Jozef Nosek
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View article: Alignment-free detection of differences between sequencing datasets
Alignment-free detection of differences between sequencing datasets Open
Summary: Comparing biological samples through sequencing is a core task in bioinformatics analyses such as variant detection, differential expression analysis, and epigenetic peak calling. Standard approaches typically rely on mapping newl…
View article: Poly (ADP-ribose) polymerase in yeasts: characterization and involvement in telomere maintenance
Poly (ADP-ribose) polymerase in yeasts: characterization and involvement in telomere maintenance Open
Poly (ADP-ribose) polymerases (PARPs) are enzymes catalyzing the post-translational addition of chains of ADP-ribose moieties to proteins. In most eukaryotic cells, their primary protein targets are involved in DNA recombination, repair, a…
View article: Translon: a single term for translated regions
Translon: a single term for translated regions Open
View article: Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3′-end processing at conserved species-specific elements
Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3′-end processing at conserved species-specific elements Open
Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondria…
View article: Reduction of ribosomal expansion segments in yeast species of the <i>Magnusiomyces/Saprochaete</i> clade
Reduction of ribosomal expansion segments in yeast species of the <i>Magnusiomyces/Saprochaete</i> clade Open
Ribosomes are ribonucleoprotein complexes highly conserved across all domains of life. The size differences of ribosomal RNAs (rRNAs) can be mainly attributed to variable regions termed expansion segments (ESs) protruding out from the ribo…
View article: Chromosome-level genome assembly of an auxotrophic strain of the pathogenic yeast <i>Candida parapsilosis</i>
Chromosome-level genome assembly of an auxotrophic strain of the pathogenic yeast <i>Candida parapsilosis</i> Open
We report the genome sequence of the pathogenic yeast Candida parapsilosis strain SR23 (CBS 7157) used in a number of experimental studies. The nuclear genome assembly consists of eight chromosome-sized contigs with a total size of 13.04 M…
View article: Chromosome-level genome assembly of the yeast <i>Lodderomyces beijingensis</i> reveals the genetic nature of metabolic adaptations and identifies subtelomeres as hotspots for amplification of mating type loci
Chromosome-level genome assembly of the yeast <i>Lodderomyces beijingensis</i> reveals the genetic nature of metabolic adaptations and identifies subtelomeres as hotspots for amplification of mating type loci Open
Lodderomyces beijingensis is an ascosporic ascomycetous yeast. In contrast to related species Lodderomyces elongisporus, which is a recently emerging human pathogen, L. beijingensis is associated with insects. To provide an insight into it…
View article: Reduction of ribosomal expansion segments in yeast species of the<i>Magnusiomyces/Saprochaete</i>clade
Reduction of ribosomal expansion segments in yeast species of the<i>Magnusiomyces/Saprochaete</i>clade Open
Ribosomes are ribonucleoprotein complexes highly conserved across all domains of life. The size differences of ribosomal RNAs (rRNAs) can be mainly attributed to variable regions termed expansion segments (ESs) protruding out from the ribo…
View article: Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection Open
Base calling in nanopore sequencing is a difficult and computationally intensive problem, typically resulting in high error rates. In many applications of nanopore sequencing, analysis of raw signal is a viable alternative. Dynamic time wa…
View article: Jaminaea angkorensis draft genome assembly
Jaminaea angkorensis draft genome assembly Open
A draft assembly of the genome of yeast Jaminaea angkorensis produced by SPAdes assembler from Illumina reads, The main purpose is to serve as a reference for analyzing DNA methylation in nanopore sequencing data produced with in vitro met…
View article: Jaminaea angkorensis draft genome assembly
Jaminaea angkorensis draft genome assembly Open
A draft assembly of the genome of yeast Jaminaea angkorensis produced by SPAdes assembler from Illumina reads, The main purpose is to serve as a reference for analyzing DNA methylation in nanopore sequencing data produced with in vitro met…
View article: Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences
Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences Open
View article: Chromosome-Level Genome Assembly of the Yeast Candida verbasci
Chromosome-Level Genome Assembly of the Yeast Candida verbasci Open
Candida verbasci is an anamorphic ascomycetous yeast. We report the genome sequence of its type strain, 11-1055 (CBS 12699). The nuclear genome assembly consists of seven chromosome-sized contigs with a total size of 12.1 Mbp and has a rel…
View article: Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources Open
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metab…
View article: Genome analysis of five recently described species of the CUG-Ser clade uncovers<i>Candida theae</i>as a new hybrid lineage with pathogenic potential in the<i>Candida parapsilosis</i>species complex
Genome analysis of five recently described species of the CUG-Ser clade uncovers<i>Candida theae</i>as a new hybrid lineage with pathogenic potential in the<i>Candida parapsilosis</i>species complex Open
Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C. metapsilosis isolates sequen…
View article: Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern
Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern Open
View article: A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020.
A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020. Open
View article: Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols Open
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pande…
View article: Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay
Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay Open
The emergence of a novel SARS-CoV-2 B.1.1.7 variant sparked global alarm due to increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to…
View article: Transcriptome and proteome profiling reveals complex adaptations of <i>Candida parapsilosis</i> cells assimilating hydroxyaromatic carbon sources
Transcriptome and proteome profiling reveals complex adaptations of <i>Candida parapsilosis</i> cells assimilating hydroxyaromatic carbon sources Open
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metab…
View article: The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids
The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids Open
Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of a…
View article: A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020
A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020 Open
SARS-CoV-2 mutants carrying the ∆H69/∆V70 deletion in the amino-terminal domain of the Spike protein emerged independently in at least six lineages of the virus (namely, B.1.1.7, B.1.1.298, B.1.160, B.1.177, B.1.258, B.1.375). We analyzed …
View article: Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report
Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report Open
We present an unofficial SARS-CoV-2 genomic surveillance report from Slovakia based on approximately 3500 samples sequenced between March 2020 and May 2021. Early samples show multiple independent imports of SARS-CoV-2 from other countries…
View article: Amplification of Telomeric Arrays via Rolling-circle Mechanism
Amplification of Telomeric Arrays via Rolling-circle Mechanism Open
Alternative (telomerase-independent) lengthening of telomeres mediated through homologous recombination is often accompanied by a generation of extrachromosomal telomeric circles (t-circles), whose role in direct promotion of recombination…
View article: Taz1 Binding to a Fission Yeast Model Telomere: FORMATION OF TELOMERIC LOOPS AND HIGHER ORDER STRUCTURES
Taz1 Binding to a Fission Yeast Model Telomere: FORMATION OF TELOMERIC LOOPS AND HIGHER ORDER STRUCTURES Open
Similar to its human homologues TRF1 and TRF2, fission yeast Taz1 protein is a component of telomeric chromatin regulating proper telomere maintenance. As mammalian TRF1 and TRF2 proteins have been shown to directly bind telomeric DNA to f…
View article: OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway
OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway Open
The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In cont…
View article: Genome analysis of <i>Candida subhashii</i> reveals its hybrid nature and dual mitochondrial genome conformations
Genome analysis of <i>Candida subhashii</i> reveals its hybrid nature and dual mitochondrial genome conformations Open
Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii wa…
View article: Technical comment on The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
Technical comment on The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia Open
Pavelka et al. (Science, Reports, 7 May 2021) claim that a single round of population-wide antigen testing in Slovakia reduced the observed COVID-19 prevalence by 58%, and that it played a substantial role in curbing the pandemic. We argue…
View article: Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols
Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols Open
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pande…
View article: Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi
Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi Open
Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times…