Functional Genomics

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  1. 2019
  2. Published

    Fatty acid starvation activates RelA by depleting lysine precursor pyruvate

    Sinha, A. K., Winther, K. S., Roghanian, Mohammad & Gerdes, K., 2019, In: Molecular Microbiology. 112, 4, p. 1339-1349

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

  3. Published

    The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+

    Skjerning, R. B., Senissar, M., Winther, K. S., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Microbiology. 111, 1, p. 221-236

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

  4. Published

    Functions of Orc1-2 in the DNA damageresponsive regulation in Sulfolobus islandicus

    Sun, M., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  5. Published

    Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells

    Svenningsen, Mikkel Skjoldan, Veress, A., Harms, A., Mitarai, Namiko & Semsey, S., 15 Apr 2019, In: Scientific Reports. 9, 13 p., 6056.

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

  6. Published

    Gene Expression Changes with Minor Effects on the Population Average Have Major Effects on the Occurrence of Cells with Extreme Protein Concentrations

    Svenningsen, Mikkel Skjoldan, Semsey, S. & Mitarai, Namiko, 2019, In: mSphere. 4, 1, p. 1-6 e00575-18.

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

  7. Published

    CRP Interacts Specifically With Sxy to Activate Transcription in Escherichia coli

    Søndberg, E., Sinha, A. K., Gerdes, K. & Semsey, S., 2019, In: Frontiers in Microbiology. 10, 8 p., 2053.

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

  8. Published

    Escherichia coli belonging to ST131 rarely transfers blactx-m-15 to fecal Escherichia coli

    Thingholm, K. R., Hertz, F. B., Løbner-Olesen, Anders, Frimodt-Møller, N. & Nielsen, K. L., 2019, In: Infection and Drug Resistance. 12, p. 2429-2435

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

  9. Published

    Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

    Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.

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

  10. Published

    Mating-type switching by homology-directed recombinational repair: a matter of choice

    Thon, Genevieve, Maki, T., Haber, J. E. & Iwasaki, H., 2019, In: Current Genetics. 65, 2, p. 351-362

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

  11. Published

    Intramolecular Interactions Dominate the Autoregulation of Escherichia coli Stringent Factor RelA

    Turnbull, K. J., Dzhygyr, I., Lindemose, Søren, Hauryliuk, V. & Roghanian, Mohammad, 2019, In: Frontiers in Microbiology. 10, 12 p., 1966.

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

  12. Published

    The Draft Genome of the Small, Spineless Green Alga Desmodesmus costato-granulatus (Sphaeropleales, Chlorophyta)

    Wang, S., Li, L., Xu, Y., Melkonian, B., Lorenz, M., Friedl, T., Petersen, Morten, Sahu, S. K., Melkonian, M. & Liu, Huan, 2019, In: Protist. 170, 6, 5 p., 125697.

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

  13. Published

    Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs)

    Xu, Y., Wang, S., Li, L., Sahu, S. K., Petersen, Morten, Liu, X., Melkonian, M., Zhang, G. & Liu, Huan, 2019, In: Scientific Reports. 9, 10 p., 12485.

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

  14. Published

    The Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) Provides Insight into the Evolution of Scenedesmaceae

    Xu, Y., Li, L., Liang, H., Melkonian, B., Lorenz, M., Friedl, T., Petersen, Morten, Liu, Huan, Melkonian, M. & Wang, S., 2019, In: Protist. 170, 6, 6 p., 125684.

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

  15. Published

    (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch

    ZHANG, YONG, Bærentsen, R. L., Fuhrer, T., Sauer, U., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Cell. 74, 6, p. 1239-1249, e1-e4

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

  16. 2018
  17. Published

    A Unified Resource for Tracking Anti-CRISPR Names

    Bondy-Denomy, J., Davidson, A. R., Doudna, J. A., Fineran, P. C., Maxwell, K. L., Moineau, S., Peng, Xu, Sontheimer, E. J. & Wiedenheft, B., 2018, In: CRISPR Journal. 1, 5, p. 304-305

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

  18. Published

    Expanding the potential of NAI-107 for treating serious ESKAPE pathogens: synergistic combinations against Gram-negatives and bactericidal activity against non-dividing cells

    Brunati, C., Thomsen, T. T., Gaspari, E., Maffioli, S., Sosio, M., Jabes, D., Løbner-Olesen, Anders & Donadio, S., 2018, In: The Journal of antimicrobial chemotherapy. 73, 2, p. 414-424 11 p.

