Functional Genomics

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  1. 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

  2. Published

    The Cycas genome and the early evolution of seed plants

    Liu, Y., Wang, S., Li, L., Yang, T., Dong, S., Wei, T., Wu, S., Liu, Y., Gong, Y., Feng, X., Ma, J., Chang, G., Huang, J., Yang, Y., Wang, H., Liu, M., Xu, Y., Liang, H., Yu, J., Cai, Y. & 45 others, Zhang, Z., Fan, Y., Mu, W., Sahu, S. K., Liu, S., Lang, X., Yang, L., Li, N., Habib, S., Yang, Y., Lindstrom, A. J., Liang, P., Goffinet, B., Zaman, S., Wegrzyn, J. L., Li, D., Liu, J., Cui, J., Sonnenschein, E. C., Wang, X., Ruan, J., Xue, J., Shao, Z., Song, C., Fan, G., Li, Z., Zhang, L., Liu, J., Liu, Z., Jiao, Y., Wang, X., Wu, H., Wang, E., Lisby, Michael, Yang, H., Wang, J., Liu, X., Xu, X., Li, N., Soltis, P. S., Van de Peer, Y., Soltis, D. E., Gong, X., Liu, H. & Zhang, S., 2022, In: Nature Plants. 8, 4, p. 389-401 13 p.

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

  3. Published

    The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

    Fan, Y., Sahu, S. K., Yang, T., Mu, W., Wei, J., Cheng, L., Yang, J., Liu, J., Zhao, Y., Lisby, Michael & Liu, Huan, 2021, In: Genomics. 113, 6, p. 3696-3704 9 p.

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

  4. 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

  5. Published

    The 3' region of human papillomavirus type 16 early mRNAs decrease expression

    Vinther, Jeppe, Rosenstierne, M. W., Kristiansen, K. & Norrild, B., 2005, In: BMC Infectious Diseases. 5, p. 83

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

  6. Published

    Temporal phosphoproteomics reveals WEE1-dependent control of 53BP1 pathway

    Petrosius, V., Benada, Jan, Nielsen, Olaf, Schoof, E. M. & Sørensen, Claus Storgaard, 2023, In: iScience. 26, 1, 24 p., 105806.

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

  7. Published

    Telomeric C-circles localize at nuclear pore complexes in Saccharomyces cerevisiae

    Aguilera, P., Dubarry, M., Hardy, J., Lisby, Michael, Simon, M. & Géli, V., 2022, In: EMBO Journal. 41, 6, 14 p., e108736.

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

  8. Published

    Targeting synthesis of the Chromosome Replication Initiator Protein DnaA by antisense PNA-peptide conjugates in Escherichia coli

    Campion, C., Charbon, Godefroid, Nielsen, Peter E. & Løbner-Olesen, Anders, 2024, In: Frontiers in Antibiotics. 3, 10 p., 1384390.

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

  9. Published

    Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

    Køhler, J. B., Tammsalu, T., Jørgensen, M. L. M., Steen, N., Hay, R. T. & Thon, Genevieve, 2015, In: Nature Communications. 6, 14 p., 8827.

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

  10. Published

    TRAP230/ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution

    Samuelsen, C. O., Baraznenok, V., Khorosjutina, O., Spahr, H., Kieselbach, T., Holmberg, Steen & Gustafsson, C. M., 2003, In: Proceedings of the National Academy of Science of the United States of America. 100, 11, p. 6422-6427 5 p.

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

  11. Published

    TOPBP1 regulates RAD51 phosphorylation and chromatin loading and determines PARP inhibitor sensitivity

    Moudry, P., Watanabe, K., Wolanin, K. M., Bartkova, J., Wassing, I. E., Watanabe, S., Strauss, R., Pedersen, R. T., Østergaard, Vibe Hallundbæk, Lisby, Michael, Andújar-Sánchez, M., Maya-Mendoza, A., Esashi, F., Lukas, Jiri & Bartek, J., 2016, In: The Journal of Cell Biology. 212, 3, p. 281-288 8 p.

