Functional Genomics

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  1. 2021
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 2020
  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

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