Publications

Selected Publications

Peer-reviewed journal articles, conference papers, and book chapters.

My publications focus primarily on genome annotation, gene prediction, and computational methods for biological sequence analysis.

2024

Tiberius: End-to-End Deep Learning with an HMM for Gene Prediction

Gabriel, L., Becker, F., Hoff, K. J. & Stanke, M.

Bioinformatics 40(12), btae685 (2024)

DOI

BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gabriel, L., Bruna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M. & Stanke, M.

Genome Research 34(5), 769–777 (2024)

DOI

A Reference Genome for Ecological Restoration of the Sunflower Sea Star, Pycnopodia helianthoides

Schiebelhut, L. M., DeBiasse, M. B., Gabriel, L., Hoff, K. J. & Dawson, M. N.

Journal of Heredity 115(1), 86–93 (2024)

DOI

2023

Galba: Genome Annotation with miniprot and AUGUSTUS

Bruna, T., Li, H., Guhlin, J., Honsel, D., Herbold, S., Stanke, M., Nenasheva, N., Ebel, M., Gabriel, L. & Hoff, K. J.

BMC Bioinformatics 24(1), 327 (2023)

DOI

The Structure of the Tetraploid Sour Cherry 'Schattenmorelle' (Prunus cerasus L.) Genome Reveals Insights into Its Segmental Allopolyploid Nature

Wohner, T. W., Emeriewen, O. F., Wittenberg, A. H. J., 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. & Flachowsky, H.

Frontiers in Plant Science 14, 1284478 (2023)

DOI

2021

TSEBRA: Transcript Selector for BRAKER

Gabriel, L., Hoff, K. J., Bruna, T., Borodovsky, M. & Stanke, M.

BMC Bioinformatics 22(1), 566 (2021)

DOI

The Draft Chromosome-Level Genome Assembly of Tetraploid Ground Cherry (Prunus fruticosa Pall.) from Long Reads

Wohner, T. W., Emeriewen, O. F., Wittenberg, A. H. J., Schneiders, H., Vrijenhoek, I., Halasz, J., Hrotko, K., Hoff, K. J., Gabriel, L., Lempe, J., Keilwagen, J., Berner, T., Schuster, M., Peil, A., Wunsche, J. & Flachowsky, H.

Genomics 113(6), 4173–4183 (2021)

DOI

Book Chapters

Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to Using BRAKER, Galba, and TSEBRA

Bruna, T., Gabriel, L. & Hoff, K. J.

In Methods in Molecular Biology 2935, 67–107 (2025)

DOI