Functional Genomics

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  1. Published

    "Population structure of drug-susceptible, -resistant and ESBL-producing Escherichia coli from community-acquired urinary tract infections"

    Hertz, F. B., Nielsen, J. B., Schønning, Kristian, Littauer, P., Knudsen, J. D., Løbner-Olesen, Anders & Frimodt-Møller, N., 11 Apr 2016, In: BMC Microbiology. 16, 6 p., 63.

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

  2. Published

    (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch

    ZHANG, YONG, Bærentsen, R. L., Fuhrer, T., Sauer, U., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Cell. 74, 6, p. 1239-1249, e1-e4

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

  3. 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

  4. 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

  5. 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

  6. Published

    57miRNA regulation during oncogene-induced senescence


    Christoffersen, N. R., Frankel, Lisa, Klausen, M., Jacobsen, A., Krogh, Anders & Lund, Anders H., May 2008.

    Research output: Contribution to conference › Conference abstract for conference › Research

  7. Published

    7. Proprioceptive evoked potentials (PEP) in man: Cerebral responses of changing weight loads on the hand

    Arnfred, Sidse Marie , CHEN, Ao, Eder, D. N., Glenthøj, Birte Yding & Hemmingsen, Ralf Peter, Oct 2001, In: Brain and Cognition. 47, 1-2, p. 54-57 4 p.

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

  8. Published

    Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development

    Næsted, H., Holm, A., Jenkins, T., Nielsen, H. B., Harris, C. A., Beale, M. H., Andersen, M., Mant, A., Scheller, H. V., Camara, B., Mattsson, O. & Mundy, J., 2004, In: Journal of Cell Science. 117, 20, p. 4807-18 12 p.

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

  9. Published

    Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance

    Petersen, Morten, Brodersen, P., Naested, H., Andreasson, E., Lindhart, U., Johansen, B., Nielsen, H. B., Lacy, M., Austin, M. J., Parker, J. E., Sharma, S. B., Klessig, D. F., Martienssen, R., Mattsson, O., Jensen, A. B. & Mundy, J. W., 2000, In: Gekkan Saibo. 103, 7, p. 1111-1120

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

  10. Published

    Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus

    Qiu, J., Fiil, Berthe Katrine, Petersen, K., Nielsen, H. B., Botanga, C. J., Thorgrimsen, S. P., Palma, K., Suarez Rodriguez, M. C., Sandbech-Clausen, S., Lichota, J., Brodersen, P., Grasser, K. D., Mattsson, O., Glazebrook, J., Mundy, J. & Petersen, Morten, 2008, In: EMBO Journal. 27, 16, p. 2214-2221 8 p.

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

  11. Published

    C-locked analogs of the antimicrobial peptide BP214

    Andersen, I. K. L., Thomsen, T. T., Rashid, J., Bobak, T. R., Oddo, A., Franzyk, Henrik, Løbner-Olesen, Anders & Hansen, Paul Robert, 2022, In: Antibiotics. 11, 8, 10 p., 1080.

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

  12. Published

    Chloranthus genome provides insights into the early diversification of angiosperms

    Guo, X., Fang, D., Sahu, S. K., Yang, S., Guang, X., Folk, R., Smith, S. A., Chanderbali, A. S., Chen, S., Liu, M., Yang, T., Zhang, S., Liu, X., Xu, X., Soltis, P. S., Soltis, D. E. & Liu, Huan, 2021, In: Nature Communications. 12, 14 p., 6930.

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

  13. Published

    Escherichia coli belonging to ST131 rarely transfers blactx-m-15 to fecal Escherichia coli

    Thingholm, K. R., Hertz, F. B., Løbner-Olesen, Anders, Frimodt-Møller, N. & Nielsen, K. L., 2019, In: Infection and Drug Resistance. 12, p. 2429-2435

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

  14. Published

    In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages

    Sinha, V., Goyal, A., Svenningsen, Sine Lo, Semsey, S. & Krishna, S., 26 Jul 2017, In: Frontiers in Microbiology. 8, 11 p., 1386.

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

  15. Published

    In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag

    Visone, V., Han, W., Perugino, G., del Monaco, G., She, Q., Rossi, M., Valenti, A. & Ciaramella, M., 3 Oct 2017, In: PLoS ONE. 12, 10, 19 p., e0185791.

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

  16. Published

    Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice

    Søndberg, E. & Jelsbak, L., 2016, In: BMC Microbiology. 16, 11 p., 30.

