Functional Genomics

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  1. 2018
  2. Published

    Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

    Ren, M., Zhang, Z., Wang, X., Zhou, Z., Chen, D., Zeng, H., Zhao, S., Chen, L., Hu, Y., Zhang, C., Liang, Y., She, Q., Zhang, Y. & Peng, N., 2018, In: Frontiers in Microbiology. 9, 14 p., 431.

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

  3. Published

    HipA-Mediated Phosphorylation of SeqA Does not Affect Replication Initiation in Escherichia coli

    Riber, Leise, Koch, B. M., Kruse, L. R., Germain, E. & Løbner-Olesen, Anders, 2 Nov 2018, In: Frontiers in Microbiology. 9, p. 1-9 2637.

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

  4. Published

    Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs

    Richard, S., Almeida, J. M. G. C. F., Cissé, O. H., Luraschi, A., Nielsen, Olaf, Pagni, M. & Hauser, P. M., 2018, In: mBio. 9, 1, 10 p., e02201-17.

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

  5. Published

    DNA damage as a consequence of NLR activation

    Rodriguez, Eleazar, Chevalier, J., El Ghoul, H., Voldum-Clausen, K., Mundy, J. & Petersen, Morten, 2018, In: PLOS Genetics. 14, 2, 17 p., e1007235.

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

  6. Published

    A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel

    Santner, P., Martins, J. M. D. S., Laursen, J. S., Behrendt, L., Riber, Leise, Olsen, Christian Adam, Arkin, I. T., Winther, Jakob R., Willemoës, Martin & Lindorff-Larsen, Kresten, 2018, In: Biochemistry. 57, 41, p. 5949-5956

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

  7. Published

    LL-37 fragments have antimicrobial activity against Staphylococcus epidermidis biofilms and wound healing potential in HaCaT cell line

    Saporito, P., Vang Mouritzen, M., Løbner-Olesen, Anders & Jenssen, H., 2018, In: Journal of Peptide Science. 24, 7, 12 p., e3080.

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

  8. 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

  9. Published

    The kinases HipA and HipA7 phosphorylate different substrate pools in Escherichia coli to promote multidrug tolerance

    Semanjski, M., Germain, E., Bratl, K., Kiessling, A., Gerdes, K. & Macek, B., 2018, In: Science Signaling. 11, 547, p. 1-13 eaat5750.

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

  10. Published

    The Interplay Between Immune Response and Bacterial Infection in COPD: Focus Upon Non-typeable Haemophilus influenzae

    Su, Y., Jalalvand, F., Thegerström, J. & Riesbeck, K., 2018, In: Frontiers in Immunology. 9, p. 1-26 2530.

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

  11. Published

    An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea

    Sun, M., Feng, X., Liu, Z., Han, W., Liang, Y. X. & She, Q., 2018, In: Nucleic Acids Research. 46, 13, p. 6697-6711

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

  12. Published

    Transcriptome-Wide Analysis of Protein-RNA and RNA-RNA Interactions in Pathogenic Bacteria

    Tree, J. J., Gerdes, K. & Tollervey, D., 2018, High-Density Sequencing Applications in Microbial Molecular Genetics. Carpousis, A. J. (ed.). Academic Press, Vol. 612. p. 467-488 (Methods in Enzymology).

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

  13. Published

    Common Chromosomal Fragile Sites - Conserved Failure Stories

    Voutsinos, Vasileios, Munk, S. H. N. & Østergaard, Vibe Hallundbæk, 2018, In: Genes. 9, 12, p. 1-16 580.

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

  14. Published

    Activation of the Stringent Response by Loading of RelA-tRNA Complexes at the Ribosomal A-Site

    Winther, K. S., Roghanian, Mohammad & Gerdes, K., 2018, In: Molecular Cell. 70, 1, p. 95-105, e1-e4 15 p.

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

  15. Published

    Discovering novel hydrolases from hot environments

    Wohlgemuth, R., Littlechild, J., Monti, D., Schnorr, K., van Rossum, T., Siebers, B., Menzel, P., Kublanov, I. V., Rike, A. G., Skretas, G., Szabo, Z., Peng, Xu & Young, M. J., 2018, In: Biotechnology Advances. 36, 8, p. 2077-2100

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

  16. Published

    Novel (p)ppGpp Binding and Metabolizing Proteins of Escherichia coli

    ZHANG, YONG, Zbornikova, E., Rejman, D. & Gerdes, K., 2018, In: mBio. 9, 2, 20 p., e02188-17.

