Functional Genomics

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  1. Published

    Countermeasures to survive excessive chromosome replication in Escherichia coli

    Charbon, Godefroid, Riber, Leise & Løbner-Olesen, Anders, 2018, In: Current Genetics. 64, 1, p. 71-79 9 p.

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

  2. Published

    Key role of Ser562/661 in Snf1-dependent regulation of Cat8p in Saccharomyces cerevisiae and Kluyveromyces lactis

    Charbon, Godefroid, Breunig, K. D., Wattiez, R., Vandenhaute, J. & Noël-Georis, I., May 2004, In: Molecular and Cellular Biology. 24, 10, p. 4083-91 9 p.

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

  3. Published

    Energy Starvation Induces a Cell Cycle Arrest in Escherichia coli by Triggering Degradation of the DnaA Initiator Protein

    Charbon, Godefroid, Mendoza-Chamizo, B., Campion, C., Li, X., Jensen, P. R., Frimodt-Møller, Jakob & Løbner-Olesen, Anders, 2021, In: Frontiers in Molecular Biosciences. 8, 9 p., 629953.

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

  4. 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

  5. Published

    Counting Replication Origins to Measure Growth of Pathogens

    Charbon, Godefroid, Haugan, M. S., Frimodt-Møller, N. & Løbner-Olesen, Anders, 2020, In: Antibiotics. 9, 5, 5 p., 239.

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

  6. Published

    Rad52 SUMOylation functions as a molecular switch that determines a balance between the Rad5- and Rad59-dependent survivors

    Charifi, F., Churikov, D., Eckert-Boulet, N., Minguet, C., Jourquin, F., Hardy, J., Lisby, Michael, Simon, M. N. & Géli, V., 2021, In: iScience. 24, 3, 26 p., 102231.

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

  7. Published

    Integrity of a heterochromatic domain ensured by its boundary elements

    Charlton, Sebastian Jespersen, Jørgensen, M. M. & Thon, Genevieve, 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 35, p. 21504-21511 8 p.

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

  8. Published

    Analysis of heterochromatin dynamics in Schizosaccharomyces pombe: With a special focus on the role of the replication factor Mrc1/Claspin in maintenance of epigenetic silencing

    Charlton, Sebastian Jespersen, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 138 p.

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

  9. 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

  10. Published

    Srs2 promotes Mus81-Mms4-mediated resolution of recombination intermediates

    Chavdarova, M., Marini, V., Sisakova, A., Sedlackova, H., Vigasova, D., Brill, S. J., Lisby, Michael & Krejci, L., 2015, In: Nucleic Acids Research. 43, 7, p. 3626-3642 17 p.

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

  11. Published

    Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

    Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., Wang, X., Lu, H., Chen, X., Liu, X., Huang, X., Li, Z., Hong, Y., Jiang, Y., Peng, J., Liu, S. & 49 others, Shen, M., Liu, C., Li, Q., Yuan, Y., Wei, X., Zheng, H., Feng, W., Wang, Z., Liu, Y., Wang, Z., Yang, Y., Xiang, H., Han, L., Qin, B., Guo, P., Lai, G., Muñoz-Cánoves, P., Maxwell, P. H., Thiery, J. P., Wu, Q., Zhao, F., Chen, B., Li, M., Dai, X., Wang, S., Kuang, H., Hui, J., Wang, L., Fei, J., Wang, O., Wei, X., Lu, H., Wang, B., Liu, S., Gu, Y., Ni, M., Zhang, W., Mu, F., Yin, Y., Yang, H., Lisby, Michael, Cornall, R. J., Mulder, J., Uhlén, M., Esteban, M. A., Li, Y., Liu, L., Xu, X. & Wang, J., 2022, In: Cell. 185, 10, p. 1777-1792.e21