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

  17. 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

  18. Published

    Age- and tactic-related paternity success in male African elephants

    Rasmussen, H. B., Okello, J. B. A., Wittemyer, G., Siegismund, Hans Redlef, Arctander, P., Vollrath, F. & Douglas-Hamilton, I., 2008, In: Behavioral Ecology. 19, 1, p. 9-15

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

  19. 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

  20. Published

    A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

    Aulitto, M., Martinez Alvarez, Laura, Fiorentino, G., Limauro, D., Peng, Xu & Contursi, P., 2022, In: International Journal of Molecular Sciences . 23, 6, 23 p., 3135.

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

  21. Published

    A Critical Role for Dna2 at Unwound Telomeres

    Markiewicz-Potoczny, M., Lisby, Michael & Lydall, D., 2018, In: Genetics. 209, 1, p. 129-141 13 p.

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

  22. Published

    A Flp-nick system to study repair of a single protein-bound nick in vivo

    Nielsen, I., Bentsen, I. B., Lisby, Michael, Hansen, S., Mundbjerg, K., Andersen, A. H. & Bjergbaek, L., 2009, In: Nature Methods. 6, 10, p. 753-757 4 p.

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

  23. Published

    A High Resolution, High Throughput Approach for Subcellular Spatial Omics

    CHEN, Ao, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 130 p.

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

  24. 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

  25. 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

  26. 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

  27. Published

    A Type III-B Cmr effector complex catalyzes the synthesis of cyclic oligoadenylate second messengers by cooperative substrate binding

    Han, W., Stella, S., Zhang, Y., Guo, T., Sulek, K., Peng-Lundgren, L., Montoya, Guillermo & She, Q., 2018, In: Nucleic Acids Research. 46, 19, p. 10319-10330 12 p.

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

  28. Published

    A Unified Nomenclature for Protein Subunits of Mediator Complexes Linking Transcriptional Regulators to RNA Polymerase II

    Bourbon, H. M., Aguilera, A., Ansari, A. Z., Asturias, F. J., Berk, A. J., Bjorklund, S., Blackwell, T. K., Borggrefe, T., Carey, M., Carlson, M., Conaway, J. W., Conaway, R. C., Emmons, S. W., Fondell, J. D., Freedman, L. P., Fukasawa, T., Gustafsson, C. M., Han, M., He, X., Herman, P. K. & 27 others, Hinnebusch, A. G., Holmberg, Steen, Holstege, F. C., Jaehning, J. A., Kim, Y., Kuras, L., Leutz, A., Lis, J. T., Meisterernest, M., Naar, A. M., Nasmyth, K., Parvin, J. D., Ptashne, M., Reinberg, D., Ronne, H., Sadowski, I., Sakurai, H., Sipiczki, M., Sternberg, P. W., Stillman, D. J., Strich, R., Struhl, K., Svejstrup, J. Q., Tuck, S., Winston, F., Roeder, R. G. & Kornberg, R. D., 2004, In: Molecular Cell. 14, 5, p. 553-557

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

  29. Published

    A Unified Resource for Tracking Anti-CRISPR Names

    Bondy-Denomy, J., Davidson, A. R., Doudna, J. A., Fineran, P. C., Maxwell, K. L., Moineau, S., Peng, Xu, Sontheimer, E. J. & Wiedenheft, B., 2018, In: CRISPR Journal. 1, 5, p. 304-305

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  30. Published

    A backward view from 16S rRNA to archaea to the universal tree of life to progenotes Reminiscences of Carl Woese

    Garrett, Roger Antony, 2014, In: R N A Biology. 11, 3, p. 232-235 4 p.

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

  31. Published

    A bacterial ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility

    ZHANG, YONG, Franco, M., Ducret, A. & Mignot, T., Jul 2010, In: PLOS Biology. 8, 7

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

  32. Published

    A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

    Chen, F., Su, L., Hu, S., Xue, J., Liu, H., Liu, G., Jiang, Y., Du, J., Qiao, Y., Fan, Y., Liu, Huan, Yang, Q., Lu, W., Shao, Z., Zhang, J., Zhang, L., Chen, F. & Cheng, Z. (., 2021, In: Horticulture Research. 8, 13 p., 141.

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

  33. Published

    A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression

    Li, X., Lozano-Madueno, C., Martinez Alvarez, Laura & Peng, Xu, 2023, In: Nucleic acids symposium series. 51, 4, 16 p.

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

  34. Published

    A comparative method for finding and folding RNA secondary structures within protein-coding regions.

