Department of Biology

 

 
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  1. 2024
  2. Published

    CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages

    Varming, A. K., Huang, Zhiyu, Hamad, G. M., Rasmussen, K. K., Ingmer, Hanne, Kilstrup, M. & Lo Leggio, Leila, 2024, In: Microbiome Research Reports. 3, 2, 16 p., 15.

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

  3. Published

    Cadmium accumulation in organisms from a spruce plantation amended with wood ash - an environmental risk?

    Ekelund, Flemming, Cruz-Paredes, C., Jørgensen, Christian Hviid Friis, Vestergård, M., Rasmussen, K. R., Mortensen, Louise Hindborg, Kindtler, Nikolaj Lunding, Rønn, Regin, Christensen, Søren, Johansen, Jesper Liengaard & Kjøller, Rasmus, 2024, In: Trees, Forests and People. 15, 6 p., 100499.

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

  4. Published

    Calls of the little auk (Alle alle) chicks reflect their behavioural contexts

    Osiecka, A. N., Briefer, Elodie, Kidawa, D., Żurawska, F. & Wojczulanis-Jakubas, K., 2024, In: PLoS ONE. 19, 2, 14 p., e0299033.

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

  5. Published

    Can large language models reason about medical questions?

    Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.

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

  6. Published

    Carving out a Glycoside Hydrolase Active Site for Incorporation into a New Protein Scaffold Using Deep Network Hallucination

    Hansen, A. L., Theisen, Frederik Friis, Crehuet, R., Marcos, E., Aghajari, N. & Willemoës, Martin, 2024, In: ACS Synthetic Biology. 13, 3, p. 862-875 14 p.

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

  7. Published

    Cellular and molecular mechanisms of aspartoacylase and its role in Canavan disease

    Grønbæk-Thygesen, Martin & Hartmann-Petersen, Rasmus, 2024, In: Cell and Bioscience. 14, 1, 33 p., 45.

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

  8. Published

    Changes in composition and function of soil microbial communities during secondary succession in oldfields on the Tibetan Plateau

    Ma, Hui, Yan, X., Gao, E., Qiu, Y., Sun, X., Wang, S., Wang, Y., Bruun, Hans Henrik, He, Z., Shi, X. & Zhao, Z., 2024, In: Plant and Soil. 495, p. 429–443 15 p.

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

  9. Published

    Characterizing glucokinase variant mechanisms using a multiplexed abundance assay

    Gersing, S., Schulze, Thea Klarsø, Cagiada, Matteo, Stein, Amelie, Roth, F. P., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2024, In: Genome Biology. 25, 1, 22 p., 98.

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

  10. Published

    Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs

    Olsen, Johan Gotthardt, Prestel, Andreas, Kassem, N., Broendum, S. S., Hossain, Mohammad Shamim, Simonsen, Signe, Grysbæk, M., Mortensen, J., Rytkjær, L. L., Haxholm, G. W., Marabini, R., Holmberg, Christian, Carr, A. M., Crehuet, R., Nielsen, Olaf & Kragelund, Birthe Brandt, 2024, In: Nucleic acids symposium series. 52, 4, p. 2030–2044 15 p.

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

  11. Published

    Cholesterol-binding motifs in STING that control endoplasmic reticulum retention mediate anti-tumoral activity of cholesterol-lowering compounds

    Zhang, B. C., Laursen, M. F., Hu, L., Hazrati, H., Narita, R., Jensen, L. S., Hansen, A. S., Huang, J., Zhang, Y., Ding, X., Muyesier, M., Nilsson, E., Banasik, A., Zeiler, C., Mogensen, T. H., Etzerodt, A., Agger, R., Johannsen, M., Kofod-Olsen, E., Paludan, S. R. & 1 others, Jakobsen, M. R., 2024, In: Nature Communications. 15, 1, 17 p., 2760.

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

  12. Published

    Chromatin image-driven modelling

    Kadlof, M., Banecki, K., Chilinski, Mateusz & Plewczynski, D., 2024, In: Methods. 226, p. 54-60 7 p.

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

  13. Published

    Circle-seq based method for eccDNA synthesis and its application as a canonical promoter independent vector for robust microRNA overexpression

    Yu, J., Zhang, H., Han, Peng, Jiang, X., Li, J., Li, B., Yang, S., He, C., Mao, S., Dang, Y. & Xiang, X., 2024, In: Computational and Structural Biotechnology Journal. 23, p. 358-368 11 p.

