Functional Genomics

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  1. Published

    Top2 and Sgs1-Top3 act redundantly to ensure rDNA replication termination

    Mundbjerg, K., Jørgensen, S. W., Fredsøe, J. C., Nielsen, I., Pedersen, J. M., Bentsen, I. B., Lisby, Michael, Bjergbaek, L. & Andersen, A. H., 2015, In: P L o S Genetics. 11, 12, 24 p., e1005697.

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

  2. Published

    TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells

    Pedersen, R. T., Kruse, Thomas, Nilsson, Jakob, Østergaard, Vibe Hallundbæk & Lisby, Michael, 2015, In: Journal of Cell Biology. 210, 4, p. 565-582 18 p.

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

  3. Published

    TopBP1 makes the final call for repair on the verge of cell division

    Østergaard, Vibe Hallundbæk & Lisby, Michael, 2016, In: Molecular & Cellular Oncology. 3, 2, 3 p., e1093066.

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

  4. Published

    TopBP1-mediated DNA processing during mitosis

    Gallina, I., Christiansen, S. K., Pedersen, R. T., Lisby, Michael & Østergaard, Vibe Hallundbæk, 2016, In: Cell Cycle. 15, 2, p. 176-183 8 p.

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

  5. Published

    TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability

    Germann, S. M., Schramke, V., Pedersen, R. T., Gallina, I., Eckert-Boulet, N., Østergaard, Vibe Hallundbæk & Lisby, Michael, 2014, In: Journal of Cell Biology. 204, 1, p. 45-59 15 p.

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

  6. Published

    Topoisomerase II deficiency leads to a postreplicative structural shift in all Saccharomyces cerevisiae chromosomes

    Ayra-Plasencia, J., Ramos-Pérez, C., Santana-Sosa, S., Quevedo, O., Medina-Suárez, S., Matos-Perdomo, E., Zamora-Dorta, M., Brown, G. W., Lisby, Michael & Machín, F., 2021, In: Scientific Reports. 11, 16 p., 14940.

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

  7. 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

  8. Published

    Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex

    Qian, H., Yu, H., Li, P., Zhu, E., Yao, Q., Tai, C., Deng, Z., Gerdes, K., He, X., Gan, J. & Ou, H., 2019, In: Nucleic Acids Research. 47, 14, p. 7690-7702

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

  9. Published

    Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

    Harms, A., Brodersen, D. E., Mitarai, Namiko & Gerdes, K., 7 Jun 2018, In: Molecular Cell. 70, 5, p. 768-784 17 p.

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

  10. Published

    Transcription of the Alginate Operon in Pseudomonas aeruginosa Is Regulated by c-di-GMP

    Liang, Z., Rybtke, Morten Levin, Kragh, K. N., Johnson, O., Schicketanz, Muriel Leandra, Zhang, Yong, Andersen, Jens Bo & Tolker-Nielsen, Tim, 2022, In: Microbiology Spectrum. 10, 4, 13 p., e00675-22.

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

  11. Published

    Transcription termination in the plasmid/virus hybrid pSSVx from Sulfolobus islandicus

    Contursi, P., Cannio, R. & She, Q., 1 Sep 2010, In: Extremophiles. 14, 5, p. 453-63 11 p.

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

  12. Published

    Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    Østergaard, Vibe Hallundbæk & Lisby, Michael, Mar 2017, In: Chromosoma. 126, 2, p. 213-222 10 p.

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

  13. Published

    Transcriptional Analysis of the Genetic Element pSSVx: Differential and Temporal Regulation of Gene Expression Reveals Correlation between Transcription and Replication

    Contursi, P., Cannio, R., Prato, S., She, Q., Rossi, M. & Bartolucci, S., 2007, In: Journal of Bacteriology. 189, 17, p. 6339-50 11 p.

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

  14. Published

    Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp 1 p and Stp2p

    Eckert-Boulet, N., Nielsen, P. S., Friis, Carsten, Moreira dos Santos, M., Nielsen, J., Kielland-Brandt, M. C. & Regenberg, Birgitte, 1 Jun 2004, In: Yeast. 21, 8, p. 635-648 14 p.

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

  15. Published

    Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

    Liu, T., Li, Y., Wang, X., Ye, Q., Li, H., Liang, Y., She, Q. & Peng, N., 30 Jan 2015, In: Nucleic Acids Research. 43, 2, p. 1044-1055 12 p.

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

  16. Published

    Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex RSC

    Moreira, José & Holmberg, Steen, 1999, In: E M B O Journal. 18, 10, p. 2836-44 9 p.