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

  19. Published

    Countermeasures to survive excessive chromosome replication in Escherichia coli

    Charbon, Godefroid, Riber, Leise & Løbner-Olesen, Anders, 2018, In: Current Genetics. 64, 1, p. 71-79 9 p.

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

  20. 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

  21. 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

  22. 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

  23. Published

    Dissection of the antimicrobial and hemolytic activity of Cap18: generation of Cap18 derivatives with enhanced specificity

    Ebbensgaard, Anna Elisabeth, Mordhorst, H., Overgaard, M. T., Aarestrup, F. M. & Hansen, E. B., May 2018, In: PLOS ONE. 13, 5, p. 1-25 e0197742.

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

  24. 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

  25. Published

    A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea

    Feng, X., Sun, M., Han, W., Liang, Y. X. & She, Q., 2018, In: Nucleic Acids Research. 46, 14, p. 7085-7096

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

  26. Published

    Identification of the archaeal regulatory network in DNA damage response

    Feng, X., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  27. Published

    A Type III-B Cmr effector complex catalyzes the synthesis of cyclic oligoadenylate second messengers by cooperative substrate binding

    Han, W., Stella, S., Zhang, Y., Guo, T., Sulek, K., Peng-Lundgren, L., Montoya, Guillermo & She, Q., 2018, In: Nucleic Acids Research. 46, 19, p. 10319-10330 12 p.

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

  28. Published

    Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

    Harms, A., Brodersen, D. E., Mitarai, Namiko & Gerdes, K., 7 Jun 2018, In: Molecular Cell. 70, 5, p. 768-784 17 p.

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

  29. Published

    Chromosome replication as a measure of bacterial growth rate during Escherichia coli infection in the mouse peritonitis model

    Haugan, M. S., Charbon, Godefroid, Frimodt-Møller, N. & Løbner-Olesen, Anders, 1 Dec 2018, In: Scientific Reports. 8, p. 1-13 14961.

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

  30. Published

    Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity

    He, F., Bhoobalan, Yuvaraj, Van, L. B., Kjeldsen, A. L., Dedola, M., Makarova, K. S., Koonin, E. V., Brodersen, D. E. & Peng, Xu, 2018, In: Nature Microbiology. 3, 4, p. 461-469 9 p.

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

  31. 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

  32. Published

    Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

    Jacquiod, S. J. A., Cyriaque, V., Riber, Leise, Al-Soud, W. A., Gillan, D. C., Wattiez, R. & Sørensen, Søren Johannes, 15 Feb 2018, In: Journal of Hazardous Materials. 344, p. 299-307 9 p.

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

  33. Published

    Dependency of Heterochromatin Domains on Replication Factors

    Jahn, L. J., Mason, B., Brøgger, Peter, Toteva, T., Nielsen, D. K. & Thon, Genevieve, 2018, In: G3: Genes, Genomes, Genetics (Bethesda). 8, 2, p. 477-489 13 p.

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

  34. Published

    Update on non-typeable Haemophilus influenzae-mediated disease and vaccine development

    Jalalvand, F. & Riesbeck, K., 3 Jun 2018, In: Expert Review of Vaccines. 17, 6, p. 503-512

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

  35. 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

  36. Published

    DNA Damage Repair and Drug Efflux as Potential Targets for Reversing Low or Intermediate Ciprofloxacin Resistance in E. coli K-12

    Klitgaard, R. N., Jana, B., Guardabassi, Luca, Nielsen, K. L. & Løbner-Olesen, Anders, 2 Jul 2018, In: Frontiers in Microbiology. 9, 6 p., 1438.

