p. 271-304 34 p.

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

  44. Published

    Catalase and NO CATALASE ACTIVITY1 promote autophagy-dependent cell death in Arabidopsis

    Hackenberg, T., Juul, T., Auzina, A., Gwizdz, S., Malolepszy, A., Van Der Kelen, K., Dam, S., Bressendorff, Simon, Lorentzen, A. M., Roepstorff, P., Nielsen, K. L., Jorgensen, J., Hofius, D., Van Breusegem, F., Petersen, Morten & Andersen, S. U., 2013, In: Plant Cell. 25, 11, p. 4616-4626 11 p.

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

  45. Published

    Characterising the CRISPR immune system in Archaea using genome sequence analysis

    Shah, S. A., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 219 p.

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

  46. Published

    Concerted action of the Ubiquitin-Fusion Degradation Protein 1 (Ufd1) and Sumo-Targeted Ubiquitin Ligases (STUbLs) in the DNA-damage response

    Køhler, J. B., Jørgensen, M. L. M., Beinoraite, G., Thorsen, M. & Thon, Genevieve, 2013, In: P L o S One. 8, 11, 15 p., e80442.

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

  47. Published

    Cyclic peptide inhibitors of the β-sliding clamp in Staphylococcus aureus

    Kjelstrup, S., Hansen, P. M. P., Thomsen, Line Elnif, Hansen, Paul Robert & Løbner-Olesen, Anders, 2013, In: P L o S One. 8, 9, 13 p., e72273.

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

  48. Published

    Discovery and seminal developments in the CRISPR field

    Mojica, F. J. M. & Garrett, Roger Antony, 2013, CRISPR-Cas Systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea. Barrangou, R. & van der Oost, J. (eds.). Springer VS, p. 1-31 31 p.

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

  49. Published

    Exposure to Cr(VI) induces organ dependent MSI in two loci related with photophosphorylation and with glutamine metabolism

    Rodriguez, E., Azevedo de Silva, R., Remédios, C., Almeida, T., Fernandes, P. & Santos, C., 2013, In: Journal of Plant Physiology. 170, 5, p. 534-538 5 p.

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

  50. Published

    Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing in Sulfolobus islandicus

    Peng, W., Li, H., Hallstrøm, S., Peng, N., Liang, Y. X. & She, Q., 2013, In: R N A Biology. 10, 5, p. 1-11 11 p.

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

  51. Published

    Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

    Zhang, C., Tian, B., Li, S., Ao, X., Dalgaard, K., Gökce, S., Liang, Y. & She, Q., 2013, In: Biochemical Society Transactions. 41, 1, p. 405-410 6 p.

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

  52. Published

    Genome Sequence of a Novel Archaeal Fusellovirus Assembled from the Metagenome of a Mexican Hot Spring

    Servin-Garciduenas, L. E., Peng, Xu, Garrett, Roger Antony & Martinez-Romero, E., 2013, In: Genome Announcements. 1, p. 1-2 2 p.

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

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