Functional Genomics

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  1. 2017
  2. 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

  3. 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

  4. 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

  5. Published

    Phosphatidylserine stimulates ceramide 1-phosphate (C1P) intermembrane transfer by C1P transfer proteins

    Zhai, X., Gao, Y., Mishra, S. K., Simanshu, D. K., Boldyrev, I. A., Benson, L. M., Bergen III, H. R., Malinina, L., Mundy, J., Molotkovsky, J. G., Patel, D. J. & Brown, R. E., 10 Feb 2017, In: Journal of Biological Chemistry. 292, 6, p. 2531-2541 11 p.

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

  6. Published

    Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

    Toteva, T., Mason, B., Kanoh, Y., Brøgger, P., Green, D., Hansen, J. V., Masai, H. & Thon, Genevieve, 31 Jan 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 1093-1098 6 p.

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

  7. 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

  8. 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

  9. Published

    Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains

    Sebesta, M., Urulangodi, M., Stefanovie, B., Szakal, B., Pacesa, M., Lisby, Michael, Branzei, D. & Krejci, L., Jan 2017, In: Nucleic Acids Research. 45, 1, p. 215-230 16 p.

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

  10. 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

  11. 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

  12. Published

    Autophagy is required for gamete differentiation in the moss Physcomitrella patens

    Sanchez-Vera, V., Kenchappa, C. S., Landberg, K., Bressendorff, Simon, Schwarzbach, S., Martin, T., Mundy, J., Petersen, Morten, Thelander, M. & Sundberg, E., 2017, In: Autophagy. 13, 11, p. 1939-1951 13 p.

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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Published

    DNA damage repair in Archaea

    She, Q., Feng, X. & Han, W., 2017, Biocommunication of Archaea. Witzany, G. (ed.). Springer, p. 305-318 14 p.

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

  20. Published

    Determination of protein turnover in E. coli cells during exit from persistence

    Semanjski, M., Germain-Maisonneuve, E., Gerdes, K. & Macek, B., 2017, In: F A S E B Journal. 31, S1, 1 p., 915.2.

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

  21. 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

  22. Published

    Elucidating the roles of MAP kinases in the moss Physcomitrella patens

    Stanimirovic, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen. 230 p.

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

  23. Published

    Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970-2016: A systematic analysis for the Global Burden of Disease Study 2016

    Wang, H., Abajobir, A. A., Abate, K. H., Abbafati, C., Abbas, K. M., Abd-Allah, F., Abera, S. F., Abraha, H. N., Abu-Raddad, L. J., Abu-Rmeileh, N. M. E., Adedeji, I. A., Adedoyin, R. A., Adetifa, I. M. O., Adetokunboh, O., Afshin, A., Aggarwal, R., Agrawal, A., Agrawal, S., Ahmad Kiadaliri, A., Ahmed, M. B. & 31 others, Aichour, A. N., Aichour, I., Aichour, M. T. E., Aiyar, S., Akanda, A. S., Akinyemiju, T. F., Akseer, N., Al-Eyadhy, A., Al Lami, F. H., Alabed, S., Alahdab, F., Al-Aly, Z., Alam, K., Alam, N., Alasfoor, D., Aldridge, R. W., Alene, K. A., Bjerregaard, P., Christensen, H., De Courten, B., Havmoeller, R., He, F., Iburg, K. M., Larsson, A., McGrath, J. J., Mengistie, M. A., Singh, Prashant, Sobngwi, E., Truelsen, Thomas Clement, Wang, Y. & GBD 2016 Mortality Collaborators, G. 2. M. C., 2017, In: The Lancet. 390, 10100, p. 1084-1150 67 p.

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

  24. Published

    Matching NLR immune receptors to autoimmunity in camta3 mutants using antimorphic NLR alleles

    Lolle, S., Greeff, M. C., Petersen, K., Roux, M. E., Jensen, M. K., Bressendorff, Simon, Rodriguez, Eleazar, Sømark, K., Mundy, J. & Petersen, Morten, 2017, In: Cell Host & Microbe. 21, 4, p. 518-529 12 p.

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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 2016
  31. Published

    Back to the roots: deep view into the evolutionary history of ADP-ribosylation opened by the DNA-targeting toxin-antitoxin module DarTG

    Harms, A. & Gerdes, K., 15 Dec 2016, In: Molecular Cell. 64, 6, p. 1020-1021 2 p.

    Research output: Contribution to journal › Comment/debate › Research

  32. Published

    Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases

    Tian, C., Roghanian, Mohammad, Jørgensen, M. G., Sneppen, Kim, Sørensen, Michael Askvad, Gerdes, K. & Mitarai, Namiko, Jul 2016, In: Journal of Bacteriology. 198, 14, p. 1918-1926

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

  33. Published

    Life cycle characterization of Sulfolobus monocaudavirus 1, an extremophilic spindle-shaped virus with extracellular tail development

    Uldahl, K. B., Jensen, S. B., Bhoobalan, Yuvaraj, Martinez Alvarez, Laura, Papathanasiou, P. & Peng, Xu, Jun 2016, In: Journal of Virology. 90, 12, p. 5693-5699 7 p.

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

  34. Published

    Configuration-dependent Presentation of Multivalent IL-15: IL-15Rα enhances the antigen-specific T cell response and anti-tumor immunity

    Hong, E., Usiskin, I. M., Bergamaschi, C., Hanlon, D. J., Edelson, R. L., Justesen, S., Pavlakis, G. N., Flavell, R. A. & Fahmy, T. M., 22 Apr 2016, In: Journal of Biological Chemistry. 291, 17, p. 8931-8950 20 p.