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

  17. Published

    Functional study of PAT mRNA decapping factors in Arabidopsis

    Zuo, Zhangli Thomsen, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  18. Published

    ALG-2 participates in recovery of cells after plasma membrane damage by electroporation and digitonin treatment

    la Cour, J. M., Gojkovic, P. W., Ambjorner, S. E. B., Bagge, J., Jensen, S. M., Panina, S. & Berchtold, Martin Werner, 2018, In: PLOS ONE. 13, 9, p. 1-13 e0204520.

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

  19. 2017
  20. Published

    The role of the Saccharomyces cerevisiae Rdh54 DNA translocase at kinetochores

    Bacinskaja, G., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  21. Published

    Remotely controlled fusion of selected vesicles and living cells

    Bahadori, Azra, Rørvig-Lund, A., Semsey, S., Oddershede, L. B. & Bendix, Poul Martin, 15 Dec 2017, In: Proceedings of SPIE. 9922, p. 992211-1

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

  22. Published

    Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding

    Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A., Pedersen, C. N. S. & Brodersen, D. E., 2017, In: Nucleic Acids Research. 45, 5, p. 2875-2886 12 p.

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

  23. Published

    Chitin-induced responses in the moss Physcomitrella patens

    Bressendorff, Simon, Rasmussen, M. W., Petersen, Morten & Mundy, J., 2017, Plant pattern recognition receptors: methods and protocols. Shan, L. & He, P. (eds.). Springer, p. 317-324 8 p. (Methods in Molecular Biology, Vol. 1578).

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

  24. Published

    Discrete structural dynamics of pseudo-palindromic motifs control DNA binding of bacterial toxin-antitoxin complexes

    Brodersen, D. E., Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A. & Pedersen, C. N. S., 2017, In: F A S E B Journal. 31, S1, 1 p., 777.2.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  25. Published

    Regulation of telomere metabolism by the RNA processing protein Xrn1

    Cesena, D., Cassani, C., Rizzo, E., Lisby, Michael, Bonetti, D. & Longhese, M. P., 20 Apr 2017, In: Nucleic Acids Research. 45, 7, p. 3860-3874 15 p.

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

  26. Published

    Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli

    Charbon, Godefroid, Campion, C., Chan, S. H. J., Bjørn, L., Weimann, A., da Silva, L. C. N., Jensen, P. R. & Løbner-Olesen, Anders, 27 Jan 2017, In: PLoS Genetics. 13, 1, 26 p., e1006590.

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

  27. Published

    Ethyl methanesulfonate mutagenesis in Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 643-646 4 p.

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

  28. Published

    Genetic analysis of Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 593-605 13 p.

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

  29. Published

    Mating-type determination in Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Aug 2017, In: Cold Spring Harbor Protocols. 2017, 8, p. 641-642 2 p.

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

  30. Published

    Selecting Schizosaccharomyces pombe diploids

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 537-540 4 p.

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

  31. Published

    Setting up Schizosaccharomyces pombe crosses/matings

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 533-536 4 p.

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

  32. Published

    Spore analysis and tetrad dissection of Schizosaccharomyces pombe

    Ekwall, K. & Thon, Genevieve, Jul 2017, In: Cold Spring Harbor Protocols. 2017, 7, p. 541-544 4 p.

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

  33. 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

  34. Published

    Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB

    Fazli, M., Rybtke, Morten Levin, Steiner, E., Weidel, E., Berthelsen, J., Groizeleau, J. D. D., Bin, W., Zhi, B. Z., Yaming, Z., Kaever, V., Givskov, Michael, Hartmann, R. W., Eberl, L. & Tolker-Nielsen, Tim, 2017, In: MicrobiologyOpen. 6, 4, 13 p., e00480.

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

  35. Published

    Novel thermostable amine transferases from hot spring metagenomes

    Ferrandi, E. E., Previdi, A., Bassanini, I., Riva, S., Peng, Xu & Monti, D., Jun 2017, In: Applied Microbiology and Biotechnology. 101, 12, p. 4963-4979 17 p.

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

  36. Published

    Deoxynucleoside salvage in fission yeast allows rescue of ribonucleotide reductase deficiency but not Spd1-mediated inhibition of replication

    Fleck, O., Fahnøe, Ulrik, Løvschal, K. V., Gasasira, M. U., Marinova, I. N., Kragelund, Birthe Brandt, Carr, A. M., Hartsuiker, E., Holmberg, Christian & Nielsen, Olaf, 25 Apr 2017, In: Genes. 8, 5, 14 p., 128.

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

  37. Published

    Control of bacterial chromosome replication by non-coding regions outside the origin

    Frimodt-Møller, Jakob, Charbon, Godefroid & Løbner-Olesen, Anders, 2017, In: Current Genetics. 63, 4, p. 607-611 5 p.