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

  14. Published

    ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data

    Duchene, David, Duchêne, S., Stiller, Josefin, Heller, Rasmus & Ho, S. Y. W., 2024, In: Genome Biology and Evolution. 16, 4, 7 p., evae064.

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

  15. Published

    Comment on “DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction”

    Vinther, Jeppe, 2024, In: Analytical Chemistry. 96, 1, p. 606-609 4 p.

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

  16. Published

    Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly

    Hu, T., Chen, J., Lin, X., He, W., Liang, H., Wang, M., Li, W., Wu, Z., Han, Mo, Jin, X., Kristiansen, Karsten, Xiao, L. & Zou, Y., 2024, In: Scientific Reports. 14, 1, 9 p., 1292.

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

  17. Published

    Comprehensive phylogeny of Pieridae butterflies reveals strong correlation between diversification and temperature

    Carvalho, A. P. S., Owens, H. L., St Laurent, R. A., Earl, C., Dexter, K. M., Messcher, R. L., Willmott, K. R., Aduse-Poku, K., Collins, S. C., Homziak, N. T., Hoshizaki, S., Hsu, Y. F., Kizhakke, A. G., Kunte, K., Martins, D. J., Mega, N. O., Morinaka, S., Peggie, D., Romanowski, H. P., Sáfián, S. & 8 others, Vila, R., Wang, H., Braby, M. F., Espeland, M., Breinholt, J. W., Pierce, N. E., Kawahara, A. Y. & Lohman, D. J., 2024, In: iScience. 27, 4, 14 p., 109336.

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

  18. Published

    Conformational ensembles of the human intrinsically disordered proteome

    Tesei, Giulio, Trolle, A. I., Jonsson, Nicolas, Betz, J., Knudsen, F. E., Pesce, Francesco, Johansson, Kristoffer Enøe & Lindorff-Larsen, Kresten, 2024, In: Nature. 626, p. 897-904 8 p.

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

  19. Published

    Controlling biases in targeted plant removal experiments

    Monteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E. J., Lett, Signe, Pedersen, Emily Pickering & Väisänen, M., 2024, In: New Phytologist. 242, 4, p. 1835-1845 11 p.

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

  20. Published

    Crispr-Cas Repurposed: Defense and Counter-defense on Mobile Genetic Elements

    Camara, Sarah, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 186 p.

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

  21. Published

    Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill‑W1 and the human colon cell line HCEC‑1CT

    Varga, E., Prause, H., Riepl, M., Hochmayr, N., Berk, D., Attakpah, E., Kiss, E., Medic, Nikola, Del Favero, G., Larsen, T. O., Hansen, Per Juel & Marko, D., 2024, In: Archives of Toxicology. 98, p. 999–1014 16 p.

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

  22. Published

    DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2

    Bjarnason, S., McIvor, J. A. P., Prestel, Andreas, Demény, K. S., Bullerjahn, J. T., Kragelund, Birthe Brandt, Mercadante, D. & Heidarsson, P. O., 2024, In: Nature Communications. 15, 1, 16 p., 1445.

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

  23. Published

    DNA metabarcoding reveals the impact of Cu2+ on soil cercozoan diversity

    Lourenço, L., Ellegaard Bager, S., Ng, D. Y. K., Sheikh, Sanea, Kindtler, Nikolaj Lunding, Nielsen, Ida Broman, Frøslev, Tobias Guldberg & Ekelund, Flemming, 2024, In: Protist. 175, 2, 9 p., 126016.

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

  24. Published

    Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs

    Ren, H., Shi, Z., Yang, F., Wang, S., Yuan, F., Li, T., Li, M., Zhu, J., Li, J., Wu, K., Zhang, Y., Ning, G., Kristiansen, Karsten, Wang, W., Gu, Y. & Zhong, H., 2024, In: iMeta. 3, 2, 9 p., e179.

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

  25. Published

    DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning

    Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2024, In: Bioinformatics. 40, 2, 10 p., btae065.

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

  26. Published

    DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

    Høie, M. H., Gade, F. S., Johansen, J., Würtzen, C., Winther, Ole, Nielsen, M. & Marcatili, P., 2024, In: Frontiers in Immunology. 15, 12 p., 1322712.

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

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