Broňa Brejová

The paper identifies noncanonical telomeric arrays in telomerase-negative yeasts and hypothesizes an ALT mechanism compensates for telomerase loss.

This study evaluates structural variant callers using long-read sequencing data, showing performance variation based on ground truth, reference genome, and genomic regions.

Pangebin improves plasmid binning in bacterial isolates by using pangenome-assembly graphs to enhance accuracy across different assemblers.

This paper introduces an assembly-free method to augment pangenome graphs using long reads from new samples, without aligning to a reference or calling variants.

The paper identifies reduced expansion segments in rRNAs of Magnusiomyces/Saprochaete yeasts compared to Saccharomyces cerevisiae, showing independent loss of ESs in multiple lineages without major changes to ribosomal protein inventories.

The paper introduces an efficient algorithm for assessing annotation colocalization with genomic context, improving speed and handling new statistical models.

The paper develops algorithms to find high-density clusters in graph representations of pangenomes by solving a path-finding problem in weighted directed graphs.

The paper improves unsupervised methylation detection in nanopore sequencing by enhancing dynamic time warping algorithms and introducing a new tool, Nadavca.

WarpSTR directly analyzes raw nanopore signals to determine STR lengths with reduced error compared to basecalling and STRique.

plASgraph uses graph neural networks to detect plasmid contigs in genome assemblies, outperforming existing methods by leveraging assembly graph information.

The paper introduces MCDP, a tool that computes p-values for genome annotation overlaps using Markov chains, improving efficiency and accuracy over existing methods.

This study profiles transcriptome and proteome of Candida parapsilosis assimilating hydroxyaromatic carbon sources, revealing pathway regulation and metabolic connections.

DeepNano-blitz is a fast base caller for MinION sequencers that runs on a laptop CPU without GPU, allowing real-time analysis and monitoring of sequencing data.