Functional Genomics

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  1. 2023
  2. Published

    Molecular Regulation of SpoT

    Schicketanz, Muriel Leandra, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 190 p.

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

  3. Published

    Molecular basis for inhibition of type III-B CRISPR-Cas by an archaeal viral anti-CRISPR protein

    Lin, Jinzhong, Alfastsen, L., Bhoobalan, Yuvaraj & Peng, Xu, 2023, In: Cell Host and Microbe. 31, 11, p. 1837-1849.e5 19 p.

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

  4. Published

    Regulation of ARF7 in Arabidopsis thaliana during lateral root formation and pluripotency acquisition

    Ebstrup, E. N., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 102 p.

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

  5. Published

    Replication Protein Rep Provides Selective Advantage to Viruses in the Presence of CRISPR-Cas Immunity

    Zhang, W., Bhoobalan-Chitty, Y., Zhai, Xichuan, Hui, Y., Hansen, Lars Hestbjerg, Deng, Ling & Peng, Xu, 2023, In: CRISPR Journal. 6, 1, p. 32-42

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

  6. Published

    Revised fission yeast gene and allele nomenclature guidelines for machine readability

    Lera-ramírez, M., Bähler, J., Mata, J., Rutherford, K., Hoffman, C. S., Lambert, S., Oliferenko, S., Martin, S. G., Gould, K. L., Du, L., Sabatinos, S. A., Forsburg, S. L., Nielsen, Olaf, Nurse, P. & Wood, V., 2023, In: Genetics. 225, 3, 10 p., iyad143.

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

  7. Published

    Ribose 5-phosphate: the key metabolite bridging the metabolisms of nucleotides and amino acids during stringent response in Escherichia coli?

    Grucela, Paulina Katarzyna, Fuhrer, T., Sauer, U., Chao, Y. & Zhang, Yong, 2023, In: Microbial Cell. 10, 7, p. 141-144

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

  8. Published

    Searches for Neutrinos from Large High Altitude Air Shower Observatory Ultra-high-energy γ-Ray Sources Using the IceCube Neutrino Observatory

