Gabriel, L., Brůna, T., Hoff, K.J., Ebel, M., Lomsadze, A., Borodovsky, M. and Stanke, M., 2023. BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. Biorxiv. https://doi.org/10.1101/2023.06.10.544449

Schiebelhut, L.M., DeBiasse, M.B., Gabriel, L., Hoff, K.J. and Dawson, M.N., 2024. A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides. Journal of Heredity, 115(1), pp.86-93. https://doi.org/10.1093/jhered/esad054

Brůna, T., Li, H., Guhlin, J., Honsel, D., Herbold, S., Stanke, M., Nenasheva, N., Ebel, M., Gabriel, L. and Hoff, K.J., 2023. Galba: genome annotation with miniprot and AUGUSTUS. BMC bioinformatics, 24(1), p.327. https://doi.org/10.1186/s12859-023-05449-z

Wöhner, T.W., Emeriewen, O.F., Wittenberg, A.H., Nijbroek, K., Wang, R.P., Blom, E.J., Schneiders, H., Keilwagen, J., Berner, T., Hoff, K.J., Gabriel, L., Thierfeldt, H., Almolla, O., Barchi, L., Schuster, M., Lempe, J., Peil, A. and Flachowsky, H., 2023. The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1284478

Gabriel, L., Hoff, K.J., Brůna, T., Borodovsky, M. and Stanke, M., 2021. TSEBRA: transcript selector for BRAKER. BMC bioinformatics, 22(1), pp.1-12. https://doi.org/10.1186/s12859-021-04482-0

Wöhner, T.W., Emeriewen, O.F., Wittenberg, A.H., Schneiders, H., Vrijenhoek, I., Halász, J., Hrotkó, K., Hoff, K.J., Gabriel, L., Lempe, J. and Keilwagen, J., 2021. The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads. Genomics, 113(6), pp.4173-4183. https://doi.org/10.1016/j.ygeno.2021.11.002

Brůna, T., Li, H., Guhlin, J., Honsel, D., Herbold, S., Stanke, M., Nenasheva, N., Ebel, M., Gabriel, L. and Hoff, K.J., Proteins Only: How Accurately Can We Annotate Large Genomes? International Plant & Animal 31 Conference 2024, U.S.A.

Gabriel, L., Hoff, K.J., Brůna, T., Lomsadze, A., Borodovsky, M. and Stanke, M. The BRAKER3 Genome Annotation Pipeline International Plant & Animal XXIX Conference 2023, U.S.A.

The BRAKER3 Genome Annotation Pipeline. International Plant & Animal Genome 30, U.S.A., 2023. https://doi.org/10.13140/RG.2.2.20047.36004

TSEBRA: Integrating various extrinsic evidence sources for more accurate genome annotation with BRAKER. International Plant & Animal Genome 29, U.S.A., 2022. https://doi.org/10.13140/RG.2.2.18144.46080

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