Functional Genomics

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  1. 2021
  2. Published

    Antibiotic Tolerance and Persistence Studied Throughout Bacterial Growth Phases

    Maffei, E., Fino, C. & Harms, A., 2021, Bacterial Persistence: Methods and Protocols. Verstraeten, N. & Michiels, J. (eds.). 2. ed. ed. Humana Press, p. 23-40 18 p. (Methods in Molecular Biology, Vol. 2357).

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

  3. Published

    Large Intronic Deletion of the Fragile Site Gene PRKN Dramatically Lowers Its Fragility Without Impacting Gene Expression

    Munk, S. H. N., Voutsinos, Vasileios & Østergaard, Vibe Hallundbæk, 2021, In: Frontiers in Genetics. 12, 9 p., 695172.

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

  4. Published

    Establishment of heterochromatin in domain-size-dependent bursts

    Nickels, Jan Fabio, Edwards, A. K., Charlton, Sebastian Jespersen, Mortensen, A. M., Hougaard, S. C. L., Trusina, Ala, Sneppen, Kim & Thon, Genevieve, 13 Apr 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 15, 11 p., e2022887118.

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

  5. Published

    Correlated transcriptional responses provide insights into the synergy mechanisms of the furazolidone, vancomycin, and sodium deoxycholate triple combination in escherichia coli

    Olivera, Catrina Diane Peralta, Cox, M. P., Rowlands, G. J. & Rakonjac, J., 2021, In: mSphere. 6, 5, 14 p., e00627-21.

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

  6. Published

    New Insights into the Antimicrobial Action of Cinnamaldehyde towards Escherichia coli and Its Effects on Intestinal Colonization of Mice

    Pereira, W. A., Pereira, C. D. S., Assunção, R. G., da Silva, I. S. C., Rego, F. S., Alves, L. S. R., Santos, J. S., Nogueira, F. J. R., Zagmignan, A., Thomsen, T. T., Løbner-Olesen, Anders, Krogfelt, K. A., da Silva, L. C. N. & Abreu, A. G., 2021, In: Biomolecules. 11, 2, 14 p., 302.

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

  7. Published

    Hibernation factors directly block ribonucleases from entering the ribosome in response to starvation: [+ erratum]

    Prossliner, T., Gerdes, K., Sørensen, Michael Askvad & Winther, K. S., 2021, In: Nucleic Acids Research. 49, 4, p. 2226-2239 14 p.

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

  8. Published

    The Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination

    Roy, U., Kwon, Y., Marie, L., Symington, L., Sung, P., Lisby, Michael & Greene, E. C., 2021, In: Molecular Cell. 81, 5, p. 1043-1057.e8 23 p.

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

  9. Published

    Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay (DRaCALA)

    Schicketanz, Muriel Leandra, Grucela, Paulina Katarzyna & ZHANG, YONG, 2021, In: Journal of visualized experiments : JoVE. 169, e62331.

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

  10. Published

    The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

    Sinha, A. K. & Winther, K. S., 2021, In: Communications Biology . 4, 10 p., 434.

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

  11. Published

    DNA Double-Strand Break-Induced Gene Amplification in Yeast

    Strucko, T., Lisby, Michael & Mortensen, U. H., 2021, Homologous Recombination: Methods and Protocols. Aguilera, A. & Carreira, A. (eds.). Humana Press, p. 239-252 14 p. (Methods in Molecular Biology, Vol. 2153).

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

  12. Published

    Algae Genome Studies Reveal the Evolutionary History of Green Plants

    Wang, S., 2021, Department of Biology, Faculty of Science, University of Copenhagen. 134 p.

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

  13. Published

    Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

    Wang, S., Liang, H., Xu, Y., Li, L., Wang, H., Sahu, D. N., Petersen, Morten, Melkonian, M., Sahu, S. K. & Liu, Huan, 2021, In: Communications Biology . 4, 11 p., 412.

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

  14. Published

    An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data

    Xu, W., Lin, Y., Zhao, K., Li, H., Tian, Y., Ngatia, J. N., Ma, Y., Sahu, S. K., Guo, H., Guo, X., Xu, Y. C., Liu, Huan, Kristiansen, Karsten, Lan, T. & Zhou, X., 2021, In: Ecology and Evolution. 11, 1, p. 390-401 12 p.

