A5006642595- Epigenetics and DNA Methylation
- Prenatal Screening and Diagnostics
- Fetal and Pediatric Neurological Disorders
- Scientific Computing and Data Management
- Research Data Management Practices
- RNA modifications and cancer
- Data Analysis with R
- Species Distribution and Climate Change
- Neuroscience and Music Perception
- Genomics and Chromatin Dynamics
- Fungal Biology and Applications
- HIV Research and Treatment
- Cancer-related gene regulation
- Microbial Natural Products and Biosynthesis
- Gut microbiota and health
- Neuroblastoma Research and Treatments
- Prostate Cancer Treatment and Research
- CRISPR and Genetic Engineering
- Music Technology and Sound Studies
- Biochemical Analysis and Sensing Techniques
- Circadian rhythm and melatonin
- Health, Environment, Cognitive Aging
- Cancer-related molecular mechanisms research
- Music and Audio Processing
- Plant Pathogens and Fungal Diseases
Centre for Addiction and Mental Health
2019-2023
Vilnius University
2017-2023
Technion – Israel Institute of Technology
2021
Galgotias University
2021
Informatics Institute of Technology
2021
Florida Museum of Natural History
2021
International Institute of Information Technology
2021
Indian Institute of Information Technology, Nagpur
2021
Only a part of prostate cancer (PCa) patients has aggressive malignancy requiring adjuvant treatment after radical prostatectomy (RP). Biomarkers capable to predict biochemical PCa recurrence (BCR) RP would significantly improve preoperative risk stratification and decisions. MicroRNA (miRNA) deregulation recently emerged as an important phenomenon in tumor development progression, however, the mechanisms remain largely unstudied. In present study, based on microarray profiling DNA...
Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health disease. Identification of oscillating signals could lead novel biological insights, yet its investigation impeded by the extensive computational statistical knowledge required perform such analysis.
Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved mammalian development and disease. brought about by collective action three AdoMet-dependent methyltransferases, whose catalytic interactions temporal interplay are poorly understood. We used structure-guided engineering the Dnmt1 methyltransferase enable transfer azide tags onto from synthetic cofactor analog, Ado-6-azide, vitro. then CRISPR-edited locus mouse embryonic stem cells...
5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on oxidative DNA demethylation pathway and implicated in regulation of embryogenesis, neurological processes, cancerogenesis. Profiling this relatively scarce genomic modification clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered...
Abstract Background Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still high cost. Building upon previous knowledge that placenta, the main source circulating DNA, hypomethylated comparison tissue counterparts cfDNA, we propose targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches material and reduces numbers...
Due to an extreme rarity of 5-carboxylcytosine (5caC) in the mammalian genome, investigation its role brings a considerable challenge. Methods based on bisulfite sequencing have been proposed for genome-wide 5caC analysis. However, bisulfite-based scarcely abundant demands significant experimental and computational resources, increasing cost. Here, we present bisulfite-free approach, caCLEAR, high-resolution mapping 5caCGs. The method uses atypical activity methyltransferase eM.SssI remove...
The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)—5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)—by the TET/JBP family dioxygenases prompted intensive studies their functional roles in mammalian cells. However, interplay these less abundant modified nucleotides other eukaryotic lineages remains poorly understood. We carried out a systematic study content distribution oxi-mCs RNA basidiomycetes Laccaria bicolor...
Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in stage differentiation and cell composition tumors. Global loss DNA methylation genomic 5-hydroxymethylcytosine (5hmC) hallmark human cancers. Here, we used our recently developed single-base resolution approaches, hmTOP-seq uTOP-seq, for construction 5hmC maps identification large partially methylated domains (PMDs) different NB subpopulations. The profiles revealed...
Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow challenging to implement and maintain. As result, record of computational steps performed on the arrive at key findings often missing. We developed Scikick, tool that eases configuration, execution, presentation analyses. Scikick allows configurations with notebooks as units defines standard structure project, automatically tracks defined interdependencies between steps, implements methods compile...
The bdverse is a collection of packages that form general framework for facilitating biodiversity science in R. We build it to serve as sustainable and agile infrastructure enhances the value data by allowing users conveniently employ R, exploration, quality assessment, cleaning, standardization. supports with without programming capabilities. It includes six unique hierarchal structure — representing different functionality levels (Fig. 1). Major features three core will be highlighted...
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and hydroxymethylation-from single library. The approach is based on chemo-enzymatic covalent tagging unmodified CG sites hydroxymethylated cytosine (5hmC) along with GC in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation the revealed its sensitivity informativity evaluating chromatin...