Functional Genomics

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  1. 2017
  2. Published

    Matching NLR immune receptors to autoimmunity in camta3 mutants using antimorphic NLR alleles

    Lolle, S., Greeff, M. C., Petersen, K., Roux, M. E., Jensen, M. K., Bressendorff, Simon, Rodriguez, Eleazar, Sømark, K., Mundy, J. & Petersen, Morten, 2017, In: Cell Host & Microbe. 21, 4, p. 518-529 12 p.

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

  3. Published

    Uncovering the roots of paranoid suicidal plants

    Lolle, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  4. 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

  5. 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

  6. 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

  7. Published

    UBL/BAG-domain co-chaperones cause cellular stress upon overexpression through constitutive activation of Hsf1

    Poulsen, E. G., Kampmeyer, Caroline, Kriegenburg, F., Johansen, Jens Vilstrup, Hofmann, K., Holmberg, Christian & Hartmann-Petersen, Rasmus, Jan 2017, In: Cell Stress & Chaperones. 22, 1, p. 143-154 12 p.

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

  8. 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

  9. Published

    Autophagy is required for gamete differentiation in the moss Physcomitrella patens

    Sanchez-Vera, V., Kenchappa, C. S., Landberg, K., Bressendorff, Simon, Schwarzbach, S., Martin, T., Mundy, J., Petersen, Morten, Thelander, M. & Sundberg, E., 2017, In: Autophagy. 13, 11, p. 1939-1951 13 p.

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

  10. 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

  11. Published

    Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains

    Sebesta, M., Urulangodi, M., Stefanovie, B., Szakal, B., Pacesa, M., Lisby, Michael, Branzei, D. & Krejci, L., Jan 2017, In: Nucleic Acids Research. 45, 1, p. 215-230 16 p.

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

  12. Published

    Determination of protein turnover in E. coli cells during exit from persistence

    Semanjski, M., Germain-Maisonneuve, E., Gerdes, K. & Macek, B., 2017, In: F A S E B Journal. 31, S1, 1 p., 915.2.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  13. 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

  14. Published

    DNA damage repair in Archaea

    She, Q., Feng, X. & Han, W., 2017, Biocommunication of Archaea. Witzany, G. (ed.). Springer, p. 305-318 14 p.

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

  15. 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

  16. Published

    Elucidating the roles of MAP kinases in the moss Physcomitrella patens

    Stanimirovic, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen. 230 p.

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

  17. 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

  18. 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

  19. 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

  20. Published

    Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

    Toteva, T., Mason, B., Kanoh, Y., Brøgger, P., Green, D., Hansen, J. V., Masai, H. & Thon, Genevieve, 31 Jan 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 1093-1098 6 p.

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

  21. 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

  22. 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

  23. 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

  24. Published

    Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970-2016: A systematic analysis for the Global Burden of Disease Study 2016

    Wang, H., Abajobir, A. A., Abate, K. H., Abbafati, C., Abbas, K. M., Abd-Allah, F., Abera, S. F., Abraha, H. N., Abu-Raddad, L. J., Abu-Rmeileh, N. M. E., Adedeji, I. A., Adedoyin, R. A., Adetifa, I. M. O., Adetokunboh, O., Afshin, A., Aggarwal, R., Agrawal, A., Agrawal, S., Ahmad Kiadaliri, A., Ahmed, M. B. & 31 others, Aichour, A. N., Aichour, I., Aichour, M. T. E., Aiyar, S., Akanda, A. S., Akinyemiju, T. F., Akseer, N., Al-Eyadhy, A., Al Lami, F. H., Alabed, S., Alahdab, F., Al-Aly, Z., Alam, K., Alam, N., Alasfoor, D., Aldridge, R. W., Alene, K. A., Bjerregaard, P., Christensen, H., De Courten, B., Havmoeller, R., He, F., Iburg, K. M., Larsson, A., McGrath, J. J., Mengistie, M. A., Singh, Prashant, Sobngwi, E., Truelsen, Thomas Clement, Wang, Y. & GBD 2016 Mortality Collaborators, G. 2. M. C., 2017, In: The Lancet. 390, 10100, p. 1084-1150 67 p.