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

  37. 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

  38. Published

    Fumarase is involved in DNA double-strand break resection through a functional interaction with Sae2

    Leshets, M., Ramamurthy, D., Lisby, Michael, Lehming, N. & Pines, O., 2018, In: Current Genetics. 64, 3, p. 697-712 16 p.

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

  39. Published

    Type III CRISPR-Cas System: Introduction And Its Application for Genetic Manipulations

    Liu, T., Pan, S., Li, Y., Peng, N. & She, Q., 1 Jan 2018, In: Current Issues in Molecular Biology. 26, p. 1-14 14 p.

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

  40. Published

    An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer

    Madsen, Jonas Stenløkke, Hylling, Ole, Jacquiod, S. J. A., Pécastaings, S., Hansen, L. H., Riber, Leise, Vestergaard, G. A. & Sørensen, Søren Johannes, 2018, In: ISME Journal. 12, 9, p. 2330-2334 5 p.

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

  41. Published

    New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe

    Maki, T., Ogura, N., Haber, J. E., Iwasaki, H. & Thon, Genevieve, May 2018, In: PLOS Genetics. 14, 5, p. 1-25 e1007424.

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

  42. Published

    A Critical Role for Dna2 at Unwound Telomeres

    Markiewicz-Potoczny, M., Lisby, Michael & Lydall, D., 2018, In: Genetics. 209, 1, p. 129-141 13 p.

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

  43. Published

    Erratum: Formation of a viral replication focus in Sulfolobus cells infected by the rudivirus Sulfolobus islandicus rod-shaped virus 2 [Journal of Virology, 91, 13, (2017), (e00486-17)] DOI:10.1128/JVI.00486-17

    Martinez Alvarez, Laura, Deng, Ling & Peng, Xu, 1 Apr 2018, In: Journal of Virology. 92, 7, e01991-17.

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

  44. Published

    Anti-CRISPR-Based and CRISPR-Based Genome Editing of Sulfolobus islandicus Rod-Shaped Virus 2

    Mayo-Muñoz, D., He, F., Jørgensen, J. B., Madsen, P. K., Bhoobalan, Yuvaraj & Peng, Xu, 2018, In: Viruses. 10, 12, p. 1-17 695.

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

  45. Published

    Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

    Mendoza-Chamizo, B., Løbner-Olesen, Anders & Charbon, Godefroid, 2018, In: Genes. 9, 11, 565.

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

  46. 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

  47. Published

    Comparative Effectiveness of Low-Volume Time-Efficient Resistance Training Versus Endurance Training in Patients With Heart Failure

    Munch, G. W., Rosenmeier, J. B., Petersen, Morten, Rinnov, A. R., Iepsen, U. W., Pedersen, Bente Klarlund & Mortensen, S. P., 2018, In: Journal of Cardiopulmonary Rehabilitation and Prevention. 38, 3, p. 175-181 7 p.

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

  48. Published

    FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells

    Pentzold, C., Shah, S. A., Hansen, Niels Richard, Le Tallec, B., Seguin-Orlando, A., Debatisse, M., Lisby, Michael & Østergaard, Vibe Hallundbæk, 2018, In: Nucleic Acids Research. 46, 3, p. 1280-1294 15 p.

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

  49. 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

  50. Published

    Fluorescence recovery allows theimplementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments

    Pinilla Redondo, Rafael, Riber, Leise & Sørensen, Søren Johannes, 2018, In: Applied and Environmental Microbiology. 84, 6, 9 p., e02507-17.

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

  51. 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

  52. Published

    Imaging of DNA Ultrafine Bridges in Budding Yeast

    Quevedo Rodriguez, O. & Lisby, Michael, 2018, Genome Instability: Methods and Protocols. Muzi-Falconi, M. & Brown, G. W. (eds.). Humana Press, p. 483-493 11 p. (Methods in Molecular Biology, Vol. 1672).

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

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