Functional Genomics

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  1. 2018
  2. Published

    Individual components of paired typical NLR immune receptors are regulated by distinct E3 ligases

    Dong, O. X., Ao, K., Xu, F., Johnson, K. C. M., Wu, Y., Li, L., Xia, S., Liu, Y., Huang, Y., Rodriguez, Eleazar, Chen, X., Chen, S., Zhang, Y., Petersen, Morten & Li, X., 2018, In: Nature Plants. 4, 9, p. 699-710

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

  3. Published

    Insights into the evolutionary conserved regulation of Rio ATPase activity

    Knüppel, R., Christensen, R. H., Gray, F. C., Esser, D., Strauss, D., Medenbach, J., Siebers, B., MacNeill, S. A., LaRonde, N. & Ferreira-Cerca, S., 2018, In: Nucleic Acids Research. 46, 3, p. 1441-1456

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

  4. Published

    Iron chelation increases the tolerance of Escherichia coli to hyper-replication stress

    Charbon, Godefroid, Klitgaard, R. N., Liboriussen, C. D., Thulstrup, Peter Waaben, Maffioli, S. I., Donadio, S. & Løbner-Olesen, Anders, 2018, In: Scientific Reports. 8, 1, 14 p., 10550.

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

  5. Published

    LL-37 fragments have antimicrobial activity against Staphylococcus epidermidis biofilms and wound healing potential in HaCaT cell line

    Saporito, P., Vang Mouritzen, M., Løbner-Olesen, Anders & Jenssen, H., 2018, In: Journal of Peptide Science. 24, 7, 12 p., e3080.

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

  6. Published

    Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives

    Pinilla Redondo, Rafael, Cyriaque, V., Jacquiod, S., Sørensen, Søren Johannes & Riber, Leise, 2018, In: Plasmid. 99, p. 56-67

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

  7. Published

    Novel (p)ppGpp Binding and Metabolizing Proteins of Escherichia coli

    ZHANG, YONG, Zbornikova, E., Rejman, D. & Gerdes, K., 2018, In: mBio. 9, 2, 20 p., e02188-17.

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

  8. Published

    Regulation of Hed1 and Rad54 binding during maturation of the meiosis-specific presynaptic complex

    Crickard, J. B., Kaniecki, K., Kwon, Y., Sung, P., Lisby, Michael & Greene, E. C., 2018, In: EMBO Journal. 37, 7, 17 p., e98728.

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

  9. Published

    Replication Fork Breakage and Restart in Escherichia coli

    Michel, B., Sinha, A. K. & Leach, D. R. F., 2018, In: Microbiology and Molecular Biology Reviews. 82, 3, 19 p., e00013-18.

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

  10. Published

    Ribosome Hibernation

    Prossliner, T., Winther, K. S., Sørensen, Michael Askvad & Gerdes, K., 2018, In: Annual Review of Genetics. 52, p. 321-348

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

  11. Published

    SLING: a tool to search for linked genes in bacterial datasets

    Horesh, G., Harms, A., Fino, C., Parts, L., Gerdes, K., Heinz, E. & Thomson, N. R., 2018, In: Nucleic Acids Research. 46, 21, p. 1-10 e128.

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

  12. Published

    Structure of the replication regulator Sap1 reveals functionally important interfaces

    Jørgensen, M. L. M., Ekundayo, B., Zaratiegui, M., Skriver, Karen, Thon, Genevieve & Schalch, T., 2018, In: Scientific Reports. 8, 9 p., 10930.

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

  13. Published

    Synthesis and Activity of Antimicrobial Peptides

    Saporito, P., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  14. Published

    The Interplay Between Immune Response and Bacterial Infection in COPD: Focus Upon Non-typeable Haemophilus influenzae

    Su, Y., Jalalvand, F., Thegerström, J. & Riesbeck, K., 2018, In: Frontiers in Immunology. 9, p. 1-26 2530.

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

  15. Published

    The Role of Outer Membrane Proteins and Lipopolysaccharides for the Sensitivity of Escherichia coli to Antimicrobial Peptides

    Ebbensgaard, Anna Elisabeth, Mordhorst, H., Aarestrup, F. M. & Hansen, E. B., 2018, In: Frontiers in Microbiology. 9, p. 1-13 2153.

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

  16. Published

    The kinases HipA and HipA7 phosphorylate different substrate pools in Escherichia coli to promote multidrug tolerance

    Semanjski, M., Germain, E., Bratl, K., Kiessling, A., Gerdes, K. & Macek, B., 2018, In: Science Signaling. 11, 547, p. 1-13 eaat5750.

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

  17. Published

    Transcriptome-Wide Analysis of Protein-RNA and RNA-RNA Interactions in Pathogenic Bacteria

    Tree, J. J., Gerdes, K. & Tollervey, D., 2018, High-Density Sequencing Applications in Microbial Molecular Genetics. Carpousis, A. J. (ed.). Academic Press, Vol. 612. p. 467-488 (Methods in Enzymology).

