Martin Bartas
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View article: Senescence-associated changes in mineral nutrients in rice leaves and their relationship with ROS homeostasis as affected by nitrogen deficiency
Senescence-associated changes in mineral nutrients in rice leaves and their relationship with ROS homeostasis as affected by nitrogen deficiency Open
View article: High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features
High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features Open
Recent advances in sequencing methods have led to major progress in the gapless assemblies of the human genome. However, until mid-2023, the complete sequence of the Y chromosome remained elusive. While only a small percentage of autosomal…
View article: Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study in <i>Drosophila</i>
Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study in <i>Drosophila</i> Open
Z-DNA is a left-handed DNA conformation linked to gene regulation, chromatin dynamics, and immunity. Despite its importance, genome-wide prediction of Z-DNA forming sequences (ZFS) remains limited by the absence of fast and accessible tool…
View article: mGem: Noncanonical nucleic acid structures—powerful but neglected antiviral targets
mGem: Noncanonical nucleic acid structures—powerful but neglected antiviral targets Open
This perspective highlights the emerging significance of noncanonical nucleic acid structures—such as G-quadruplexes, Z-DNA/Z-RNA, and cruciforms—in viral genomes. Once considered structural oddities, these motifs are now recognized as cri…
View article: CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome
CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome Open
With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often req…
View article: Abiotic Stresses in Plants: From Molecules to Environment
Abiotic Stresses in Plants: From Molecules to Environment Open
Plants face several challenges during their growth and development, including environmental factors (mainly abiotic ones), that can lead to/induce oxidative stress—specifically, adverse temperatures (both hot and cold), drought, salinity, …
View article: Special Issue “Bioinformatics of Unusual DNA and RNA Structures”
Special Issue “Bioinformatics of Unusual DNA and RNA Structures” Open
Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...]
View article: RNA analysis of the longest living vertebrate Greenland shark revealed an abundance of LINE-like elements in its transcriptome
RNA analysis of the longest living vertebrate Greenland shark revealed an abundance of LINE-like elements in its transcriptome Open
The Greenland shark (Somniosus microcephalus) is an enigmatic species known for its exceptional longevity and extraordinary adaptations to the cold environment. This animal lives in the arctic and subarctic regions of the North Atlantic Oc…
View article: Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions
Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions Open
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, “bubbles”, R-loops, and other outcomes of supercoiling…
View article: Variability of Inverted Repeats in All Available Genomes of Bacteria
Variability of Inverted Repeats in All Available Genomes of Bacteria Open
Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence a…
View article: Identification of annotation artifacts concerning the chalcone synthase (CHS)
Identification of annotation artifacts concerning the chalcone synthase (CHS) Open
View article: Identification of annotation artifacts concerning the<i>CHALCONE SYNTHASE</i>(CHS)
Identification of annotation artifacts concerning the<i>CHALCONE SYNTHASE</i>(CHS) Open
Objective Chalcone synthase (CHS) catalyzes the initial step of the flavonoid biosynthesis. The CHS encoding gene is well studied in numerous plant species. Rapidly growing sequence databases contain hundreds of CHS entries that are the re…
View article: New Low Morphine Opium Poppy Genotype Obtained by TILLING Approach
New Low Morphine Opium Poppy Genotype Obtained by TILLING Approach Open
The opium poppy’s ability to produce various alkaloids is both useful and problematic. Breeding of new varieties with varying alkaloid content is therefore an important task. In this paper, the breeding technology of new low morphine poppy…
View article: Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana
Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana Open
Sequences of nucleic acids with the potential to form four-stranded G-quadruplex structures are intensively studied mainly in the context of human diseases, pathogens, or extremophile organisms; nonetheless, the knowledge about their occur…
View article: What Do We Know about Barley miRNAs?
What Do We Know about Barley miRNAs? Open
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immun…
View article: The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation
The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation Open
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional releva…
View article: Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance
Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance Open
Photosynthetically active radiation (PAR) is an important environmental cue inducing the production of many secondary metabolites involved in plant oxidative stress avoidance and tolerance. To examine the complex role of PAR irradiance and…
View article: Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA Open
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known R…
View article: Are There Hidden Genes in DNA/RNA Vaccines?
Are There Hidden Genes in DNA/RNA Vaccines? Open
Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus – 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Alt…
View article: Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain
Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain Open
Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid se…
View article: Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation
Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation Open
G-quadruplexes are four-stranded nucleic acid structures occurring in the genomes of all living organisms and viruses. It is increasingly evident that these structures play important molecular roles; generally, by modulating gene expressio…
View article: Transcriptomic and Proteomic Analysis of Drought Stress Response in Opium Poppy Plants during the First Week of Germination
Transcriptomic and Proteomic Analysis of Drought Stress Response in Opium Poppy Plants during the First Week of Germination Open
Water deficiency is one of the most significant abiotic stresses that negatively affects growth and reduces crop yields worldwide. Most research is focused on model plants and/or crops which are most agriculturally important. In this resea…
View article: The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity Open
Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifesp…
View article: G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story
G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story Open
G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene…
View article: G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story Open
Supplementary material to the journal article Consist of: Supplementary material S1: Analyzed RPB1 sequences in 40 plant species together with detailed characteristics and G-quadruplex prediction using four differ…
View article: G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story Open
Supplementary material to the journal article Consist of: Supplementary material S1: Analyzed RPB1 sequences in 40 plant species together with detailed characteristics and G-quadruplex prediction using four differ…
View article: G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story Open
Supplementary material to the journal article Consist of: Supplementary material S1: Analyzed RPB1 sequences in 40 plant species together with detailed characteristics and G-quadruplex prediction using four differ…
View article: G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story Open
Supplementary material to the journal article: Consist of: Difference CD spectra - comparison without and with previous UV treatment (Difference CD spectra - comparison without and with previous UV treatment.pdf) 40 bp long potential G4 lo…
View article: Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection
Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection Open
G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putat…
View article: Tracing dsDNA Virus–Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences
Tracing dsDNA Virus–Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences Open
The importance of gene expression regulation in viruses based upon G-quadruplex may point to its potential utilization in therapeutic targeting. Here, we present analyses as to the occurrence of putative G-quadruplex-forming sequences (PQS…