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

  15. Published

    Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis

    Yang, Nan, Nesme, Joseph, Røder, Henriette Lyng, Li, Xuan Ji, Zuo, Zhangli Thomsen, Petersen, Morten, Burmølle, Mette & Sørensen, Søren Johannes, 2021, In: npj Biofilms and Microbiomes. 7, 11 p., 82.

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

  16. Published

    Characterization of an archaeal virus replication initiator protein and first insights into virus assembly of spindle-shaped virus SMV1

    Zhang, W., 2021, Department of Biology, Faculty of Science, University of Copenhagen. 140 p.

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

  17. Published

    The Arabidopsis thaliana mRNA decay factor PAT1 functions in osmotic stress responses and decaps ABA-responsive genes

    Zuo, Zhangli Thomsen, Roux, M. E., Sæmundsson, H. P., Müller, M., Bosch, S. M. & Petersen, Morten, 2021, In: FEBS Letters. 595, 2, p. 253-263 11 p.

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

  18. 2020
  19. Published

    The ZGRF1 Helicase Promotes Recombinational Repair of Replication-Blocking DNA Damage in Human Cells

    Brannvoll, A., Xue, X., Kwon, Y., Kompocholi, Smaragda, Simonsen, Anne Katrine Wrist, Bagge, Keerthana Stine Viswalingam, Gonzalez, L., Hickson, Ian David, Østergaard, Vibe Hallundbæk, Mankouri, H. W., Sung, P. & Lisby, Michael, 2020, In: Cell Reports. 32, 1, 25 p., 107849.

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

  20. Published

    Counting Replication Origins to Measure Growth of Pathogens

    Charbon, Godefroid, Haugan, M. S., Frimodt-Møller, N. & Løbner-Olesen, Anders, 2020, In: Antibiotics. 9, 5, 5 p., 239.

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

  21. Published

    Integrity of a heterochromatic domain ensured by its boundary elements

    Charlton, Sebastian Jespersen, Jørgensen, M. M. & Thon, Genevieve, 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 35, p. 21504-21511 8 p.

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

  22. Published

    Autophagy mediate cellular reprogramming

    Chevalier, J. R., 2020, Department of Biology, Faculty of Science, University of Copenhagen.

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

  23. Published

    Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

    Bjørnkjær, Lene, Stein, Amelie, Grønbæk-Thygesen, Martin, Nygaard, L., Søltoft, C. L., Nielsen, S. V., Lisby, Michael, Ravid, T., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: PLOS Genetics. 16, 11, 28 p., e1009187.

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

  24. Published

    Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments

    Cyriaque, V., Jacquiod, S. J. A., Riber, Leise, Abu Al-Soud, W., Gillan, D. C., Sørensen, Søren Johannes & Wattiez, R., 2020, In: Journal of Hazardous Materials. 382, 10 p., 121173.

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

  25. Published

    The Role of Efflux Pumps in the Transition from Low-Level to Clinical Antibiotic Resistance

    Ebbensgaard, Anna Elisabeth, Løbner-Olesen, Anders & Frimodt-Møller, Jakob, 2020, In: Antibiotics. 9, 12, 7 p., 855.

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

  26. Published

    Origins: It takes a well rooted trunk to bear a tree - reductionist models of divergent evolution and further aspects of reality

    Egel, Richard, 2020, Untangling Molecular Biodiversity: Explaining Unity and Diversity Principles of Organization with Molecular Structure and Evolutionary Genomics. Caetano-Anollés, G. (ed.). World Scientific, p. 223-282 60 p.

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

  27. Published

    Dissecting the genome of star fruit (Averrhoa carambola L.)

    Fan, Y., Sahu, S. K., Yang, T., Mu, W., Wei, J., Cheng, L., Yang, J., Mu, R., Liu, J., Zhao, J., Zhao, Y., Xu, X., Liu, X. & Liu, Huan, 2020, In: Horticulture Research. 7, 10 p., 94.

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

  28. Published

    Discovery and Characterization of a Novel Thermostable β-Amino Acid Transaminase from a Meiothermus Strain Isolated in an Icelandic Hot Spring

    Ferrandi, E. E., Bassanini, I., Sechi, B., Vanoni, M., Tessaro, D., Gudbergsdóttir, S. R., Riva, S., Peng, Xu & Monti, D., 2020, In: Biotechnology Journal. 15, 11, 9 p., 2000125.

