Kristian Vlahoviček

Hidden Contaminants in Sponge Genomes: Large-Scale Decontamination of 30 Public Assemblies

The paper decontaminates 30 sponge genome assemblies using a pipeline that combines k-mer analysis, DIAMOND, and Kraken2, achieving high accuracy and precision in identifying and removing contaminants.

Comprehensive Transcriptome Quality Assessment Using CATS: Reference-free and Reference-based Approaches

The paper introduces CATS, a tool for assessing transcriptome assembly quality using reference-free and reference-based approaches, showing improved accuracy and sensitivity over existing methods.

Somatic embryogenesis of grapevine (Vitis vinifera) expresses a transcriptomic hourglass

The paper investigates whether the hourglass-shaped ontogeny-phylogeny correlation observed in Arabidopsis zygotic embryogenesis is preserved in grapevine somatic embryogenesis, finding that the heart stage has the most conserved transcriptome.

Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization

This study profiles HIV-1 integration sites in microglia and links viral insertions to topologically associated domain organization.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1

The paper identifies spatially clustered genes with multiple enhancers as frequent targets of HIV-1 integration in T cells.

Tumor mutational landscape is a record of the pre-malignant state

The paper predicts cancer cell-of-origin from DNA sequences by matching mutational landscapes to chromatin modification patterns in normal tissues.

Role of Cnot6l in maternal mRNA turnover

This study shows that Cnot6l is essential for maternal mRNA turnover during oocyte-to-embryo transition in mice, with loss of Cnot6l leading to reduced litter size and developmental arrest.