    Abbasi, R., Ackermann, M., Adams, J., Aggarwal, N., Aguilar, J. A., Ahlers, M., Alameddine, J. M., Alves, A. A., Amin, N. M., Andeen, K., Anderson, T., Anton, G., Argüelles, C., Ashida, Y., Athanasiadou, S., Axani, S. N., Bai, X., Balagopal, V. A., Baricevic, M., Barwick, S. W. & 369 others, Basu, V., Bay, R., Beatty, J. J., Becker, K. H., Tjus, J. B., Beise, J., Bellenghi, C., Benda, S., BenZvi, S., Berley, D., Bernardini, E., Besson, D. Z., Binder, G., Bindig, D., Blaufuss, E., Blot, S., Bontempo, F., Book, J. Y., Borowka, J., Meneguolo, C. B., Böser, S., Botner, O., Böttcher, J., Bourbeau, E., Braun, J., Brinson, B., Brostean-Kaiser, J., Burley, R. T., Busse, R. S., Campana, M. A., Carnie-Bronca, E. G., Chang, Y. L., Chen, C., Chen, Z., Chirkin, D., Choi, K., Clark, B. A., Classen, L., Coleman, A., Collin, G. H., Connolly, A., Conrad, J. M., Coppin, P., Correa, P., Countryman, S., Cowen, D. F., Dappen, C., Dave, P., De Clercq, C., DeLaunay, J. J., López, D. D., Dembinski, H., Deoskar, K., Desai, A., Desiati, P., de Vries, K. D., de Wasseige, G., DeYoung, T., Diaz, A., Díaz-Vélez, J. C., Dittmer, M., Dujmovic, H., DuVernois, M. A., Ehrhardt, T., Eller, P., Engel, R., Erpenbeck, H., Evans, J., Evenson, P. A., Fan, K. L., Fazely, A. R., Fedynitch, A., Feigl, N., Fiedlschuster, S., Fienberg, A. T., Finley, C., Fischer, L., Fox, D., Franckowiak, A., Friedman, E., Fritz, A., Fürst, P., Gaisser, T. K., Gallagher, J., Ganster, E., Garcia, A., Garrappa, S., Gerhardt, L., Ghadimi, A., Glaser, C., Glauch, T., Glüsenkamp, T., Goehlke, N., Gonzalez, J. G., Goswami, S., Grant, D., Gray, Simon, Grégoire, T., Griswold, S., Günther, C., Gutjahr, P., Haack, C., Hallgren, A., Halliday, R., Halve, L., Halzen, F., Hamdaoui, H., Minh, M. H., Hanson, K., Hardin, J., Harnisch, A. A., Hatch, P., Haungs, A., Helbing, K., Hellrung, J., Henningsen, F., Heuermann, L., Hickford, S., Hidvegi, A., Hill, C., Hill, G. C., Hoffman, K. D., Hoshina, K., Hou, W., Huber, T., Hultqvist, K., Hünnefeld, M., Hussain, R., Hymon, K., In, S., Iovine, N., Ishihara, A., Jansson, M., Japaridze, G. S., Jeong, M., Jin, M., Jones, B. J. P., Kang, D., Kang, W., Kang, X., Kappes, A., Kappesser, D., Kardum, L., Karg, T., Karl, M., Karle, A., Katz, U., Kauer, M., Kelley, J. L., Kheirandish, A., Kin, K., Kiryluk, J., Klein, S. R., Kochocki, A., Koirala, R., Kolanoski, H., Kontrimas, T., Köpke, L., Kopper, C., Koskinen, D. Jason, Koundal, P., Kovacevich, M., Kowalski, M., Kozynets, T., Kruiswijk, K., Krupczak, E., Kun, E., Kurahashi, N., Lad, N., Gualda, C. L., Lamoureux, M., Larson, M. J., Lauber, F., Lazar, J. P., Lee, J. W., DeHolton, K. L., Leszczyńska, A., Lincetto, M., Liu, Q. R., Liubarska, M., Lohfink, E., Love, C., Mariscal, C. J. L., Lu, L., Lucarelli, F., Ludwig, A., Luszczak, W., Lyu, Y., Ma, W. Y., Madsen, J., Mahn, K. B. M., Makino, Y., Mancina, S., Sainte, W. M., Mariş, I. C., Marka, S., Marka, Z., Marsee, M., Martinez-Soler, I., Maruyama, R., Mayhew, F., McElroy, T., McNally, F., Mead, J. V., Meagher, K., Mechbal, S., Medina, A., Meier, M., Meighen-Berger, S., Merckx, Y., Micallef, J., Mockler, D., Montaruli, T., Moore, R. W., Morse, R., Moulai, M., Mukherjee, T., Naab, R., Nagai, R., Naumann, U., Nayerhoda, A., Necker, J., Neumann, M., Niederhausen, H., Nisa, M. U., Noell, A., Nowicki, S. C., Pollmann, A. O., Oehler, M., Oeyen, B., Olivas, A., Orsoe, R., Osborn, J., O’Sullivan, E., Pandya, H., Pankova, D. V., Park, N., Parker, G. K., Paudel, E. N., Paul, L., de los Heros, C. P., Peterson, J., Philippen, S., Pieper, S., Pizzuto, A., Plum, M., Popovych, Y., Porcelli, A., Rodriguez, M. P., Pries, B., Procter-Murphy, R., Przybylski, G. T., Raab, C., Rack-Helleis, J., Rameez, M., Rawlins, K., Rechav, Z., Rehman, A., Reichherzer, P., Renzi, G., Resconi, E., Reusch, S., Rhode, W., Richman, M., Riedel, B., Roberts, E. J., Robertson, S., Rodan, S., Roellinghoff, G., Rongen, M., Rott, C., Ruhe, T., Ruohan, L., Ryckbosch, D., Cantu, D. R., Safa, I., Saffer, J., Salazar-Gallegos, D., Sampathkumar, P., Sanchez Herrera, S. E., Sandrock, A., Santander, M., Sarkar, S., Sarkar, S., Savelberg, J., Schaufel, M., Schieler, H., Schindler, S., Schlueter, B., Schmidt, T., Schneider, J., Schröder, F. G., Schumacher, L., Schwefer, G., Sclafani, S., Seckel, D., Seunarine, S., Sharma, A., Shefali, S., Shimizu, N., Silva, M., Skrzypek, B., Smithers, B., Snihur, R., Soedingrekso, J., Søgaard, A., Soldin, D., Spannfellner, C., Spiczak, G. M., Spiering, C., Stamatikos, M., Stanev, T., Stein, R., Stezelberger, T., Stürwald, T., Stuttard, Thomas Simon, Sullivan, G. W., Taboada, I., Ter-Antonyan, S., Thompson, W. G., Thwaites, J., Tilav, S., Tollefson, K., Tönnis, C., Toscano, S., Tosi, D., Trettin, A., Tung, C. F., Turcotte, R., Twagirayezu, J. P., Ty, B., Elorrieta, M. A. U., Upshaw, K., Valtonen-Mattila, N., Vandenbroucke, J., Eijndhoven, N. V., Vannerom, D., Santen, J. V., Vara, J., Veitch-Michaelis, J., Verpoest, S., Veske, D., Walck, C., Wang, W., Watson, T. B., Weaver, C., Weigel, P., Weindl, A., Weldert, J., Wendt, C., Werthebach, J., Weyrauch, M., Whitehorn, N., Wiebusch, C. H., Willey, N., Williams, D. R., Wolf, M., Wrede, G., Wulff, J., Xu, D. L., Xu, X. W., Yanez, J. P., Yasutsugu, M., Yildizci, E., Yoshida, S., Yu, S., Yuan, T., Zhang, Z. & Zhelnin, P., 2023, In: Astrophysical Journal Letters. 945, 1, 11 p., L8.