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

  17. Published

    Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system

    Fusco, S., Liguori, R., Limauro, D., Bartolucci, S., She, Q. & Contursi, P., 2015, In: Biochimie. 118, p. 322-332 11 p.

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

  18. Published

    Transcriptome and genome size analysis of the venus flytrap

    Jensen, M. K., Vogt, J. K., Bressendorff, Simon, Seguin-Orlando, A., Petersen, Morten, Sicheritz-Pontén, T. & Mundy, J., 2015, In: P L o S One. 10, 4, 13 p., e0123887.

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

  19. Published

    Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition

    León Sobrino, C., Kot, W. P. & Garrett, Roger Antony, 2016, In: Molecular Microbiology. 99, 4, p. 719-728 10 p.

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

  20. Published

    Transcriptome responses to combinations of stresses in Arabidopsis

    Rasmussen, S., Barah, P., Suarez Rodriguez, M. C., Bressendorff, Simon, Friis, P., Costantino, P., Bones, A. M., Nielsen, H. B. & Mundy, J., 2013, In: Plant Physiology. 161, 4, p. 1783-1794 12 p.

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

  21. 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

  22. Published

    Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

    Suarez Rodriguez, M. C., Edsgärd, D., Hussain, S. S., Alquezar Planas, D. E., Rasmussen, M., Gilbert, M Thomas P, Nielsen, B. H., Bartels, D. & Mundy, J., Jul 2010, In: The Plant Journal. 63, 2, p. 212-228 17 p.

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

  23. Published

    Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi

    Ren, Y., She, Q. & Huang, L., 2013, In: Virology. 441, 2, p. 126-134 9 p.

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

  24. Published

    Translocation of non-lytic antimicrobial peptides and bacteria penetrating peptides across the inner membrane of the bacterial envelope

    Frimodt-Møller, Jakob, Campion, C., Nielsen, Peter E. & Løbner-Olesen, Anders, 2022, In: Current Genetics. 68, 1, p. 83-90

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

  25. Published

    Transposon tagging and gene targeting in Lotus japonicus

    Handberg, K., Thykjaer, T., Stiller, J., She, Q. & Stougaard, J., 1993, Current Plant Science and Biotechnology in Agriculture; New horizons in nitrogen fixation (R. Palacios, J. Mora W. E. Newton eds). p. 342 1 p.

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

  26. Published

    Truncated glucagon-like peptide I, an insulin-releasing hormone from the distal gut

    Holst, Jens Juul, Ørskov, Cathrine, Nielsen, Olaf & Schwartz, Thue W., 1987, In: F E B S Letters. 211, 2, p. 169-74 6 p.

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

  27. Published

    Trypanosome variable surface glycoproteins: composite genes and order of expression

    Thon, Genevieve, Baltz, T., Giroud, C. & Eisen, H., 1990, In: Genes & Development. 4, 8, p. 1374-1383 10 p.

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

  28. Published

    Two conserved modules of Schizosaccharomyces pombe Mediator regulate distinct cellular pathways

    Linder, T., Rasmussen, N., Samuelsen, C. O., Chatzidaki, E., Baraznenok, V., Beve, J., Henriksen, P., Gustafsson, C. M. & Holmberg, Steen, 2008, In: Nucleic Acids Research. 36, 8, p. 2489-504 15 p.

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

  29. Published

    Two differentially regulated Arabidopsis genes define a new branch of the DFR superfamily.

    Østergaard, L., Lauvergeat, V., Naested, H., Mattsson, O. & Mundy, J., 2001, In: Plant Science. 160, 3, p. 463-472 9 p.

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

  30. Published

    Two portable recombination enhancers direct donor choice in fission yeast heterochromatin

    Jakociunas, T., Holm, L. R., Hansen, J. V., Trusina, Ala & Thon, Genevieve, 2013, In: P L o S Genetics. 9, 10, 14 p., e1003762.

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

  31. Published

    Two-step activation of meiosis by the mat1 locus in Schizosaccharomyces pombe

    Willer, M., Hoffmann, U., Styrkársdóttir, U., Egel, Richard, Davey, W. J., Nielsen, O. & Nielsen, Olaf, 1 Sep 1995, In: Molecular and Cellular Biology. 15, 9, p. 4964-70 7 p.