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

  12. Published

    Tlys, a newly identified Sulfolobus spindle-shaped virus 1 transcript expressed in the lysogenic state, encodes a DNA-binding protein interacting at the promoters of the early genes

    Fusco, S., She, Q., Bartolucci, S. & Contursi, P., 2013, In: Journal of Virology. 87, 10, p. 5926-5936 11 p.

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

  13. 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

  14. Published

    Synthesis and Activity of Antimicrobial Peptides

    Saporito, P., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  15. Published

    Synergy between Mecillinam and Ceftazidime/Avibactam or Avibactam against Multi-Drug-Resistant Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae

    List, K. K., Kolpen, Mette, Kragh, K. N., Charbon, Godefroid, Radmer, S., Hansen, F., Løbner-Olesen, Anders, Frimodt-Møller, N. & Hertz, F. B., 2022, In: Antibiotics. 11, 10, 13 p., 1280.

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

  16. Published

    Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation

    Tian, C., Semsey, S. & Mitarai, Namiko, 21 Aug 2017, In: Nucleic Acids Research. 45, 14, p. 8180-8189 10 p.

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

  17. Published

    Synchronization of S phase in Schizosaccharomyces pombe cells by transient exposure to M-factor pheromone

    Nielsen, Olaf, 2016, In: Cold Spring Harbor Protocols. 2016, 9, p. 768-772 5 p.

    Research output: Contribution to journal › Journal article › Research

  18. Published

    Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals

    Xu, D., Peng, Xu, Xie, L. & Chen, L., 2022, In: Diversity. 14, 5, 23 p., 350.

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

  19. Published

    Suppressors of Hyperinitiation in Escherichia coli Couple DNA Replication to Precursor Biosynthesis and Energy Metabolism

    Bjørn, L., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  20. Published

    Suppressing autoimmunity in Arabidopsis thaliana with dominant negative immune receptors

    Greeff, M. C., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  21. Published

    Sulfolobus genomes: mechanisms of rearrangement and change

    Brügger, K., Peng, Xu & Garrett, Roger Antony, 2006, Archaea: Evolution, physiology and Molecular Biolog.

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

  22. 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

  23. Published

    Sulfolobus Turreted Icosahedral Virus c92 Protein Responsible for the Formation of Pyramid-Like Cellular Lysis Structures

    Snyder, J. C., Brumfield, S. K., Peng, N., She, Q. & Young, M. J., 2011, In: Journal of Virology. 85, 13, p. 6287-92 6 p.

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

  24. Published

    Sulfolobus Replication Factor C stimulates the activity of DNA Polymerase B1

    Xing, X., Zhang, L., Guo, L., She, Q. & Huang, L., 2014, In: Journal of Bacteriology. 196, 13, p. 2367-2375 9 p.

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

  25. Published

    Sugar metabolism of the first thermophilic Planctomycete Thermogutta terrifontis: comparative genomic and transcriptomic approaches

    Elcheninov, A. G., Menzel, P., Gudbergsdottir, S. R., Slesarev, A. I., Kadnikov, V. V., Krogh, Anders, Bonch-Osmolovskaya, E. A., Peng, Xu & Kublanov, I. V., 2 Nov 2017, In: Frontiers in Microbiology. 8, 11 p., 2140.

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

  26. Published

    Substrate specificity and gene expression of the amino acid permeases in Saccharomyces cerevisiae

    Regenberg, Birgitte, Düring-Olsen, L., Kielland-Brandt, M. C. & Holmberg, Steen, 1 Jan 1999, In: Current Genetics. 36, 6, p. 317-328 12 p.

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

  27. Published

    Subnuclear relocalization and silencing of a chromosomal region by an ectopic ribosomal DNA repeat

    Jakociunas, T., Domange Jordö, M. E., Mebarek, M. A., Bünner, C. M., Hansen, J. V., Oddershede, L. B. & Thon, Genevieve, 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 47, p. E4465-E4473 9 p.

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

  28. Published

    Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system

    Vestergaard, G. A., Shah, S. A., Bize, A., Reitberger, W., Reuter, M., Phan, H., Briegel, A., Rachel, R., Garrett, Roger Antony & Prangishvili, D., 2008, In: Journal of Bacteriology. 190, 20, p. 6837-6845 8 p.