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

  25. 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

  26. 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

  27. Published

    Phosphatidylserine stimulates ceramide 1-phosphate (C1P) intermembrane transfer by C1P transfer proteins

    Zhai, X., Gao, Y., Mishra, S. K., Simanshu, D. K., Boldyrev, I. A., Benson, L. M., Bergen III, H. R., Malinina, L., Mundy, J., Molotkovsky, J. G., Patel, D. J. & Brown, R. E., 10 Feb 2017, In: Journal of Biological Chemistry. 292, 6, p. 2531-2541 11 p.

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

  28. 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

  29. 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

  30. Published

    Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    Østergaard, Vibe Hallundbæk & Lisby, Michael, Mar 2017, In: Chromosoma. 126, 2, p. 213-222 10 p.

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

  31. 2016
  32. Published

    The transcriptional regulator GalR self-assembles to form highly regular tubular structures

    Agerschou, E. D., Christiansen, G., Schafer, N. P., Madsen, D. J., Brodersen, D. E., Semsey, S. & Otzen, D. E., 2016, In: Scientific Reports. 6, 13 p., 27672 .

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

  33. Published

    Characterizing leader sequences of CRISPR loci

    Alkhnbashi, O., Shah, S. A., Garrett, Roger Antony, Saunders, S. J., Costa, F. & Backofen, R., 2016, In: Bioinformatics. 32, 17, p. i576-i585 10 p.

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

  34. Published

    Protein Kinase Signalling in the Moss Physcomitrella patens

    Azevedo de Silva, R., 2016, Department of Biology, Faculty of Science, University of Copenhagen. 109 p.

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

  35. Published

    An innate immunity pathway in the moss Physcomitrella patens

    Bressendorff, Simon, Azevedo da Silva, R., Kenchappa, C. S., Ponce de León, I., Olsen, J. V., Rasmussen, M. W., Erbs, G., Newman, Mari-Anne, Petersen, Morten & Mundy, J., 2016, In: The Plant Cell. 28, 6, p. 1328-1342 16 p.

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

  36. Published

    Isolation of a novel protein, P12-from adult Drosophila melanogaster that inhibits deoxyribonucleoside and protein kinase activities and activates 3'-5'-exonuclease activity

    Christiansen, L. S., Zanten, G. V., Berenstein, D., Lauridsen, M., Kjærulff, S., Søndergaard, Leif & Munch-Petersen, B., 2016, In: Nucleosides, Nucleotides and Nucleic Acids. 35, 10-12, p. 699-706 8 p.

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

  37. Published

    Barley plants over-expressing the NAC transcription factor gene HvNAC005 show stunting and delay in development combined with early senescence

    Christiansen, M. W., Matthewman, C., Podzimska-Sroka, D. A., O'Shea, Charlotte, Lindemose, Søren, Møllegaard, Niels Erik, Holme, I. B., Hebelstrup, K., Skriver, Karen & Gregersen, P. L., 2016, In: Journal of Experimental Botany. 67, 17, p. 5259-5273 15 p.

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

  38. Published

    SUMO-dependent relocalization of eroded telomeres to nuclear pore complexes controls telomere recombination

    Churikov, D., Charifi, F., Eckert-Boulet, N. V., Pinela da Silva, S. C., Simon, M., Lisby, Michael & Géli, V., 2016, In: Cell Reports. 15, 6, p. 1242-1253 12 p.

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

  39. Published

    DNA replication control is linked to genomic positioning of control regions in Escherichia coli

    Frimodt-Møller, Jakob, Charbon, Godefroid, Krogfelt, K. A. & Løbner-Olesen, Anders, 2016, In: P L o S Genetics. 12, 9, 27 p., e1006286.