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

  29. Published

    Short-term kinetics of rRNA degradation in Escherichia coli upon starvation for carbon, amino acid, or phosphate

    Fessler, M., Gummesson, Bertil, Charbon, Godefroid, Svenningsen, Sine Lo & Sørensen, Michael Askvad, 2020, In: Molecular Microbiology. 113, 5, p. 951-963 13 p.

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

  30. Published

    Antimicrobial and Antivirulence Action of Eugenia brejoensis Essential Oil in vitro and in vivo Invertebrate Models

    Filho, C. M. B., da Silva, L. C. N., da Silva, M. V., Løbner-Olesen, Anders, Struve, C., Krogfelt, K. A., Correia, M. T. D. S. & Oliva, M. L. V., 2020, In: Frontiers in Microbiology. 11, 11 p., 424.

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

  31. Published

    Diversity of type II toxin-antitoxin systems of enterobacteria and their contribution to antibiotic persistence

    Fino, C., 2020, Department of Biology, Faculty of Science, University of Copenhagen.

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

  32. Published

    PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10

    Fino, C., Vestergaard, M., Ingmer, Hanne, Pierrel, F., Gerdes, K. & Harms, A., 2020, In: MicrobiologyOpen. 9, 8, 36 p., e1064.

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

  33. Published

    Virulence, Resistance, and Genomic Fingerprint Traits of Vibrio cholerae Isolated from 12 Species of Aquatic Products in Shanghai, China

    Fu, H., Yu, P., Liang, W., Kan, B., Peng, Xu & Chen, L., 2020, In: Microbial Drug Resistance. 26, 12, p. 1526-1539 14 p.

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

  34. Published

    Archaeal Viruses and Their Interactions with CRISPR-Cas Systems

    Garrett, Roger Antony, Shah, S. A., Martinez Alvarez, Laura & Peng, Xu, 2020, Biocommunication of Phages. 1 ed. Springer, p. 199-220 22 p.

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

  35. Published

    Thresholds for clinical importance were defined for the European Organisation for Research and Treatment of Cancer Computer Adaptive Testing Core-an adaptive measure of core quality of life domains in oncology clinical practice and research

    Giesinger, J. M., Loth, F. L. C., Aaronson, N. K., Arraras, J. I., Caocci, G., Efficace, F., Grønvold, Mogens, van Leeuwen, M., Petersen, Morten, Ramage, J., Tomaszewski, K. A., Young, T., Holzner, B. & EORTC Quality of Life Group, E. Q. O. L. G., 2020, In: Journal of Clinical Epidemiology. 117, p. 117-125 9 p.

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

  36. Published

    Thresholds for clinical importance were established to improve interpretation of the EORTC QLQ-C30 in clinical practice and research

    Giesinger, J. M., Loth, F. L. C., Aaronson, N. K., Arraras, J. I., Caocci, G., Efficace, F., Grønvold, Mogens, van Leeuwen, M., Petersen, Morten, Ramage, J., Tomaszewski, K. A., Young, T., Holzner, B. & EORTC Quality of Life Group, E. Q. O. L. G., 2020, In: Journal of Clinical Epidemiology. 118, p. 1-8 8 p.

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

  37. Published

    Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing

    Gummesson, Bertil, Shah, S. A., Borum, A. S., Fessler, M., Mitarai, Namiko, Sørensen, Michael Askvad & Svenningsen, Sine Lo, 2020, In: Frontiers in Genetics. 11, 17 p., 144.

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

  38. Published

    Effects of Antibiotics on the Intestinal Microbiota of Mice

    Hertz, F. B., Budding, A. E., van der Lugt-Degen, M., Savelkoul, P. H., Løbner-Olesen, Anders & Frimodt-Møller, N., 2020, In: Antibiotics. 9, 4, 11 p., 191.

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

  39. Published

    Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population

    Horesh, G., Fino, C., Harms, A., Dorman, M. J., Parts, L., Gerdes, K., Heinz, E. & Thomson, N. R., 2020, In: Nucleic Acids Research. 48, 8, p. 4357-4370 14 p.

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

  40. Published

    Novel Cyclic Lipopeptide Antibiotics: Effects of Acyl Chain Length and Position

    Jensen, S. K., Thomsen, T. T., Oddo, A., Franzyk, Henrik, Løbner-Olesen, Anders & Hansen, Paul Robert, 2020, In: International Journal of Molecular Sciences . 21, 16, 18 p., 5829.