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

  12. Published

    Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex

    Chen, A., Sun, Y., Lei, Y., Li, C., Liao, S., Meng, J., Bai, Y., Liu, Z., Liang, Z., Zhu, Z., Yuan, N., Yang, H., Wu, Z., Lin, F., Wang, K., Li, M., Zhang, S., Yang, M., Fei, T., Zhuang, Z. & 85 others, Huang, Y., Zhang, Y., Xu, Y., Cui, L., Zhang, R., Han, L., Sun, X., Chen, B., Li, W., Huangfu, B., Ma, K., Ma, J., Li, Z., Lin, Y., Wang, H., Zhong, Y., Zhang, H., Yu, Q., Wang, Y., Liu, X., Peng, J., Liu, C., Chen, W., Pan, W., An, Y., Xia, S., Lu, Y., Wang, M., Song, X., Liu, S., Wang, Z., Gong, C., Huang, X., Yuan, Y., Zhao, Y., Chai, Q., Tan, X., Liu, J., Zheng, M., Li, S., Huang, Y., Hong, Y., Huang, Z., Li, M., Jin, M., Li, Y., Zhang, H., Sun, S., Gao, L., Bai, Y., Cheng, M., Hu, G., Liu, S., Wang, B., Xiang, B., Li, S., Li, H., Chen, M., Wang, S., Li, M., Liu, W., Liu, X., Zhao, Q., Lisby, Michael, Wang, J., Fang, J., Lin, Y., Xie, Q., He, J., Xu, H., Huang, W., Mulder, J., Yang, H., Sun, Y., Uhlen, M., Poo, M., Wang, J., Yao, J., Wei, W., Li, Y., Shen, Z., Liu, L., Liu, Z., Xu, X. & Li, C., 2023, In: Cell. 186, 17, p. 3726-3743.e24 43 p.

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

  13. 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

  14. Published

    RPA coordinates DNA end resection and prevents formation of DNA hairpins

    Chen, H., Lisby, Michael & Symington, L. S., 2013, In: Molecular Cell. 50, 4, p. 589-600 12 p.

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

  15. E-pub ahead of print

    International consensus guidelines for the definition, detection, and interpretation of autophagy-dependent ferroptosis

    Chen, X., Tsvetkov, A. S., Shen, H., Isidoro, C., Ktistakis, N. T., Linkermann, A., Koopman, W. J. H., Simon, H., Galluzzi, L., Luo, S., Xu, D., Gu, W., Peulen, O., Cai, Q., Rubinsztein, D. C., Chi, J., Zhang, D. D., Li, C., Toyokuni, S., Liu, J. & 49 others, Roh, J., Dai, E., Juhasz, G., Liu, W., Zhang, J., Yang, M., Liu, J., Zhu, L., Zou, W., Piacentini, M., Ding, W., Yue, Z., Xie, Y., Petersen, Morten, Gewirtz, D. A., Mandell, M. A., Chu, C. T., Sinha, D., Eftekharpour, E., Zhivotovsky, B., Besteiro, S., Gabrilovich, D. I., Kim, D., Kagan, V. E., Bayir, H., Chen, G., Ayton, S., Lünemann, J. D., Komatsu, M., Krautwald, S., Loos, B., Baehrecke, E. H., Wang, J., Lane, J. D., Sadoshima, J., Yang, W. S., Gao, M., Münz, C., Thumm, M., Kampmann, M., Yu, D., Lipinski, M. M., Jones, J. W., Jiang, X., Zeh, H. J., Kang, R., Klionsky, D. J., Kroemer, G. & Tang, D., 2024, (E-pub ahead of print) In: Autophagy. p. 1-34

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

  16. Published

    Novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates

    Chen, Z., Liu, Y., Wu, J., She, Q., Jiang, C. & Liu, S., 2007, In: Applied Microbiology and Biotechnology. 74, 3, p. 688-98 10 p.

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

  17. Published

    Characterization of pMC11, a plasmid with dual origins of replication isolated from Lactobacillus casei MCJ and construction of shuttle vectors with each replicon

    Chen, Z., Lin, J., Ma, C., Zhao, S., She, Q. & Liang, Y., 2014, In: Applied Microbiology and Biotechnology. 98, 13, p. 5977-5989 13 p.

