Computational and RNA Biology

  1. 2022
  2. E-pub ahead of print

    NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

    Høie, Magnus Haraldson, Kiehl, E. N., Petersen, Bent, Nielsen, M., Winther, Ole, Nielsen, H., Hallgren, J. & Marcatili, P., 1 Jun 2022, (E-pub ahead of print) In: Nucleic Acids Research. 6 p., gkac439.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. E-pub ahead of print

    Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

    YANG, Meng, Huang, L., Huang, H., Tang, H., Zhang, N., Yang, H., Wu, J. & Mu, F., 10 May 2022, (E-pub ahead of print) In: Nucleic Acids Research. 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. E-pub ahead of print

    PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

    Thieffry, A., Lopéz Márquez, Diego, Bornholdt, J., Gholami Malekroudi, Mojgan, Bressendorff, S., Barghetti, A., Sandelin, Albin Gustav & Brodersen, Peter, 11 Apr 2022, (E-pub ahead of print) In: The Plant Cell. 23 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. E-pub ahead of print

    DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

    Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, Ole, Apr 2022, (E-pub ahead of print) In: Nucleic Acids Research.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    African climate and geomorphology drive evolution and ghost introgression in sable antelope

    Rocha, J. L., Vaz Pinto, P., Siegismund, Hans Redlef, Meyer, M., Jansen van Vuuren, B., Veríssimo, L., Ferrand, N. & Godinho, R., 2022, In: Molecular Ecology. 31, 10, p. 2968-2984 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    An update on principles of m6A targeting

    Bai, Bing, 2022, In: Trends in Plant Science. 27, 3, p. 224-226 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Ancient and historical DNA in conservation policy

    Jensen, E. L., Díez-del-Molino, D., Gilbert, M Thomas P, Bertola, Laura, Borges, F., Cubric-Curik, V., de Navascués, M., Frandsen, P., Heuertz, M., Hvilsom, C., Jiménez-Mena, B., Miettinen, A., Moest, M., Chrzanová Pecnerová, Patrícia, Barnes, I. & Vernesi, C., 2022, In: Trends in Ecology and Evolution. 37, 5, p. 420-429 10 p.

    Research output: Contribution to journalReviewResearchpeer-review

  9. Published

    Bioinformatics of transcription factor binding prediction

    Navarro-Delgado, E. I., Salgado-Albarrán, M., Torres-Arciga, K., Alcaraz, N., Soto-Reyes, E., Herrera, L. A. & González-Barrios, R., 2022, Bioinformatics and Human Genomics Research. CRC Press, p. 203-221 19 p.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  10. Published

    CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

    Corsi, Giulia, Qu, Kunli, Alkan, F., Pan, X., Luo, Y. & Gorodkin, Jan, 2022, In: Nature Communications. 13, 14 p., 3006.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Calibrated uncertainty for molecular property prediction using ensembles of message passing neural networks

    Busk, J., Jørgensen, P. B., Bhowmik, A., Schmidt, M. N., Winther, Ole & Vegge, T., 2022, In: Machine Learning: Science and Technology. 3, 1, 12 p., 015012.

    Research output: Contribution to journalJournal articleResearchpeer-review

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