    Pedersen, J. S., Meyer, I. M., Forsberg, R., Simmonds, P. & Hein, J., 2004, In: Nucleic Acids Research. 32, 16, p. 4925-36 11 p.

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

  35. Published

    A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination

    Ambjørn, Sara Marie, Duxin, Julien, Hertz, Emil Peter Thrane, Nasa, I., Duro, Joana Maria, Kruse, Thomas, Lopez-Mendez, B., Rymarczyk, B., Cressey, L. E., van Overeem Hansen, T., Kettenbach, A. N., Østergaard, Vibe Hallundbæk, Lisby, Michael & Nilsson, Jakob, 2021, In: Nature Communications. 12, 1, 11 p., 5748.

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

  36. Published

    A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA

    Nielsen, Henrik, Einvik, C., Lentz, T. E., Hedegaard, M. M. & Johansen, S. D., 2009, In: RNA: A publication of the RNA Society. 15, 5, p. 958-67 9 p.

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

  37. Published

    A context-dependent and disordered ubiquitin-binding motif

    Dreier, Jesper Elmsted, Prestel, Andreas, Martins, J. M., Brøndum, S. S., Nielsen, Olaf, Garbers, Anna Engstrøm, Suga, H., Boomsma, Wouter, Rogers, Joseph Matthew, Hartmann-Petersen, Rasmus & Kragelund, Birthe Brandt, 2022, In: Cellular and molecular life sciences : CMLS. 79, 9, 21 p., 484.

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

  38. 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

  39. Published

    A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication

    Oke, M., Kerou, M., Liu, H., Peng, Xu, Garrett, Roger Antony, Prangishvili, D., Naismith, J. H. & White, M. F., 2011, In: Journal of Virology. 85, 2, p. 925-31 7 p.

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

  40. 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

  41. Published

    A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway

    Wang, J., Xie, J., Chen, H., Qiu, X., Cui, H., Liu, Y., Sahu, S. K., Fang, D., Li, T., Wang, M., Chen, Y., Liu, Huan, Zhang, J. & Wang, B., 2022, In: Communications Biology . 5, 12 p., 1294.

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

  42. Published

    A guanosine quadruplex and two stable hairpins flank a major cleavage site in insulin-like growth factor II mRNA

    Christiansen, Jan, Kofod, M. & Nielsen, F. C., 1994, In: Nucleic Acids Research. 22, 25, p. 5709-16 7 p.

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

  43. Published

    A human topoisomerase IIα heterodimer with only one ATP binding site can go through successive catalytic cycles

    Skouboe, C., Bjergbaek, L., Østergaard, Vibe Hallundbæk, Larsen, M. K., Knudsen, B. R. & Andersen, A. H., 21 Feb 2003, In: Journal of Biological Chemistry. 278, 8, p. 5768-5774 7 p.

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

  44. Published

    A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

    Lorenzen, Eline, Masembe, C., Arctander, P. & Siegismund, Hans Redlef, 2010, In: Journal of Biogeography. 37, 3, p. 571-581 11 p.

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

  45. Published

    A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

    Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. & Huang, L., 2007, In: Virology. 363, 1, p. 124-33 9 p.

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

  46. Published

    A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates

    Li, Y., Pan, Y., She, Q. & Chen, L., 2013, In: B M C Biotechnology. 13, 13 p., 89.

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

  47. Published

    A novel esterase from Saccharomyces carlsbergensis, a possible function for the yeast TIP1 gene

    Horsted, M. W., Dey, E. S., Holmberg, Steen & Kielland-Brandt, M. C., 1998, In: Yeast. 14, 9, p. 793-803 10 p.

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

  48. Published

    A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus

    Deng, Ling, Garrett, Roger Antony, Shah, S. A., Peng, Xu & She, Q., 2013, In: Molecular Microbiology. 87, 5, p. 1088-1099 12 p.

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

  49. Published

    A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus

    Vestergaard, G. A., Häring, M., Peng, Xu, Rachel, R., Garrett, Roger Antony & Prangishvili, D., 2005, In: Virology. 336, 1, p. 83-92 10 p.

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

  50. Published

    A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species

    Erdmann, S., Chen, B., Huang, X., Deng, Ling, Liu, C., Shah, S. A., Bauer, S. L. M., León Sobrino, C., Wang, H., Wei, Y., She, Q., Garrett, Roger Antony, Huang, L. & Lin, L., 2014, In: Extremophiles. 18, 1, p. 51-60 10 p.

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

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