Matej Lexa
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View article: Factors determining chromosomal localization of transposable elements in plants
Factors determining chromosomal localization of transposable elements in plants Open
Transposable elements (TEs) constitute a significant part of plant genomes and shape their genomic landscape. While some TEs are ubiquitously dispersed, other elements specifically occupy discrete genomic loci. The evolutionary forces behi…
View article: Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
View article: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
View article: Y chromosome-coded HSATII repeats may contribute to higher incidence of cancer in men
Y chromosome-coded HSATII repeats may contribute to higher incidence of cancer in men Open
It has been observed that men have a shorter lifespan and higher incidence of certain cancers than women. We postulate here that this phenomenon may be attributed to the toxicity of the Y chromosome, owing to the expression of normally sil…
View article: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
Background Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes. LTRs contain regulatory sequences essential for the life cycle of th…
View article: A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools
A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools Open
Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overv…
View article: High-Throughput Spike Detection in Greenhouse Cultivated Grain Crops with Attention Mechanisms-Based Deep Learning Models
High-Throughput Spike Detection in Greenhouse Cultivated Grain Crops with Attention Mechanisms-Based Deep Learning Models Open
View article: HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization Open
Motivation The role of repetitive DNA in the 3D organization of the interphase nucleus is a subject of intensive study. In studies of 3D nucleus organization, mutual contacts of various loci can be identified by Hi-C sequencing. Typical an…
View article: Additional files for Lexa et al. HiC-TE publication
Additional files for Lexa et al. HiC-TE publication Open
Additional files for Lexa et al. HiC-TE publication Additional file 1 Suplementary Figure — Flow chart of the Nextflow HiC-TE pipeline (output from running Nextflow with the -graph switch) Additional file 2
View article: HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization
HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization Open
The role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA …
View article: Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates
Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates Open
Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses and low levels of immunoglobulins including IgA that is involved in the maintenance of the intestinal homeost…
View article: Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both <i>In Vitro</i> and <i>In Vivo</i> Conditions
Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both <i>In Vitro</i> and <i>In Vivo</i> Conditions Open
Increasing levels of antibiotic resistance among bacteria also increase the need for alternatives to conventional antibiotic treatment. Pathogenic Escherichia coli represents a major diarrheic infectious agent of piglets in their postweani…
View article: Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains
Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains Open
In a recently published paper, we have found that SARS-CoV-2 hot-spot mutations are significantly associated with inverted repeat loci and CG dinucleotides. However, fast-spreading strains with new mutations (so-called mink farm mutations,…
View article: SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci
SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci Open
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby c…
View article: TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting Open
Motivation Transposable elements (TEs) in eukaryotes often get inserted into one another, forming sequences that become a complex mixture of full-length elements and their fragments. The reconstruction of full-length elements and the order…
View article: What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? Open
LTR retrotransposons constitute a significant part of plant genomes and their evolutionary dynamics play an important role in genome size changes. Current methods of LTR retrotransposon age estimation are based only on LTR (long terminal r…
View article: Correction to: Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
Correction to: Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study Open
View article: Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study Open
View article: Bacterial but Not Fungal Gut Microbiota Alterations Are Associated With Common Variable Immunodeficiency (CVID) Phenotype
Bacterial but Not Fungal Gut Microbiota Alterations Are Associated With Common Variable Immunodeficiency (CVID) Phenotype Open
Common Variable Immunodeficiency (CVID) is the most frequent symptomatic immune disorder characterized by reduced serum immunoglobulins. Patients often suffer from infectious and serious non-infectious complications which impact their life…
View article: High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing
High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing Open
Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by …
View article: The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery
The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery Open
Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biase…
View article: Referee report. For: seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data [version 1; peer review: 1 approved with reservations]
Referee report. For: seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data [version 1; peer review: 1 approved with reservations] Open
View article: MOESM6 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
MOESM6 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study Open
Additional file 6. Python scripts used for recalculation of genomic coordinates of protein domains in analyzed LTR retrotransposons annotated using DANTE tool, RepeatExplorer.
View article: High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing
High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing Open
Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by …
View article: MOESM7 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
MOESM7 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study Open
Additional file 7. GFF3 files of fully annotated nested-original pairs and non-nested LTR retrotransposons used in this study.
View article: Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast Open
View article: Additional file 4: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
Additional file 4: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast Open
Overview of families, PQS and average lengths. Table S1. Families possessing PQS score > 64. Table S2. Number of PQS score > 64 in superfamilies. Table S3. Average lengths of LTRs, non-LTR regios and whole elements. (XLSX 13 kb)
View article: Additional file 2: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
Additional file 2: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast Open
Overview of oligonucleotides, BAC clones and primers used in study. Name is derived from Maize TE Database. BAC referes to ZMMBBc library coordinates of clones containing given element. G4 motif coresponds to oligonucleotides used for CD m…
View article: pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R Open
Motivation G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These f…
View article: p53 Specifically Binds Triplex DNA In Vitro and in Cells
p53 Specifically Binds Triplex DNA In Vitro and in Cells Open
Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different ty…