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

  41. Published

    Mutations in a Single Signaling Pathway Allow Cell Growth in Heavy Water

    Kampmeyer, Caroline, Johansen, Jens Vilstrup, Holmberg, Christian, Karlson, M., Andersen, Sarah Gersing, Nunes Bordallo, Heloisa, Kragelund, Birthe Brandt, Lerche, M. H., Jourdain, I., Winther, Jakob R. & Hartmann-Petersen, Rasmus, 2020, In: A C S Synthetic Biology. 9, 4, p. 733-748 16 p.

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

  42. Published

    The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

    Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., Xu, Y., Liang, H., Li, Z., Cheng, S., Reder, T., Çebi, Z., Wittek, S., Petersen, M., Melkonian, B., Du, H., Yang, H., Wang, J., Wong, G. K-S., Xu, X. & 4 others, Liu, X., Van de Peer, Y., Melkonian, M. & Liu, Huan, 2020, In: Nature Ecology and Evolution. 4, 9, p. 1220-1231

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

  43. Published

    The Draft Genome of Coelastrum proboscideum (Sphaeropleales, Chlorophyta)

    Liang, H., Wang, H., Xu, Y., Li, L., Melkonian, B., Lorenz, M., Friedl, T., Sahu, S. K., Yu, J., Liu, Huan, Melkonian, M. & Wang, S., 2020, In: Protist. 171, 5, 7 p., 125758.

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

  44. Published

    Characterization of a novel type III CRISPR-Cas effector provides new insights into the allosteric activation and suppression of the Cas10 DNase

    Lin, Jinzhong, Feng, M., Zhang, H. & She, Q., 2020, In: Cell Discovery. 6, 16 p., 29.

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

  45. Published

    DNA targeting by subtype I-D CRISPR-Cas shows type I and type III features

    Lin, Jinzhong, Fuglsang, Anders, Kjeldsen, A. L., Sun, K., Bhoobalan, Yuvaraj & Peng, Xu, 2020, In: Nucleic Acids Research. 48, 18, p. 10470-10478 9 p.

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

  46. Published

    Protocol for Purification of Human ZGRF1 and Its Regulatory Function on RAD51-Mediated D-Loop Formation

    Lisby, Michael & Xue, X., 2020, In: STAR Protocols. 1, 2

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

  47. Published

    A CRISPR-associated factor Csa3a regulates DNA damage repair in Crenarchaeon Sulfolobus islandicus

    Liu, Z., Sun, M., Liu, J., Liu, T., Ye, Q., Li, Y. & Peng, N., 2020, In: Nucleic Acids Research. 48, 17, p. 9681-9693 13 p.

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

  48. Published

    Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12

    Madsen, D., Jørgensen, F. P., Palmer, D., Roux, M. E., Olsen, J. V., Bols, Mikael, Schoffelen, S., Diness, Frederik & Meldal, Morten Peter, 2020, In: ACS Combinatorial Science. 22, 3, p. 156-164

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

  49. Published

    Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

    Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Scott, D., Shah, S. A., Siksnys, V., Terns, M. P., Venclovas, Č., White, M. F., Yakunin, A. F., Yan, W. & 6 others, Zhang, F., Garrett, Roger Antony, Backofen, R., van der Oost, J., Barrangou, R. & Koonin, E. V., 2020, In: Nature Reviews. Microbiology. 18, p. 67-83

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

  50. Published

    Structural basis for inhibition of an archaeal CRISPR–Cas type I-D large subunit by an anti-CRISPR protein

    Manav, M. C., Van, L. B., Lin, Jinzhong, Fuglsang, Anders, Peng, Xu & Brodersen, D. E., 2020, In: Nature Communications. 11, 10 p., 5993.

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

  51. Published

    Anti-CRISPR Proteins in Archaea

    Peng, Xu, Mayo-Muñoz, D., Bhoobalan, Yuvaraj & Martinez Alvarez, Laura, 2020, In: Trends in Microbiology. 28, 11, p. 913-921 9 p.

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

  52. Published

    Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

    Pinilla Redondo, Rafael, Mayo-Muñoz, D., Russel, J., Garrett, Roger Antony, Randau, L., Sørensen, Søren Johannes & Shah, S. A., 2020, In: Nucleic Acids Research. 48, 4, p. 2000-2012 13 p.

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

  53. Published

    Inhibition of Escherichia coli chromosome replication by rifampicin treatment or during the stringent response is overcome by de novo DnaA protein synthesis

    Riber, Leise & Løbner-Olesen, Anders, 2020, In: Molecular Microbiology. 114, 6, p. 906-919

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

  54. Published

    Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells

    Rodriguez, Eleazar, Chevalier, J., Olsen, J., Ansbøl, J., Kapousidou, V., Zuo, Zhangli Thomsen, Svenning, S., Loefke, C., Koemeda, S., Drozdowskyj, P. S., Jez, J., Durnberger, G., Kuenzl, F., Schutzbier, M., Mechtler, K., Ebstrup, E. N., Lolle, S., Dagdas, Y. & Petersen, Morten, 2020, In: EMBO Journal. 39, 4, 11 p., e103315.

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

  55. Published

    Draft genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

    Sahu, S. K., Liu, M., Yssel, A., Kariba, R., Muthemba, S., Jiang, S., Song, B., Hendre, P. S., Muchugi, A., Jamnadass, R., Kao, S., Featherston, J., Zerega, N. J. C., Xu, X., Yang, H., Van Deynze, A., Van de Peer, Y., Liu, X. & Liu, Huan, 2020, In: Genes. 11, 1, 27.

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

  56. Published

    A distinct role for recombination repair factors in an early cellular response to transcription-replication conflicts

    Shao, Xin, Joergensen, A. M., Howlett, N. G., Lisby, Michael & Østergaard, Vibe Hallundbæk, 2020, In: Nucleic Acids Research. 48, 10, p. 5467-5484 18 p.

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

  57. Published

    Bacterial Chromosome Replication and DNA Repair During the Stringent Response

    Sinha, A. K., Løbner-Olesen, Anders & Riber, Leise, 2020, In: Frontiers in Microbiology. 11, 9 p., 582113.

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

  58. Published

    The Roles of Bacterial DNA Double-Strand Break Repair Proteins in Chromosomal DNA Replication

    Sinha, A. K., Possoz, C. & Leach, D. R. F., 2020, In: FEMS Microbiology Reviews. 44, 3, p. 351-368

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

  59. Published

    Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas

    Sofos, N., Feng, M., Stella, S., Pape, T., Fuglsang, Anders, Lin, Jinzhong, Huang, Q., Li, Y., She, Q. & Montoya, Guillermo, 2020, In: Molecular Cell. 79, 5, p. 741-757

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

  60. Published

    A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

    Song, J., Klümper, U., Riber, Leise, Dechesne, A., Smets, B. F., Sørensen, Søren Johannes & Brandt, Kristian Koefoed, 2020, In: FEMS Microbiology Ecology. 96, 11, 10 p., fiaa200.

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

  61. Published

    Analogues of a Cyclic Antimicrobial Peptide with a Flexible Linker Show Promising Activity Against Pseudomonas aeruginosa and Staphylococcus aureus

    Thomsen, T. T., Mendel, H. C., Al-Mansour, W., Oddo, A., Løbner-Olesen, Anders & Hansen, Paul Robert, 2020, In: Antibiotics. 9, 7, 13 p., 366.

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

  62. Published

    Ethanol exposure increases mutation rate through error-prone polymerases

    Voordeckers, K., S.Colding-Christensen, Camilla, Grasso, L., Pardo, B., Hoes, L., Kominek, J., Gielens, K., Dekoster, K., Gordon, J., Van der Zande, E., Bircham, P., Swings, T., Michiels, J., Van Loo, P., Nuyts, S., Pasero, P., Lisby, Michael & Verstrepen, K. J., 2020, In: Nature Communications. 11, 16 p., 3664.

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

  63. Published

    Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica

    Wang, H., Li, Y., Wang, S., Kong, D., Sahu, S. K., Bai, M., Li, H., Li, L., Xu, Y., Liang, H., Liu, Huan & Wu, H., 2020, In: PeerJ. 8, 24 p., e8690.

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

  64. Published

    Genomes of early-diverging streptophyte algae shed light on plant terrestrialization

    Wang, S., Li, L., Li, H., Sahu, S. K., Wang, H., Xu, Y., Xian, W., Song, B., Liang, H., Cheng, S., Chang, Y., Song, Y., Çebi, Z., Wittek, S., Reder, T., Peterson, M., Yang, H., Wang, J., Melkonian, B., Van de Peer, Y. & 5 others, Xu, X., Wong, G. K., Melkonian, M., Liu, Huan & Liu, X., 2020, In: Nature Plants. 6, 2, p. 95-106

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

  65. Published

    Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25

    Yang, L., Wang, Y., Yu, P., Ren, S., Zhu, Z., Jin, Y., Yan, J., Peng, Xu & Chen, L., 2020, In: Frontiers in Cellular and Infection Microbiology. 10, 18 p., 595709.

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

  66. Published

    The draft genome of mandrill (Mandrillus sphinx): an Old World monkey

    Yin, Y., Yang, T., Liu, Huan, Huang, Z., Zhang, Y., Song, Y., Wang, W., Guang, X., Sahu, S. K. & Kristiansen, Karsten, 2020, In: Scientific Reports. 10, 8 p., 2431.

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

  67. Published

    A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger

    Zhao, R., Yang, Y., Zheng, F., Zeng, Z., Feng, W., Jin, X., Wang, J., Yang, K., Liang, Y. X., She, Q. & Han, W., 2020, In: Cell Reports. 32, 11, 16 p., 108133.

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

  68. Published

    Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

    Zhu, Z., Yang, L., Yu, P., Wang, Y., Peng, Xu & Chen, L., 2020, In: Frontiers in Microbiology. 11, 31 p., 1453.

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

  69. 2019
  70. Published

    Regulation of BRCA2 by the Protein Phosphatase 2A

    Ambjørn, Sara Marie, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  71. Published

    Quantitative sensing and signalling of single-stranded DNA during the DNA damage response

    Bantele, S. C. S., Lisby, Michael & Pfander, B., 2019, In: Nature Communications. 10, p. 1-12 944.

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

  72. Published

    The FANCM family Mph1 helicase localizes to the mitochondria and contributes to mtDNA stability

    Bernal, M., Yang, X., Lisby, Michael & Mazón, G., 2019, In: DNA Repair. 82, 11 p., 102684.

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

  73. Published

    Sulfolobus and SIRV2: An Enduring Love Story

    Bhoobalan, Yuvaraj, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  74. Published

    Inhibition of Type III CRISPR-Cas Immunity by an Archaeal Virus-Encoded Anti-CRISPR Protein

    Bhoobalan, Yuvaraj, Johansen, T. B., Di Cianni, N. & Peng, Xu, 2019, In: Cell. 179, 2, p. 448-458, e1-e11

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

  75. Published

    Evolution of the bacterial nucleosidase PpnN and its relation to the stringent response

    Bærentsen, R. L., Brodersen, D. E. & ZHANG, YONG, 2019, In: Microbial Cell Factories. 6, 9, p. 450-453

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

  76. Published

    Development and Psychometric Evaluation of an Item Bank for Computerized Adaptive Testing of the EORTC Insomnia Dimension in Cancer Patients (EORTC CAT-SL)

    Dirven, L., Petersen, Morten, Aaronson, N. K., Chie, W., Conroy, T., Costantini, A., Hammerlid, E., Velikova, G., Verdonck-de Leeuw, I. M., Young, T. & Grønvold, Mogens, 6 Dec 2019, In: Applied Research in Quality of Life. 18 p.

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

  77. Published

    Current View of the Mechanisms Controlling the Transcription of the TOL Plasmid Aromatic Degradation Pathways

    Domínguez-Cuevas, P. & Marqués, S., 2019, Aerobic Utilization of Hydrocarbons, Oils, and Lipids. Rojo, F. (ed.). Springer, p. 573-594 (Handbook of Hydrocarbon and Lipid Microbiology).

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

  78. Published

    Efflux-Pump Upregulation: From Tolerance to High-level Antibiotic Resistance?

    Frimodt-Møller, Jakob & Løbner-Olesen, Anders, 2019, In: Trends in Microbiology. 27, 4, p. 291-293

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

  79. Published

    Comparative genomics for non-O1/O139 Vibrio cholerae isolates recovered from the Yangtze River Estuary versus V. cholerae representative isolates from serogroup O1

    Gong, L., Yu, P., Zheng, H., Gu, W., He, W., Tang, Y., Wang, Y., Dong, Y., Peng, Xu, She, Q., Xie, L. & Chen, L., 2019, In: Molecular Genetics and Genomics. 294, 2, p. 417-430

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

  80. Published

    Cmr3 regulates the suppression on cyclic oligoadenylate synthesis by tag complementarity in a Type III-B CRISPR-Cas system

    Guo, T., Zheng, F., Zeng, Z., Yang, Y., Li, Q., She, Q. & Han, W., 2019, In: RNA Biology. 16, 10, p. 1513-1520

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

  81. Published

    Investigation of the Sulfolobus islandicus III-B Cmr-α CRISPR-Cas system and SMV1 anti-CRISPR activity

    Guo, T., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  82. Published

    Tolerance of Sulfolobus SMV1 virus to the immunity of I-A and III-B CRISPR-Cas systems in Sulfolobus islandicus

    Guo, T., Han, W. & She, Q., 2019, In: RNA Biology. 16, 4, p. 549-556 8 p.

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

  83. Published

    Comparative activity of ceftriaxone, ciprofloxacin and gentamicin as a function of bacterial growth rate probed by Escherichia coli chromosome replication in the mouse peritonitis model

    Haugan, M. S., Løbner-Olesen, Anders & Frimodt-Møller, N., 2019, In: Antimicrobial Agents and Chemotherapy. 63, 2, 13 p., e-02133-18.

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

  84. Published

    Examination of bacterial growth rate during host infection and its importance for antimicrobial treatment

    Haugan, M. S., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  85. Published

    Growth Rate of Escherichia coli During Human Urinary Tract Infection: Implications for Antibiotic Effect

    Haugan, M. S., Hertz, F. B., Charbon, Godefroid, Sahin, B., Løbner-Olesen, Anders & Frimodt-Møller, N., 2019, In: Antibiotics. 8, 3, 12 p., 92.

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

  86. Published

    Synthesis of Shld Derivatives, Their Binding to the Destabilizing Domain, and Influence on Protein Accumulation in Transgenic Plants

    Jørgensen, F. P., Madsen, D., Meldal, Morten Peter, Olsen, J. V., Petersen, Morten, Granhøj, J. & Bols, Mikael, 2019, In: Journal of Medicinal Chemistry. 62, 10, p. 5191-5216 26 p.

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

  87. Published

    Esc2 promotes telomere stability in response to DNA replication stress

    Jørgensen, S. W., Liberti, S. E., Larsen, N. B., Lisby, Michael, Mankouri, H. W. & Hickson, Ian David, 2019, In: Nucleic Acids Research. 47, 9, p. 4597-4611 15 p.

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

  88. Published

    Guidelines for DNA recombination and repair studies: cellular assays of DNA repair pathways

    Klein, H. L., Bacinskaja, G., Che, J., Cheblal, A., Elango, R., Epshtein, A., Fitzgerald, D. M., Gómez-González, B., Khan, S. R., Kumar, S., Leland, B. A., Marie, L., Mei, Q., Miné-Hattab, J., Piotrowska, A., Polleys, E. J., Putnam, C. D., Radchenko, E. A., Saada, A. A., Sakofsky, C. J. & 28 others, Shim, E. Y., Stracy, M., Xia, J., Yan, Z., Yin, Y., Aguilera, A., Argueso, J. L., Freudenreich, C. H., Gasser, S. M., Gordenin, D. A., Haber, J. E., Ira, G., Jinks-Robertson, S., King, M. C., Kolodner, R. D., Kuzminov, A., Lambert, S. A. E., Lee, S. E., Miller, K. M., Mirkin, S. M., Petes, T. D., Rosenberg, S. M., Rothstein, R., Symington, L. S., Zawadzki, P., Kim, N., Lisby, Michael & Malkova, A., 2019, In: Microbial Cell Factories. 6, 1, p. 1-64

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

  89. Published

    A Novel Fluorescence-Based Screen for Inhibitors of the Initiation of DNA Replication in Bacteria

    Klitgaard, R. N. & Løbner-Olesen, Anders, 2019, In: Current Drug Discovery Technologies. 16, 3, p. 272-277

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

  90. Published

    Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida

    Liang, H., Wei, T., Xu, Y., Li, L., Sahu, S. K., Wang, H., Li, H., Fu, X., Zhang, G., Melkonian, M., Liu, X., Wang, S. & Liu, Huan, 2019, In: International Journal of Molecular Sciences (Online). 20, 12, 14 p., 3020.

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

  91. Published

    Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages

    Lima, I. M. D. S. F., Zagmignan, A., Santos, D. M., Maia, H. S., Silva, L. D. S., Cutrim, B. D. S., Vieira, S. L., Filho, C. M. B., de Sousa, E. M., Napoleão, T. H., Krogfelt, K. A., Løbner-Olesen, Anders, Paiva, P. M. G. & da Silva, L. C. N., 2019, In: Scientific Reports. 9, 14 p., 18159.

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

  92. Published

    A novel type III CRISPR-Cas system in Lactobacilli: Molecular mechanisms and its application potential

    Lin, Jinzhong, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  93. Published

    Structure-Activity Study of an All-D Antimicrobial Octapeptide D2D

    Lone, A., Thomsen, T. T., Nielsen, J. E., Thulstrup, Peter Waaben, Klitgaard, R. N., Løbner-Olesen, Anders, Lund, R., Jenssen, H. & Hansen, Paul Robert, 2019, In: Molecules. 24, 24, 17 p., 4571.

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

  94. Published

    Regulation of Ribonucleotide Reductase and Screening for Species-Specific Inhibitors in Fission Yeast

    Løvschal, K. V., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  95. Published

    Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array

    Makarova, K. S., Karamycheva, S., Shah, S. A., Vestergaard, G. A., Garrett, Roger Antony & Koonin, E. V., 2019, In: FEMS Microbiology Letters. 366, 7, 5 p., fnz079.

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

  96. Published

    The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain

    Manav, M. C., Turnbull, K. J., Jurėnas, D., Garcia-Pino, A., Gerdes, K. & Brodersen, D. E., 2019, In: Structure. 27, 11, p. 1675-1685, e1-e3

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

  97. Published

    Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas

    Molina, R., Stella, S., Feng, M., Sofos, N., Jauniskis, V., Pozdnyakova, I., López-Méndez, B., She, Q. & Montoya, Guillermo, 2019, In: Nature Communications. 10, 14 p., 4302.

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

  98. Published

    Serine-Threonine Kinases Encoded by Split hipA Homologs Inhibit Tryptophanyl-tRNA Synthetase

    Nielsen, S. V., Turnbull, K. J., Roghanian, Mohammad, Bærentsen, R., Semanjski, M., Brodersen, D. E., Macek, B. & Gerdes, K., 2019, In: mBio. 10, 3, 16 p., e-01138-19.

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

  99. Published

    A seed motif for target RNA capture enables efficient immune defence by a type III-B CRISPR-Cas system

    Pan, S., Li, Q., Deng, Ling, Jiang, S., Jin, X., Peng, N., Liang, Y., She, Q. & Li, Y., 2019, In: RNA Biology. 16, 9, p. 1166-1178

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

  100. Published

    Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1

    Papathanasiou, P., Erdmann, S., Leon-Sobrino, C., Sharma, K., Urlaub, H., Garrett, Roger Antony & Peng, Xu, 2019, In: RNA Biology. 16, 4, p. 557-565

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

  101. Published

    The PCNA interaction motifs revisited: thinking outside the PIP-box

    Prestel, Andreas, Wichmann, N., Martins, J. M., Marabini, R., Kassem, N., Broendum, S. S., Otterlei, M., Nielsen, Olaf, Willemoës, Martin, Ploug, Michael, Boomsma, Wouter & Kragelund, Birthe Brandt, 2019, In: Cellular and Molecular Life Sciences. 76, 24, p. 4923-4943

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

  102. Published

    Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex

    Qian, H., Yu, H., Li, P., Zhu, E., Yao, Q., Tai, C., Deng, Z., Gerdes, K., He, X., Gan, J. & Ou, H., 2019, In: Nucleic Acids Research. 47, 14, p. 7690-7702

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

  103. Published

    (p)ppGpp-mediated stress response induced by defects in outer membrane biogenesis and ATP production promotes survival in Escherichia coli

    Roghanian, Mohammad, Semsey, S., Løbner-Olesen, Anders & Jalalvand, F., 2019, In: Scientific Reports. 9, p. 1-11 2934.

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

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