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

  38. Published

    Determination of the optimal chromosomal location(s) for a DNA element in Escherichia coli using a novel transposon-mediated approach

    Frimodt-Møller, Jakob, Charbon, Godefroid, Krogfelt, K. A. & Løbner-Olesen, Anders, 11 Sep 2017, In: Journal of Visualized Experiments. 127, e55946.

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

  39. Published

    Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a β-strand sliding mechanism

    Hadži, S., Garcia-Pino, A., Haesaerts, S., Jurėnas, D., Gerdes, K., Lah, J. & Loris, R., 5 May 2017, In: Nucleic Acids Research. 45, 8, p. 4972-4983 12 p.

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

  40. Published

    A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction

    Han, W., Li, Y., Deng, Ling, Feng, M., Peng, W., Hallstrøm, S., Zhang, J., Peng, N., Liang, Y. X., White, M. F. & She, Q., 2017, In: Nucleic Acids Research. 45, 4, p. 1983–1993 11 p., gkw1274.

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

  41. Published

    Allosteric regulation of Csx1, a type IIIB-associated CARF domain ribonuclease by RNAs carrying a tetraadenylate tail

    Han, W., Pan, S., López-Méndez, B., Montoya, Guillermo & She, Q., 13 Oct 2017, In: Nucleic Acids Research. 45, 18, p. 10740-10750 11 p., gkx726.

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

  42. Published

    CRISPR History: Discovery, Characterization, and Prosperity

    Han, W. & She, Q., 2017, CRISPR in Animals and Animal Models. Torres-Ruiz, R. & Rodriguez-Perales, S. (eds.). Elsevier, p. 1-21 20 p. (Progress in Molecular Biology and Translational Science, Vol. 152).

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

  43. Published

    NQO-induced DNA-less cell formation is associated with chromatin protein degradation and dependent on A0A1-ATPase in Sulfolobus

    Han, W., Xu, Y., Feng, X., Liang, Y. X., Huang, L., Shen, Y. & She, Q., 14 Aug 2017, In: Frontiers in Microbiology. 8, 12 p., 1480.

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

  44. Published

    Reverse gyrase functions in genome integrity maintenance by protecting DNA breaks in vivo

    Han, W., Feng, X. & She, Q., Jul 2017, In: International Journal of Molecular Sciences. 18, 7, 13 p., 1340.

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

  45. Published

    Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells

    Harms, A., Fino, C., Sørensen, Michael Askvad, Semsey, S. & Gerdes, K., 12 Dec 2017, In: mBio. 8, 6, 18 p., e01964-17.

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

  46. Published

    CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b

    He, F., Vestergaard, G. A., Peng, W., She, Q. & Peng, Xu, 2017, In: Nucleic Acids Research. 45, 4, p. 1902-1913 12 p.

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

  47. Published

    Chitin and stress induced protein kinase activation

    Kenchappa, C. S., Azevedo da Silva, R., Bressendorff, Simon, Stanimirovic, S., Olsen, J. V., Petersen, Morten & Mundy, J., 2017, Plant pattern recognition receptors: methods and protocols. Shan, L. & He, P. (eds.). Springer, p. 185-194 10 p. (Methods in Molecular Biology, Vol. 1578).

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

  48. Published

    The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

    Lafuente-Barquero, J., Luke-Glaser, S., Graf, M., Pinela da Silva, S. C., Gómez-González, B., Lockhart, A., Lisby, Michael, Aguilera, A. & Luke, B., 27 Dec 2017, In: PLOS Genetics. 13, 12, 25 p., e1007136.

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

  49. Published

    Cmr1 enables efficient RNA and DNA interference of a III-B CRISPR–Cas system by binding to target RNA and crRNA

    Li, Y., Zhang, Y., Lin, Jinzhong, Pan, S., Han, W., Peng, N., Liang, Y. X. & She, Q., 2 Nov 2017, In: Nucleic Acids Research. 45, 19, p. 11305-11314 10 p., gkx791.

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

  50. Published

    3Rs tightly intertwined to maintain genome stability

    Lisby, Michael & Mortensen, U. H., Jan 2017, In: FEMS Yeast Research. 17, 1, 2 p., fox003.

    Research output: Contribution to journal › Editorial › Research

  51. Published

    Coupling transcriptional activation of CRISPR–Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus

    Liu, T., Liu, Z., Ye, Q., Pan, S., Wang, X., Li, Y., Peng, W., Liang, Y., She, Q. & Peng, N., 2017, In: Nucleic Acids Research. 45, 15, p. 8978–8992 15 p., gkx612.

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

  52. Published

    Type III CRISPR/Cas system: introduction and its application for genetic manipulations

    Liu, T., Pan, S., Li, Y., Peng, N. & She, Q., 2017, The CRISPR/Cas system: emerging technology and application. Jamal, M. (ed.). Caister Academic Press, p. 1-13 13 p.

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

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