Katharina J. Hoff

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

The paper reports the genome of Candidatus Argioplasma dusa, a spider symbiont, and finds it has a small genome with limited biosynthetic capabilities, suggesting an endosymbiotic lifestyle.

This study identifies ancient RNA virus genomes in Adelie penguin mummies, revealing viral sequences from specimens up to 2000 years old.

The paper annotates 200 insect genomes using BRAKER3 and VARUS to enable consistent comparative genomics analyses across species.

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

Tiberius is a deep learning gene predictor that integrates HMMs with CNNs and LSTMs, achieving high accuracy in mammalian genomes.

BRAKER3 improves eukaryotic genome annotation by integrating RNA-seq, protein data, and statistical models, achieving higher accuracy than previous tools.

The paper sequences and analyzes the genome of the sour cherry cultivar Schattenmorelle to reveal its segmental allopolyploid structure and evolutionary history.

GALBA is a fully automated gene annotation pipeline combining miniprot and AUGUSTUS, achieving high accuracy in large vertebrate genomes and new species.

TSEBRA selects gene predictions from BRAKER1 and BRAKER2 outputs by comparing transcript scores based on RNA-seq and protein evidence, achieving higher accuracy than either pipeline alone.

The paper presents a chromosome-level genome assembly of tetraploid ground cherry using long-read sequencing technology and reports annotated genes and plastid sequences.

BRAKER2 improves eukaryotic genome annotation by integrating GeneMark-EP+ and AUGUSTUS with cross-species protein sequences, achieving higher accuracy than MAKER2 and BRAKER1 in certain conditions.

VARUS samples RNA reads from the Sequence Read Archive to enable automated genome annotation with high sensitivity and specificity.

MakeHub automates the creation of UCSC Genome Browser Assembly Hubs, simplifying the process for non-bioinformatics users.