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

  32. 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

  33. Published

    Type III CRISPR-Cas System: Introduction And Its Application for Genetic Manipulations

    Liu, T., Pan, S., Li, Y., Peng, N. & She, Q., 1 Jan 2018, In: Current Issues in Molecular Biology. 26, p. 1-14 14 p.

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

  34. 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

  35. 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

  36. Published

    UBL/BAG-domain co-chaperones cause cellular stress upon overexpression through constitutive activation of Hsf1

    Poulsen, E. G., Kampmeyer, Caroline, Kriegenburg, F., Johansen, Jens Vilstrup, Hofmann, K., Holmberg, Christian & Hartmann-Petersen, Rasmus, Jan 2017, In: Cell Stress & Chaperones. 22, 1, p. 143-154 12 p.

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

  37. Published

    Uncovering the roots of paranoid suicidal plants

    Lolle, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  38. Published

    Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus

    Deng, L., Zhu, H., Chen, Z., Liang, Y. X. & She, Q., 2009, In: Extremophiles. 13, 4, p. 735-46 11 p.

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

  39. Published

    Unravelling the role of the F55 regulator in the transition from lysogeny to UV induction of sulfolobus spindle-shaped virus 1

    Fusco, S., She, Q., Fiorentino, G., Bartolucci, S. & Contursi, P., 2015, In: Journal of Virology. 89, 12, p. 6453-6461 9 p.

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

  40. Published

    Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry

    Deng, Ling, He, F., Bhoobalan, Yuvaraj, Martinez Alvarez, Laura, Guo, Y. & Peng, Xu, 2014, In: Journal of Virology. 88, 17, p. 10264-10268 5 p.

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

  41. Published

    Update on non-typeable Haemophilus influenzae-mediated disease and vaccine development

    Jalalvand, F. & Riesbeck, K., 3 Jun 2018, In: Expert Review of Vaccines. 17, 6, p. 503-512

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

  42. Published

    Upregulated baseline plasma CCL19 and CCR7 cell-surface expression on monocytes in early rheumatoid arthritis normalized during treatment and CCL19 correlated with radiographic progression

    Ellingsen, T., Hansen, I., Thorsen, J., Møller, B. K., Tarp, U., Lottenburger, T., Andersen, L. S., Skjødt, H., Pedersen, J. K., Lauridsen, U. B., Svendsen, A., Lindegaard, H., Jacobsen, S., Østergaard, M., Vestergaard, A., Jurik, A. G., Junker, P., Christensen, A. F., Hetland, M. L., Hørslev-Petersen, K. & 1 others, Stengaard-Pedersen, K., 2014, In: Scandinavian Journal of Rheumatology. 43, 2, p. 91-100 10 p.

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

  43. Published

    Uropathogenic Escherichia coli metabolite-dependent quiescence and persistence may explain antibiotic tolerance during urinary tract infection

    Leatham-Jensen, M. P., Mokszycki, M. E., Rowley, D. C., Deering, R., Camberg, J. L., Sokurenko, E. V., Tchesnokova, V. L., Frimodt-Møller, Jakob, Krogfelt, K. A., Nielsen, K. L., Frimodt-Møller, N., Sun, G. & Cohen, P. S., 2016, In: mSphere. 1, 1, 22 p., e00055-15.

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

  44. Published

    Using an alignment of fragment strings for comparing protein structures.

    Friedberg, I., Harder, T., Kolodny, R., Sitbon, E., Li, Z. & Godzik, A., 2007, In: Bioinformatics. 23, 2, p. e219-24

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

  45. Published

    Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia

    Stephens, N. A., Gallagher, I. J., Rooyackers, O., Skipworth, R. J., Tan, B. H., Marstrand, T. T., Ross, J. A., Guttridge, D. C., Lundell, L., Fearon, K. C. & Timmons, J. A., 2010, In: Genome Medicine. 2, 12 p., 1.

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

  46. 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

  47. Published

    VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation

    Winther, K. S., Tree, J. J., Tollervey, D. & Gerdes, K., 2016, In: Nucleic Acids Research. 44, 20, p. 9860-9871 12 p.

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

  48. Published

    Vesicles in electric fields: some novel aspects of membrane behavior

    Dimova, R., Bezlyepkina, N. & Domange Jordö, M. E., 2009, In: Soft Matter. 5, 17, p. 3201-3212 12 p.

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

  49. Published

    Virology: Independent virus development outside a host

    Häring, M., Vestergaard, G. A., Rachel, R., Chen, L., Garrett, Roger Antony & Prangishvili, D., 2005, In: Nature. 436, 7054, p. 1101-1102

    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

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