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

  35. 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

  36. Published

    The role of HERC2 and RNF8 ubiquitin E3 ligases in the promotion of translesion DNA synthesis in the chicken DT40 cell line

    Mohiuddin, M., Kobayashi, S., Keka, I. S., Guilbaud, G., Sale, J., Narita, Takeo, Abdel-Aziz, H. I., Wang, X., Ogawa, S., Sasanuma, H., Chiu, R., Østergaard, Vibe Hallundbæk, Lisby, Michael & Takeda, S., Apr 2016, In: DNA Repair. 40, p. 67-76 10 p.

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

  37. 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

  38. Published

    Adipokinetic hormones and their G protein-coupled receptors emerged in Lophotrochozoa

    Li, S., Hauser, Frank, Skadborg, S. K., Nielsen, S. V., Kirketerp-Møller, N. & Grimmelikhuijzen, Cornelis (Cok), 2016, In: Scientific Reports. 6, 13 p., 32789.

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

  39. Published

    Alarmone (p)ppGpp regulates the transition from pathogenicity to mutualism in Photorhabdus luminescens

    Skjerning, R. B., Roghanian, Mohammad, Gerdes, K. & Clarke, D. J., 2016, In: Molecular Microbiology. 100, 4, p. 735-747 13 p.

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

  40. Published

    An amphipathic undecapeptide with all D-amino acids shows promising activity against colistin-resistant strains of Acinetobacter baumannii and a dual mode of action

    Oddo, A., Thomsen, T. T., Kjelstrup, S., Gorey, C., Franzyk, Henrik, Frimodt-Møller, N., Løbner-Olesen, Anders & Hansen, Paul Robert, 2016, In: Antimicrobial Agents and Chemotherapy. 60, 1, p. 592-599 8 p.

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

  41. Published

    An innate immunity pathway in the moss Physcomitrella patens

    Bressendorff, Simon, Azevedo da Silva, R., Kenchappa, C. S., Ponce de León, I., Olsen, J. V., Rasmussen, M. W., Erbs, G., Newman, Mari-Anne, Petersen, Morten & Mundy, J., 2016, In: The Plant Cell. 28, 6, p. 1328-1342 16 p.

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

  42. Published

    Archaeal physiology: the secrets of termination

    Garrett, Roger Antony, 2016, In: Nature Microbiology. 1, 2 p., 16159.

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

  43. Published

    Barley plants over-expressing the NAC transcription factor gene HvNAC005 show stunting and delay in development combined with early senescence

    Christiansen, M. W., Matthewman, C., Podzimska-Sroka, D. A., O'Shea, Charlotte, Lindemose, Søren, Møllegaard, Niels Erik, Holme, I. B., Hebelstrup, K., Skriver, Karen & Gregersen, P. L., 2016, In: Journal of Experimental Botany. 67, 17, p. 5259-5273 15 p.

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

  44. Published

    Cdc14 phosphatase: warning, no delay allowed for chromosome segregation!

    Machín, F., Quevedo Rodriguez, O., Ramos-Pérez, C. & García-Luis, J., 2016, In: Current Genetics. 62, 1, p. 7-13 7 p.

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

  45. Published

    Characterizing leader sequences of CRISPR loci

    Alkhnbashi, O., Shah, S. A., Garrett, Roger Antony, Saunders, S. J., Costa, F. & Backofen, R., 2016, In: Bioinformatics. 32, 17, p. i576-i585 10 p.

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

  46. Published

    Construction and characterization of three protein-targeting expression system in Lactobacillus casei

    Lin, J., Zou, Y., Ma, C., Liang, Y., Ge, X., Chen, Z. & She, Q., 2016, In: F E M S Microbiology Letters. 363, 7, 8 p.

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

  47. Published

    DNA replication control is linked to genomic positioning of control regions in Escherichia coli

    Frimodt-Møller, Jakob, Charbon, Godefroid, Krogfelt, K. A. & Løbner-Olesen, Anders, 2016, In: P L o S Genetics. 12, 9, 27 p., e1006286.

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

  48. Published

    Discovery and characterization of a thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate

    Zarafeta, D., Kissas, D., Sayer, C., Islin, S. R., Ladoukakis, E., Isupov, M. N., Chatziioannou, A., Peng, Xu, Littlechild, J. A., Skretas, G. & Kolisis, F. N., 2016, In: P L o S One. 11, 1, 18 p., e0146454.

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

  49. Published

    Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species

    Guannan, L., She, Q. & Garrett, Roger Antony, 2016, In: Nucleic Acids Research. 44, 9, p. 4233-4242 10 p.

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

  50. Published

    Diverse gene functions in a soil mobilome

    Luo, W., Xu, Z., Riber, Leise, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2016, In: Soil Biology & Biochemistry. 101, p. 175-183 9 p.

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

  51. Published

    Epidemiological factors associated with ESBL- and non ESBL-producing E. coli causing urinary tract infection in general practice

    Hertz, F. B., Schønning, K., Rasmussen, S. C., Littauer, P., Knudsen, J. D., Løbner-Olesen, Anders & Frimodt-Møller, N., 2016, In: Infectious Diseases. 48, 3, p. 241-245 5 p.

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

  52. Published

    EstDZ3: a new esterolytic enzyme exhibiting remarkable thermostability

    Zarafeta, D., Szabo, Z., Moschidi, D., Phan, Safir Hien, Chrysina, E. D., Peng, Xu, Ingham, C. J., Kolisis, F. N. & Skretas, G., 2016, In: Frontiers in Microbiology. 7, 14 p., 1779.

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

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