A5009135905- Chronic Lymphocytic Leukemia Research
- Genomics and Phylogenetic Studies
- Immunodeficiency and Autoimmune Disorders
- Lymphoma Diagnosis and Treatment
- Biosensors and Analytical Detection
- SARS-CoV-2 detection and testing
- Advanced biosensing and bioanalysis techniques
- Monoclonal and Polyclonal Antibodies Research
- SARS-CoV-2 and COVID-19 Research
- RNA Research and Splicing
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- Marine and environmental studies
- Food Industry and Aquatic Biology
- Environmental DNA in Biodiversity Studies
- Genomics and Chromatin Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Glycosylation and Glycoproteins Research
- Multiple Myeloma Research and Treatments
- Immune Cell Function and Interaction
- CAR-T cell therapy research
- Biomedical Text Mining and Ontologies
Centre for Research and Technology Hellas
2020-2024
Aristotle University of Thessaloniki
2021-2024
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity, which can be used to identify viral lineages (including variants concern) that are circulating in local...
Abstract The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread virus. Recently, SARS-CoV-2 RNA in wastewater has emerged as a useful tool monitor prevalence virus community. Here, we propose methodology, called lineagespot , for monitoring mutations lineages samples using next-generation sequencing (NGS). Our proposed method was tested evaluated NGS data...
Abstract Almost one‐third of all splenic marginal zone lymphoma (SMZL) cases express B‐cell receptor immunoglobulin (BcR IG) encoded by the IGHV1‐2*04 gene, implicating antigen selection in disease ontogeny. Evidence supporting this notion mostly derives from low‐throughput sequencing approaches, which have limitations capturing full complexity BcR IG gene repertoire. This hinders comprehensive assessment subclonal architecture SMZL as shaped selection. To address this, we conducted a...
A recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on library preparation steps. UMI adds a identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias this step. Here, we propose an alignment free framework serving as preprocessing step fastq files, called UMIc, for deduplication and correction reads building consensus...
Abstract Background Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era high-throughput immunoprofiling next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers opportunity for in-depth analysis based on processing output files IMGT/HighV-Quest tool, a standard NGS immunoprofiling, through number interoperable modules. These provide detailed...
Background Microenvironmental interactions of the malignant clone with T cells are critical throughout natural history chronic lymphocytic leukemia (CLL). Indeed, clonal expansions and shared clonotypes exist between different CLL patients, strongly implying selection by antigens. Moreover, immunogenic neoepitopes have been isolated from clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated (TR) gene repertoire...
Abstract Subset #201 is a clinically indolent subgroup of patients with chronic lymphocytic leukemia defined by the expression stereotyped, mutated IGHV4-34/IGLV1-44 BCR Ig. characterized recurrent somatic hypermutations (SHMs) that frequently lead to creation and/or disruption N-glycosylation sites within Ig H and L chain variable domains. To understand relevance this observation, using next-generation sequencing, we studied how SHM shapes subclonal architecture repertoire in subset #201,...
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disease caused by a trinucleotide (CAG) repeat expansion in the ATXN1 gene. It characterized presence of polyglutamine (polyQ) intranuclear inclusion bodies (IIBs) within affected neurons. In order to investigate impact polyQ IIBs SCA1 pathogenesis, we generated novel protein aggregation model inducible overexpression mutant ATXN1(Q82) isoform human neuroblastoma SH-SY5Y cells. Moreover, developed simple and...
Abstract Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity which can be used to identify viral lineages (including variants concern) that are circulating in local...
Abstract The SARS-CoV-2 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread virus. Recently, RNA in wastewater has emerged as a useful tool monitor prevalence virus community. Here, we propose methodology, called lineagespot , for lineages samples using next-generation sequencing. Our proposed method was tested evaluated NGS data produced by sequencing three from...
ABSTRACT The integration of multi-omics data can greatly facilitate the advancement research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful integration. Here, we present a robust framework, called InterTADs, integrating derived from same sample, and considering chromatin configuration genome, i.e. topologically associating domains (TADs). Following process, statistical analysis highlights differences between groups...
T cell large granular lymphocyte (T-LGL) lymphoproliferations constitute a disease spectrum ranging from poly/oligo to monoclonal. Boundaries within this of proliferations are not well established. T-LGL co-occur with wide variety other diseases autoimmune disorders, solid tumors, hematological malignancies, post organ, and hematopoietic stem transplantation, can therefore arise as consequence antigenic triggers. Persistence dominant malignant clone is established through continuous STAT3...
Automating data analysis pipelines is a key requirement to ensure reproducibility of results, especially when dealing with large volumes data. Here we assembled automated for the High-throughput Sequencing (HTS) originating from RNA-Seq, ChIP-Seq and Germline variant calling experiments. We implemented these workflows in Common workflow language (CWL) evaluated their performance by: i) reproducing results two previously published studies on Chronic Lymphocytic Leukemia (CLL), ii) analyzing...
Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a user-friendly platform that integrates 220+ tool suites 65+ curated workflows microbial analyses, including taxonomic profiling, assembly, annotation, functional analysis. Hosted on the main EU Galaxy server (microgalaxy.usegalaxy.eu), it supports workflow creation & customization, sharing,...
The severe deforestation, as indicated in national forest data, is a recurring problem many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion these areas, one the major drivers having adverse consequences on local plant biodiversity. Conserving biodiversity mainly dependent biological monitoring species distribution and population sizes. However, existing conventional approaches for are rather limited.Here, we explored soil DNA at four types Park...
Increasing evidence supports a role for the vaginal microbiome (VM) in severity of HPV infection and its potential link to cervical intraepithelial neoplasia. However, lot remains unclear regarding precise certain bacteria context positivity persistence infection. Here, using next generation sequencing (NGS), we comprehensively profiled VM series 877 women who tested positive at least one high risk (hrHPV) type with COBAS® 4,800 assay, after self-collection cervico-vaginal sample. Starting...
Classification of patients with chronic lymphocytic leukemia (CLL) based on the somatic hypermutation (SHM) status clonotypic immunoglobulin heavy variable (IGHV) gene has established predictive and prognostic relevance. The SHM is assessed number mutations within IG domain sequence, albeit only over rearranged IGHV excluding complementarity determining region 3 (VH CDR3). This may lead to an underestimation actual impact SHM, in fact overlooking most critical for antigen-antibody...