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

  18. 2017
  19. Published

    The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

    Lafuente-Barquero, J., Luke-Glaser, S., Graf, M., Pinela da Silva, S. C., Gómez-González, B., Lockhart, A., Lisby, Michael, Aguilera, A. & Luke, B., 27 Dec 2017, In: PLOS Genetics. 13, 12, 25 p., e1007136.

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

  20. Published

    Remotely controlled fusion of selected vesicles and living cells

    Bahadori, Azra, Rørvig-Lund, A., Semsey, S., Oddershede, L. B. & Bendix, Poul Martin, 15 Dec 2017, In: Proceedings of SPIE. 9922, p. 992211-1

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

  21. Published

    Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells

    Harms, A., Fino, C., Sørensen, Michael Askvad, Semsey, S. & Gerdes, K., 12 Dec 2017, In: mBio. 8, 6, 18 p., e01964-17.

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

  22. Published

    Cmr1 enables efficient RNA and DNA interference of a III-B CRISPR–Cas system by binding to target RNA and crRNA

    Li, Y., Zhang, Y., Lin, Jinzhong, Pan, S., Han, W., Peng, N., Liang, Y. X. & She, Q., 2 Nov 2017, In: Nucleic Acids Research. 45, 19, p. 11305-11314 10 p., gkx791.

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

  23. Published

    Sugar metabolism of the first thermophilic Planctomycete Thermogutta terrifontis: comparative genomic and transcriptomic approaches

    Elcheninov, A. G., Menzel, P., Gudbergsdottir, S. R., Slesarev, A. I., Kadnikov, V. V., Krogh, Anders, Bonch-Osmolovskaya, E. A., Peng, Xu & Kublanov, I. V., 2 Nov 2017, In: Frontiers in Microbiology. 8, 11 p., 2140.

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

  24. Published

    SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract

    Uldahl, K. B., Walk, S. T., Olshefsky, S. C., Young, M. J. & Peng, Xu, Nov 2017, In: Journal of Applied Microbiology. 123, 5, p. 1286-1297 12 p.

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

  25. Published

    Allosteric regulation of Csx1, a type IIIB-associated CARF domain ribonuclease by RNAs carrying a tetraadenylate tail

    Han, W., Pan, S., López-Méndez, B., Montoya, Guillermo & She, Q., 13 Oct 2017, In: Nucleic Acids Research. 45, 18, p. 10740-10750 11 p., gkx726.

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

  26. Published

    In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag

    Visone, V., Han, W., Perugino, G., del Monaco, G., She, Q., Rossi, M., Valenti, A. & Ciaramella, M., 3 Oct 2017, In: PLoS ONE. 12, 10, 19 p., e0185791.

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

  27. Published

    Genome-scale genetic interactions and cell imaging confirm cytokinesis as deleterious to transient topoisomerase II deficiency in Saccharomyces cerevisiae

    Ramos-Pérez, C., Ayra-Plasencia, J., Matos-Perdomo, E., Lisby, Michael, Brown, G. W. & Machín, F., Oct 2017, In: G3: Genes, Genomes, Genetics (Bethesda). 7, 10, p. 3379-3391 13 p.

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

  28. Published

    Interaction of extremophilic archaeal viruses with human and mouse complement system and viral biodistribution in mice

    Wu, L., Uldahl, K. B., Chen, F., Benasutti, H., Logvinski, D., Vu, V., Banda, N. K., Peng, Xu, Simberg, D. & Moghimi, S. M., Oct 2017, In: Molecular Immunology. 90, p. 273-279 7 p.

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

  29. Published

    Novel method for quantitative estimation of biofilms

    Syal, K., Oct 2017, In: Current Microbiology. 74, 10, p. 1194-1199 6 p.

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

  30. Published

    Determination of the optimal chromosomal location(s) for a DNA element in Escherichia coli using a novel transposon-mediated approach

    Frimodt-Møller, Jakob, Charbon, Godefroid, Krogfelt, K. A. & Løbner-Olesen, Anders, 11 Sep 2017, In: Journal of Visualized Experiments. 127, e55946.

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

  31. Published

    The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications

    Stiefler-Jensen, D., Schwarz-Linnet, T., de Lichtenberg, C., Nguyen, T. T. T. N., Rand, Kasper Dyrberg, Huang, L., She, Q. & Teilum, Kaare, Sep 2017, In: Protein Science. 26, 9, p. 1819-1827 9 p.

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

  32. Published

    Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation

    Tian, C., Semsey, S. & Mitarai, Namiko, 21 Aug 2017, In: Nucleic Acids Research. 45, 14, p. 8180-8189 10 p.