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

  40. Published

    TopBP1-mediated DNA processing during mitosis

    Gallina, I., Christiansen, S. K., Pedersen, R. T., Lisby, Michael & Østergaard, Vibe Hallundbæk, 2016, In: Cell Cycle. 15, 2, p. 176-183 8 p.

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

  41. Published

    Archaeal physiology: the secrets of termination

    Garrett, Roger Antony, 2016, In: Nature Microbiology. 1, 2 p., 16159.

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

  42. Published

    Isolation and characterization of the first Xylanolytic hyperthermophilic euryarchaeon Thermococcus sp strain 2319x1 and its unusual multidomain glycosidase

    Gavrilov, S. N., Stracke, C., Jensen, K., Menzel, P., Kallnik, V., Slesarev, A., Sokolova, T., Zayulina, K., Bräsen, C., Bonch-Osmolovskaya, E. A., Peng, Xu, Kublanov, I. V. & Siebers, B., 2016, In: Frontiers in Microbiology. 7, 17 p., 552.

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

  43. Published

    Hypothesis: type I toxin - antitoxin genes enter the persistence field-a feedback mechanism explaining membrane homoeostasis

    Gerdes, K., 2016, In: Royal Society of London. Philosophical Transactions B. Biological Sciences. 371, 1707, 9 p., 20160189.

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

  44. Published

    Microbiology: pumping persisters

    Gerdes, K. & Semsey, S., 2016, In: Nature. 534, 7605, p. 41-42 2 p.

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

  45. Published

    Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species

    Guannan, L., She, Q. & Garrett, Roger Antony, 2016, In: Nucleic Acids Research. 44, 9, p. 4233-4242 10 p.

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

  46. Published

    Back to the roots: deep view into the evolutionary history of ADP-ribosylation opened by the DNA-targeting toxin-antitoxin module DarTG

    Harms, A. & Gerdes, K., 15 Dec 2016, In: Molecular Cell. 64, 6, p. 1020-1021 2 p.

    Research output: Contribution to journal › Comment/debate › Research

  47. Published

    Mechanisms of bacterial persistence during stress and antibiotic exposure

    Harms, A., Maisonneuve, E. & Gerdes, K., 2016, In: Science. 354, 6318, 10 p., aaf4268.

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

  48. Published

    "Population structure of drug-susceptible, -resistant and ESBL-producing Escherichia coli from community-acquired urinary tract infections"

    Hertz, F. B., Nielsen, J. B., Schønning, Kristian, Littauer, P., Knudsen, J. D., Løbner-Olesen, Anders & Frimodt-Møller, N., 11 Apr 2016, In: BMC Microbiology. 16, 6 p., 63.

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

  49. Published

    Epidemiological factors associated with ESBL- and non ESBL-producing E. coli causing urinary tract infection in general practice

    Hertz, F. B., Schønning, K., Rasmussen, S. C., Littauer, P., Knudsen, J. D., Løbner-Olesen, Anders & Frimodt-Møller, N., 2016, In: Infectious Diseases. 48, 3, p. 241-245 5 p.

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

  50. Published

    Configuration-dependent Presentation of Multivalent IL-15: IL-15Rα enhances the antigen-specific T cell response and anti-tumor immunity

    Hong, E., Usiskin, I. M., Bergamaschi, C., Hanlon, D. J., Edelson, R. L., Justesen, S., Pavlakis, G. N., Flavell, R. A. & Fahmy, T. M., 22 Apr 2016, In: Journal of Biological Chemistry. 291, 17, p. 8931-8950 20 p.

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

  51. Published

    Mining Hot Springs for Biodiversity and Novel Enzymes

    Islin, S. R., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

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

  52. Published

    Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs

    Islin, S. R., Menzel, P., Krogh, Anders, Young, M. & Peng, Xu, 2016, In: Environmental Microbiology. 18, 3, p. 863-874 12 p.

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

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