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

  18. Published

    Autophagy mediate cellular reprogramming

    Chevalier, J. R., 2020, Department of Biology, Faculty of Science, University of Copenhagen.

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

  19. Published

    Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2013, In: PLoS ONE. 8, 12, 10 p., e84123.

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

  20. Published

    Mik1 levels accumulate in S phase and may mediate an intrinsic link between S phase and mitosis

    Christensen, P. U., Bentley, N. J., Martinho, R. G., Nielsen, O., Carr, A. & Nielsen, Olaf, 14 Mar 2000, In: Proceedings of the National Academy of Sciences of the United States of America. 97, 6, p. 2579-84 6 p.

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

  21. Published

    Abc1: a new ABC transporter from the fission yeast Schizosaccharomyces pombe

    Christensen, P. U., Davis, K., Nielsen, O., Davey, W. J. & Nielsen, Olaf, 1 Feb 1997, In: F E M S Microbiology Letters. 147, 1, p. 97-102 6 p.

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

  22. Published

    The Schizosaccharomyces pombe mam1 gene encodes an ABC transporter mediating secretion of M-factor

    Christensen, P. U., Davey, W. J., Nielsen, O. & Nielsen, Olaf, 1 Jun 1997, In: Molecular and General Genetics MGG. 255, 2, p. 226-36 11 p.

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

  23. 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

  24. Published

    Isolation of a novel protein, P12-from adult Drosophila melanogaster that inhibits deoxyribonucleoside and protein kinase activities and activates 3'-5'-exonuclease activity

    Christiansen, L. S., Zanten, G. V., Berenstein, D., Lauridsen, M., Kjærulff, S., Søndergaard, Leif & Munch-Petersen, B., 2016, In: Nucleosides, Nucleotides and Nucleic Acids. 35, 10-12, p. 699-706 8 p.

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

  25. 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

  26. 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

  27. Published

    SUMO-dependent relocalization of eroded telomeres to nuclear pore complexes controls telomere recombination

    Churikov, D., Charifi, F., Eckert-Boulet, N. V., Pinela da Silva, S. C., Simon, M., Lisby, Michael & Géli, V., 2016, In: Cell Reports. 15, 6, p. 1242-1253 12 p.

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

  28. Published

    Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium

    Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W. & 31 others, Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Garcia, A. C. L., Nielsen, Rasmus, Pedersen, J. S., Vieira, Filipe Garrett & Drosophila 12 Genomes Consortium, D. 1. G. C., 2007, In: Nature. 450, 7167, p. 203-18 15 p.

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

  29. Published

    Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

    Bjørnkjær, Lene, Stein, Amelie, Grønbæk-Thygesen, Martin, Nygaard, L., Søltoft, C. L., Nielsen, S. V., Lisby, Michael, Ravid, T., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: PLOS Genetics. 16, 11, 28 p., e1009187.

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

  30. Published

    The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress

    Clausing, E., Mayer, A., Chanarat, S., Müller, B., Germann, S. M., Cramer, P., Lisby, Michael & Strässer, K., 31 Dec 2010, In: Journal of Biological Chemistry. 285, 53, p. 41665-41674 10 p.

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

  31. 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

  32. 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

  33. Published

    Molecular biology of fuselloviruses and their satellites

    Contursi, P., Fusco, S., Cannio, R. & She, Q., 2014, In: Extremophiles. 18, 3, p. 473-489 17 p.

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

  34. Published

    C68 from the Sulfolobus islandicus plasmid-virus pSSVx is a novel member of the AbrB-like transcription factor family

    Contursi, P., D'Ambrosio, K., Pirone, L., Pedone, E., Aucelli, T., She, Q., De Simone, G. & Bartolucci, S., 2011, In: Biochemical Journal. 435, 1, p. 157-66 10 p.

