Andrej Baláž
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View article: Advancing molecular diagnostics of myotonic dystrophy type 1 using short-read whole genome sequencing
Advancing molecular diagnostics of myotonic dystrophy type 1 using short-read whole genome sequencing Open
Myotonic dystrophy type 1 (DM1) is a serious multisystem disorder caused by GCA repeat expansions in the DMPK gene. Early and accurate diagnosis, often requiring reliable DNA-diagnostic techniques, is critical for preventing life-threateni…
View article: Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?
Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? Open
Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the associat…
View article: Advancing Myotonic Dystrophy Type 2 Diagnostics: Insights from Short-Read Whole-Genome Sequencing-Based Genotyping
Advancing Myotonic Dystrophy Type 2 Diagnostics: Insights from Short-Read Whole-Genome Sequencing-Based Genotyping Open
View article: Suffixient Sets
Suffixient Sets Open
We define a suffixient set for a text $T [1..n]$ to be a set $S$ of positions between 1 and $n$ such that, for any edge descending from a node $u$ to a node $v$ in the suffix tree of $T$, there is an element $s \in S$ such that $u$'s path …
View article: SnakeLines: integrated set of computational pipelines for sequencing reads
SnakeLines: integrated set of computational pipelines for sequencing reads Open
With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics pr…
View article: Wheeler maps
Wheeler maps Open
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can prepro…
View article: Prefix-free graphs and suffix array construction in sublinear space
Prefix-free graphs and suffix array construction in sublinear space Open
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and re…
View article: PHERI—Phage Host ExploRation Pipeline
PHERI—Phage Host ExploRation Pipeline Open
Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most…
View article: VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples Open
Background The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.1.617.2 or Omicron variant B.1.1.529). Proportions of these variants circulating in a human pop…
View article: MARIA: Multiple-alignment $r$-index with aggregation
MARIA: Multiple-alignment $r$-index with aggregation Open
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the d…
View article: VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples
VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples Open
Background The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the delta variant B.1.617.2 or omicron variant B.1.1.529). Proportions of these variants in a population are typica…
View article: Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs
Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs Open
We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this …
View article: SnakeLines: integrated set of computational pipelines for sequencing reads
SnakeLines: integrated set of computational pipelines for sequencing reads Open
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioin…