Functional Genomics

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  1. 2020
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. Published

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

    Kampmeyer, Caroline, Johansen, Jens Vilstrup, Holmberg, Christian, Karlson, M., Gersing, S. K., 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

  30. 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

  31. 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

  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

    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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 2021
  52. Published

    (p)ppGpp-Dependent Regulation of the Nucleotide Hydrolase PpnN Confers Complement Resistance in Salmonella enterica Serovar Typhimurium

    Chau, N. Y. E., Pérez-Morales, D., Elhenawy, W., Bustamante, V. H., ZHANG, YONG & Coombes, B. K., 2021, In: Infection and Immunity. 89, 2, 14 p., e00639-20.

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

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