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

  35. Published

    Overexpression of putative NADH oxidases from the hyperthermophilic archaeons Sulfolobus solfataricus and Pyrococcus horikoshii

    Crane III, E. J., Ward, D. E., van der Oost, J., She, Q. & Garrett, Roger Antony, 1999, Flavins and Flavoproteins 1999 (Ghisla, S., Kroneck, P., Macheroux, P., and Sund, H. ed.). Berlin, p. 281-284 4 p.

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

  36. Published

    Regulation of Hed1 and Rad54 binding during maturation of the meiosis-specific presynaptic complex

    Crickard, J. B., Kaniecki, K., Kwon, Y., Sung, P., Lisby, Michael & Greene, E. C., 2018, In: EMBO Journal. 37, 7, 17 p., e98728.

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

  37. Published

    Four additional natural 7-deazaguanine derivatives in phages and how to make them

    Cui, L., Balamkundu, S., Liu, C. F., Ye, H., Hourihan, J., Rausch, A., Hauß, C., Nilsson, E., Hoetzinger, M., Holmfeldt, K., Zhang, W., Martinez-Alvarez, L., Peng, X., Tremblay, D., Moinau, S., Solonenko, N., Sullivan, M. B., Lee, Y. J., Mulholland, A., Weigele, P. R. & 3 others, de Crécy-Lagard, V., Dedon, P. C. & Hutinet, G., 2023, In: Nucleic Acids Research. 51, 17, p. 9214-9226 13 p.

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

  38. Published

    Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments

    Cyriaque, V., Jacquiod, S. J. A., Riber, Leise, Abu Al-Soud, W., Gillan, D. C., Sørensen, Søren Johannes & Wattiez, R., 2020, In: Journal of Hazardous Materials. 382, 10 p., 121173.

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

  39. Published

    A site-specific endonuclease encoded by a typical archaeal intron.

    Dalgaard, J., Garrett, Roger Antony & Belfort, M., 1993, In: Proceedings of the National Academy of Science of the United States of America. 90, 12, p. 5414-5417

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

  40. Published

    Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum

    Dalgaard, J. & Garrett, Roger Antony, 1992, In: Gene. 121, p. 103-110

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

  41. Published

    Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonucleose encoded by an archaeal intron

    Dalgaard, J., Garrett, Roger Antony & Belfort, M., 1994, In: Journal of Biological Chemistry. Vol 269, p. 28885-28892

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

  42. Published

    Identification of the transporter for the M-factor mating pheromone in fission yeast

    Davey, W. J., Christensen, P. U., Nielsen, O. & Nielsen, Olaf, 1 May 1997, In: Biochemical Society Transactions. 25, 2, p. 224S

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

  43. Published

    Mutations in cyr1 and pat1 reveal pheromone-induced G1 arrest in the fission yeast Schizosaccharomyces pombe

    Davey, W. J., Nielsen, O. & Nielsen, Olaf, 1 Aug 1994, In: Current Genetics. 26, 2, p. 105-12 8 p.

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

  44. 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

  45. 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

  46. 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

  47. Published

    Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus

    Deng, Ling, Kenchappa, C. S., Peng, Xu, She, Q. & Garrett, Roger Antony, 2012, In: Nucleic Acids Research. 40, 6, p. 2470-2480 11 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

    Development and Psychometric Evaluation of an Item Bank for Computerized Adaptive Testing of the EORTC Insomnia Dimension in Cancer Patients (EORTC CAT-SL)

    Dirven, L., Petersen, Morten, Aaronson, N. K., Chie, W., Conroy, T., Costantini, A., Hammerlid, E., Velikova, G., Verdonck-de Leeuw, I. M., Young, T. & Grønvold, Mogens, 6 Dec 2019, In: Applied Research in Quality of Life. 18 p.

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

  50. Published

    Theoretical analysis of epigenetic cell memory by nucleosome modification

    Dodd, I. B., Micheelsen, M. A., Sneppen, Kim & Thon, Genevieve, 2007, In: Cell. 129, 4, p. 813-22 10 p.

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

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