Publications & Talks

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Gabriel, L., Brůna, T., Kaur, A., Krishnan, A., Ortmann, F., Salamov, A., Talbot, S., Becker, F., Krieg, R., Wheat, C. W., Grigoriev, I. V., Stanke, M. & Hoff, K. J.

bioRxiv · (2026)

Extends Tiberius toward accurate ab initio gene prediction across multiple eukaryotic clades.

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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)

Introduces a deep learning-based gene prediction tool that end-to-end integrates a Hidden Markov Model for eukaryotic genome annotation.

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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)

Describes a fully automated genome annotation workflow integrating RNA-seq and protein evidence.

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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)

Contributes genome annotation expertise to a reference genome supporting ecological restoration work.

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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)

Presents a protein-informed annotation workflow using miniprot and AUGUSTUS.

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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)

Applies genome annotation methods in a plant genome project focused on polyploid genome structure.

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TSEBRA: Transcript Selector for BRAKER

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

BMC Bioinformatics · 22(1), 566 (2021)

Presents a transcript selection method for combining and filtering gene predictions in BRAKER workflows.

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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)

Contributes genome annotation to a chromosome-level plant genome assembly project.

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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)

Provides practical guidance for using BRAKER, Galba, and TSEBRA in eukaryotic genome annotation workflows.

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Tiberius: Progress on Gene Prediction with Deep Learning

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

Plant and Animal Genomes Conference 32 · January 2025

Talk

Ab Initio Gene Prediction with Tiberius Matches Gene Prediction Accuracy of BRAKER3

Gabriel, L., Brůna, T., Kaur, A., Krishnan, A., Ortmann, F., Salamov, A., Grigoriev, I. V., Talbot, S., Wheat, C. W., Becker, F., Krieg, R., Hoff, K. J. & Stanke, M.

AI & Genome Annotation Workshop · Hinxton, United Kingdom (2025)

Talk

The BRAKER3 Genome Annotation Pipeline

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

Plant and Animal Genomes XXX · January 15, 2023

Talk, Poster

TSEBRA: Integrating Various Extrinsic Evidence Sources for More Accurate Genome Annotation with BRAKER

Gabriel, L., Hoff, K. J., Thierfeldt, H., Brůna, T., Borodovsky, M. & Stanke, M.

Plant and Animal Genomes XXIX · January 9, 2022

Talk, Poster