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

  33. Published

    Archaea and CRISPR biology

    She, Q. & Han, W., 17 Aug 2017, In: Microbiology Today. 44, 3, p. 122-125 4 p.

    Research output: Contribution to journal › Journal article › Communication

  34. Published

    NQO-induced DNA-less cell formation is associated with chromatin protein degradation and dependent on A0A1-ATPase in Sulfolobus

    Han, W., Xu, Y., Feng, X., Liang, Y. X., Huang, L., Shen, Y. & She, Q., 14 Aug 2017, In: Frontiers in Microbiology. 8, 12 p., 1480.

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

  35. Published

    Ethyl methanesulfonate mutagenesis in Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 643-646 4 p.

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

  36. Published

    Genetic analysis of Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 593-605 13 p.

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

  37. Published

    Mating-type determination in Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 641-642 2 p.

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

  38. Published

    In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages

    Sinha, V., Goyal, A., Svenningsen, Sine Lo, Semsey, S. & Krishna, S., 26 Jul 2017, In: Frontiers in Microbiology. 8, 11 p., 1386.

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

  39. Published

    Formation of a viral replication focus in Sulfolobus cells infected by the rudivirus Sulfolobus islandicus rod-shaped virus 2

    Martinez Alvarez, Laura, Deng, Ling & Peng, Xu, Jul 2017, In: Journal of Virology. 91, 13, 12 p., e00486-17.

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

  40. Published

    Reverse gyrase functions in genome integrity maintenance by protecting DNA breaks in vivo

    Han, W., Feng, X. & She, Q., Jul 2017, In: International Journal of Molecular Sciences. 18, 7, 13 p., 1340.

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

  41. Published

    Selecting Schizosaccharomyces pombe diploids

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 537-540 4 p.

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

  42. Published

    Setting up Schizosaccharomyces pombe crosses/matings

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 533-536 4 p.

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

  43. Published

    Spore analysis and tetrad dissection of Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 541-544 4 p.

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

  44. Published

    Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

    Zhu, C., Sun, B., Liu, T., Zheng, H., Gu, W., He, W., Sun, F., Wang, Y., Yang, M., Bei, W., Peng, Xu, She, Q., Xie, L. & Chen, L., 5 Jun 2017, In: BMC Genomics. 18, 19 p., 436.

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

  45. Published

    HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin

    Turnbull, K. & Gerdes, K., Jun 2017, In: Molecular Microbiology. 104, 5, p. 781-792 12 p.

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

  46. Published

    Novel thermostable amine transferases from hot spring metagenomes

    Ferrandi, E. E., Previdi, A., Bassanini, I., Riva, S., Peng, Xu & Monti, D., Jun 2017, In: Applied Microbiology and Biotechnology. 101, 12, p. 4963-4979 17 p.

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

  47. Published

    Ciprofloxacin intercalated in fluorohectorite clay: identical pure drug activity and toxicity with higher adsorption and controlled release rate

    dos Santos, E. C., Rozynek, Z., Hansen, E. L., Hartmann-Petersen, Rasmus, Klitgaard, R. N., Løbner-Olesen, Anders, Michels, L., Mikkelsen, A., Plivelic, Nunes Bordallo, Heloisa & Fossum, J. O., 17 May 2017, In: R S C Advances. 7, 43, p. 26537-26545

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

  48. Published

    Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a β-strand sliding mechanism

    Hadži, S., Garcia-Pino, A., Haesaerts, S., Jurėnas, D., Gerdes, K., Lah, J. & Loris, R., 5 May 2017, In: Nucleic Acids Research. 45, 8, p. 4972-4983 12 p.

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

  49. Published

    High intracellular c-di-GMP levels antagonize quorum sensing and virulence gene expression in Burkholderia cenocepacia H111

    Schmid, N., Suppiger, A., Steiner, E., Pessi, G., Kaever, V., Fazli, M., Tolker-Nielsen, Tim, Jenal, U. & Eberl, L., 1 May 2017, In: Microbiology. 163, 5, p. 754-764 11 p.

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

  50. Published

    Analysis of RNA metabolism in fission yeast

    Wise, J. A. & Nielsen, Olaf, May 2017, In: Cold Spring Harbor Protocols. 2017, 5, p. 365-372 8 p.

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

  51. Published

    Peptide-nucleotide antibiotic Microcin C is a potent inducer of stringent response and persistence in both sensitive and producing cells

    Piskunova, J., Maisonneuve, E., Germain-Maisonneuve, E., Gerdes, K. & Severinov, K., May 2017, In: Molecular Microbiology. 104, 3, p. 463-471 9 p.

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

  52. Published

    Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea

    Peng, N., Han, W., Li, Y., Liang, Y. & She, Q., 30 Apr 2017, In: Science China Life Sciences. 60, 4, p. 370-385 16 p.

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

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