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

  29. Published

    Studying Extrachromosomal Genetic Elements in Sulfolobus

    Guannan, L., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 85 p.

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

  30. Published

    Studies on DNA Damage Response in Sulfolobus islandicus

    Han, W., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 139 p.

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

  31. Published

    Studies of archaeal virus-host systems in thermal environments

    Erdmann, S., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 147 p.

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

  32. 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

  33. Published

    Structured RNAs in the ENCODE selected regions of the human genome.

    Washietl, S., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S. E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T. R., Guigó, R., Snyder, M. & 4 others, Gerstein, M. B., Reymond, A., Hofacker, I. L. & Stadler, P. F., 2007, In: Genome Research. 17, 6, p. 852-64 12 p.

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

  34. 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

  35. Published

    Structure, function and networks of transcription factors involved in abiotic stress responses

    Lindemose, Søren, O'Shea, Charlotte, Jensen, M. K. & Skriver, Karen, 2013, In: International Journal of Molecular Sciences (Online). 14, 3, p. 5842-78 37 p.

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

  36. 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

  37. Published

    Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses

    Vestergaard, G. A., Aramayo, R., Basta, T., Häring, M., Peng, Xu, Brügger, K., Chen, L., Rachel, R., Boisset, N., Garrett, Roger Antony & Prangishvili, D., 2008, In: Journal of Virology. 82, 1, p. 371-381 11 p.

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

  38. Published

    Structure of Leptin Receptor Related with Obesity

    Toleikis, Z., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  39. 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

  40. Published

    Structure of African elephant populations

    Siegismund, Hans Redlef & Arctander, P., 1996, In: Journal of Heredity. 86, 6, p. 467-9 2 p.

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

  41. Published

    Structure and organ specificity of an anionic peroxidase from Arabidopsis thaliana cell suspension culture

    Ostergaard, L., Abelskov, A. K., Mattsson, O. & Welinder, K. G., 1996, In: FEBS Letters. 398, 2-3, p. 243-7 4 p.

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

  42. Published

    Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures

    Häring, M., Vestergaard, G. A., Brügger, K., Rachel, R., Garrett, Roger Antony & Prangishvili, D., 2005, In: Journal of Bacteriology. 187, 11, p. 3855-8 4 p.

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

  43. Published

    Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response

    Bisiak, F., Chrenková, A., Zhang, S., Pedersen, J. N., Otzen, D. E., ZHANG, YONG & Brodersen, D. E., 2022, In: Journal of Biological Chemistry. 298, 7, 16 p., 102142.

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

  44. Published

    Structural basis for kinase inhibition in the tripartite E. coli HipBST toxin-antitoxin system

    Bærentsen, R. L., Nielsen, S. V., Skjerning, R. B., Lyngsø, J., Bisiak, F., Pedersen, J. S., Gerdes, K., Sørensen, Michael Askvad & Brodersen, D. E., 2023, In: eLife. 12, 20 p., RP90400.

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

  45. 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

  46. Published

    Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle

    Prangishvili, D., Vestergaard, G. A., Häring, M., Aramayo, R., Basta, T., Rachel, R. & Garrett, Roger Antony, 2006, In: Journal of Molecular Biology. 359, 5, p. 1203-1216 13 p.

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

  47. Published

    Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

    Lintner, N. G., Kerou, M., Brumfield, S. K., Graham, S., Liu, H., Naismith, J. H., Sdano, M., Peng, N., She, Q., Copié, V., Young, M. J., White, M. F. & Lawrence, C. M., 2011, In: The Journal of Biological Chemistry. 286, 24, p. 21643-56 14 p.

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

  48. Published

    Structural analysis of sumoylated proteins in Schizosaccharomyces pombe : with a special focus on the DNA binding protein Sap1

    Jørgensen, M. L. M., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

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

  49. Published

    Statistical evidence for miscoding lesions in ancient DNA templates

    Hansen, Anders Johannes, Willerslev, Eske, Wiuf, C., Mourier, T. & Arctander, P., 2001, In: Molecular Biology and Evolution. 18, 2, p. 262-65 4 p.

    Research output: Contribution to journal › Letter › Research

  50. 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

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