Tomáš Brůna

The paper describes Sissivirus, a giant virus with a 4-megabase genome and a large repeatome, identifying repeat accumulation as a key driver of its genome expansion.

GLARE is a TE classifier that outperforms existing methods across multiple taxonomic groups and sequence quality conditions using a genomic language model fine-tuned on harmonized reference data.

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.

This study shows that cold acclimation in Brassica rapa involves diel retiming, paralog-specific regulation, and conserved regulatory programs masked by paralog diversification.

This study identifies WOX1 mutations as the genetic basis of the prickleless S locus in blackberry and red raspberry, enabling gene editing to create prickleless cultivars.

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

The paper catalogs structural and sequence variation in the pennycress pangenome, revealing contrasting evolutionary modes across genomic regions and highlighting the utility of pangenomic resources for crop development.

The paper evaluates challenges in creating consistent pangene sets across pangenomes, showing that annotation inconsistencies lead to misleading presence-absence variation interpretations.

This study identifies a genomic region on chromosome Ra03 associated with primocane-fruiting in tetraploid blackberries and develops diagnostic markers for breeding.

The paper identifies dopamine biosynthesis pathway in plants using metabolite-based genome-wide association studies and demonstrates its role in tissue browning and stress tolerance.

This study presents a chromosome-level genome of Myrothamnus flabellifolia and transcriptomic data, revealing its desiccation tolerance mechanisms and sex determination system.

The paper expands the database of giant virus genomes, identifies new viral taxa and functions, and highlights potential biotechnological applications.

The paper presents an improved haplotype-resolved genome assembly for Eucalyptus grandis, increasing gene annotation completeness and revealing structural variations and tandem duplicates.

GVClass identifies and classifies giant virus genomes with high precision and provides quality assessments for genome completeness and contamination.

This paper presents an updated soybean genome assembly (Wm82.a6) and compares it with other assemblies and Fiskeby III, revealing genomic heterogeneity and polymorphisms.

GeneMark-ETP improves gene prediction accuracy in large eukaryotic genomes by integrating genomic, transcriptomic, and protein evidence, outperforming existing tools.

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

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

The paper presents a chromosome-length genome assembly and annotation of the blackberry species Rubus argutus, identifying candidate genes for primocane-fruiting.

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.

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.

The paper identifies a disproportionate incorporation of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii compared to nuclear DNA, linked to elevated ATP levels.

The paper introduces GeneMark-EP and -EP+, which improve eukaryotic gene prediction by integrating protein database information, showing better accuracy than previous methods, especially in large genomes.