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

  9. 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

  10. Published

    Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma

    Zhang, R., Feng, Y., Ma, W., Guo, Y., Luo, M., Li, Y., Zang, Y., Dong, X., Lu, S., Guo, Q., Xu, Q., Chen, H., Li, Y., Liu, L., CHEN, Ao, Chen, G. & Xu, X., 2023, In: Fundamental Research. 3, 4, 7 p.

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

  11. Published

    Structural basis for kinase inhibition in the tripartite E. coli HipBST toxin-antitoxin system

    Bærentsen, R. L., Nielsen, S. V., Skjerning, R. B., Lyngsø, J., Bisiak, F., Pedersen, J. S., Gerdes, K., Sørensen, Michael Askvad & Brodersen, D. E., 2023, In: eLife. 12, 20 p., RP90400.

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

  12. Published

    Temporal phosphoproteomics reveals WEE1-dependent control of 53BP1 pathway

    Petrosius, V., Benada, Jan, Nielsen, Olaf, Schoof, E. M. & Sørensen, Claus Storgaard, 2023, In: iScience. 26, 1, 24 p., 105806.

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

  13. Published

    The Discovery of Anti-defense Genes in Archaea

    Xu, Shuanshuan, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 117 p.

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

  14. Published

    The Role of ZGRF1 in Recombinational Repair and Telomere Stability Maintenance

    Bagge, Keerthana Stine Viswalingam, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 179 p.

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

  15. Published

    The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development

    Zuo, Zhangli Thomsen, Roux, M. E., Chevalier, J. R., Dagdas, Y. F., Yamashino, T., Højgaard, S. D., Knight, E., Østergaard, L., Rodriguez, Eleazar & Petersen, Morten, 2023, In: Life Science Alliance. 6, 9, 11 p.

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

  16. Published

    Where is the field of autophagy research heading?

    Abeliovich, H., Debnath, J., Ding, W. X., Jackson, W. T., Kim, D. H., Klionsky, D. J., Ktistakis, N., Margeta, M., Münz, C., Petersen, Morten, Sadoshima, J. & Vergne, I., 2023, In: Autophagy. 19, 4, 6 p.

    Research output: Contribution to journal › Editorial › Research

  17. Published

    ZGRF1 Contributes to DNA Repair, Secondary DNA Structure Regulation, and Transcriptional Alteration

    Simonsen, Anne Katrine Wrist, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 153 p.

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

  18. Published

    cAMP competitively inhibits periplasmic phosphatases to coordinate nutritional growth with competence of Haemophilus influenzae

    Kronborg, Kristina & Zhang, Yong, 2023, In: Journal of Biological Chemistry. 299, 12, 13 p., 105404.

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

  19. 2022
  20. Published

    Investigating the value of immersive virtual reality tools for organizational training: An applied international study in the biotech industry

    Baceviciute, S., Cordoba, A. L., Wismer, P., Jensen, T. V., Klausen, M. & Makransky, Guido, Apr 2022, In: Journal of Computer Assisted Learning. 38, 2, p. 470-487

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

  21. 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

  22. 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

  23. 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

  24. 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

  25. Published

    CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

    Pinilla Redondo, Rafael, Russel, J., Mayo-Muñoz, D., Shah, S. A., Garrett, Roger Antony, Nesme, Joseph, Madsen, Jonas Stenløkke, Fineran, P. C. & Sørensen, Søren Johannes, 2022, In: Nucleic Acids Research. 50, 8, p. 4315-4328

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

  26. Published

    Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets

    Han, L., Lan, T., Li, D., Li, H., Deng, L., Peng, Z., He, S., Zhou, Y., Han, R., Li, L., Lu, Y., Lu, H., Wang, Q., Yang, S., Zhu, Y., Huang, Y., Cheng, X., Yu, J., Wang, Y., Sun, H. & 8 others, Chai, H., Yang, H., Xu, X., Lisby, Michael, Liu, Q., Kristiansen, Karsten, Liu, Huan & Hou, Z., 2022, In: Molecular Ecology Resources. 22, 2, p. 768-785 18 p.

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

  27. Published

    Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

    Yang, T., Sahu, S. K., Yang, L., Liu, Y., Mu, W., Liu, X., Strube, M. L., Liu, Huan & Zhong, B., 2022, In: Frontiers in Plant Science. 13, 13 p., 808156.

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

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