A5103138297- RNA modifications and cancer
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Inflammatory Bowel Disease
- Circular RNAs in diseases
- Single-cell and spatial transcriptomics
- Insect behavior and control techniques
- Genomics and Phylogenetic Studies
- IL-33, ST2, and ILC Pathways
- Insect Resistance and Genetics
- Insect-Plant Interactions and Control
- Microscopic Colitis
- Immune Cell Function and Interaction
- Cancer Immunotherapy and Biomarkers
- Pharmacology and Obesity Treatment
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- Cell death mechanisms and regulation
- Galectins and Cancer Biology
- NF-κB Signaling Pathways
- interferon and immune responses
- RNA regulation and disease
- Machine Learning in Bioinformatics
Takeda (United Kingdom)
2025
University of Thessaly
2013-2024
Takeda (United States)
2022-2023
Takeda (Japan)
2023
Tufts Medical Center
2017-2022
Molecular Oncology (United States)
2012-2022
Tufts University
2020
Pasteur Hellenic Institute
2015-2019
National and Kapodistrian University of Athens
2012-2013
Academy of Athens
2013
The functional characterization of miRNAs is still an open challenge.Here, we present DIANA-miRPath v3.0 (http://www.microrna.gr/miRPathv3)an online software suite dedicated to the assessment miRNA regulatory roles and identification controlled pathways.The new miRPath web server renders possible annotation one or more using standard (hypergeometric distributions), unbiased empirical distributions and/or meta-analysis statistics.DIANA-miRPath database functionality have been significantly...
MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it being widely used from the scientific community, since its initial launch in 2009. v5.0, new version of microT server, has been significantly enhanced with an improved prediction algorithm,...
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version first >1 million entries, corresponding ∼670 000 unique miRNA-target pairs. The interactions are by >33 experimental methodologies, applied ∼600 cell types/tissues under ∼451 conditions. It integrates information on cell-type specific miRNA–gene regulation, while hundreds thousands miRNA-binding locations reported. TarBase...
microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds thousands miRNA:gene interactions have been experimentally identified. However, this wealth information fragmented and hidden in manuscripts raw next-generation sequencing data sets. DIANA-TarBase was initially released 2006 it the first database aiming catalog published validated...
microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function lncRNAs introduces an extra layer complexity in the miRNA interactome. DIANA-LncBase v1 provided a database experimentally supported and silico predicted Recognition Elements (MREs) on lncRNAs. second version LncBase (www.microrna.gr/LncBase) presents extensive collection...
MicroRNAs (miRNAs) are key regulators of diverse biological processes and their functional analysis has been deemed central in many research pipelines. The new version DIANA-miRPath web server was redesigned from the ground-up. user DNA Intelligent Analysis (DIANA) v2.0 can now utilize miRNA targets predicted with high accuracy based on DIANA-microT-CDS and/or experimentally verified TarBase v6; combine results merging meta-analysis algorithms; perform hierarchical clustering miRNAs pathways...
Recently, the attention of research community has been focused on long non-coding RNAs (lncRNAs) and their physiological/pathological implications. As number experiments increase in a rapid rate transcriptional units are better annotated, databases indexing lncRNA properties function gradually become essential tools to this process. Aim DIANA-LncBase (www.microrna.gr/LncBase) is reinforce researchers' attempts unravel microRNA (miRNA)–lncRNA putative functional interactions. This study...
Abstract DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half million entries, corresponding to ∼240 000 unique tissue and cell type specific miRNA–lncRNA pairs. This compilation of interactions derived from the manual curation publications analysis >300 high-throughput datasets. are by 14 experimental methodologies, applied 243 distinct types tissues in...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences all types from broad range organisms. We have recently added new genome mapping pipeline that identifies genomic locations for in 296 species. also several functional annotations, such as tRNA secondary structures, Gene Ontology and miRNA-target interactions. A quality control mechanism based Rfam family assignments potential contamination, incomplete more. The has become...
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides single entry point for accessing all types organisms. Since its launch in 2014, has integrated twelve new resources, taking the total number collaborating to 22, began importing data, such as modified nucleotides MODOMICS PDB. We created species-specific identifiers refer unique within context species. The website been subject continuous improvements focusing on...
The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits unique ability invade adapt ecological niches throughout tropical subtropical regions the world, though medfly infestations have been prevented controlled by sterile technique (SIT) as part integrated management programs (IPMs). genetic analysis manipulation has subject intensive study in an effort improve SIT...
microRNAs (miRNAs) are small non-coding RNAs that actively fine-tune gene expression. The accurate characterization of the mechanisms underlying miRNA transcription regulation will further expand our knowledge regarding their implication in homeostatic and pathobiological networks. Aim DIANA-miRGen v3.0 (http://www.microrna.gr/mirgen) is to provide for first time cell-line-specific start sites (TSSs), coupled with genome-wide maps factor (TF) binding order unveil regulation. To this end,...
Abstract Background Understanding the cellular and molecular mechanisms underlying response to treatment in patients with inflammatory bowel disease (IBD) is crucial guide development of new drugs. We have used transcriptomic approaches assess biomarkers among active ulcerative colitis (UC) receiving integrin inhibitor vedolizumab (VDZ) or systemic tumor necrosis factor (TNF) therapy. Methods In VARSITY, 769 moderately severely were randomized receive VDZ (n = 383) adalimumab (ADA; n 386)...
Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA mRNAs microRNAs (miRNAs) to uncover miRNAs transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded analysis. Users combine their...
microRNAs (miRNAs) are short non-coding RNAs (∼22 nts) present in animals, plants, and viruses. They considered central post-transcriptional regulators of gene expression key components a great number physiological pathological conditions. The accurate characterization their targets is essential to series applications basic or applied research settings. DIANA-TarBase (http://www.microrna.gr/tarbase) was initially launched 2006. It reference repository indexing experimentally derived...
Argonaute crosslinking and immunoprecipitation (CLIP) experiments are the most widely used high-throughput methodologies for miRNA targetome characterization. The analysis of Photoactivatable Ribonucleoside-Enhanced (PAR) CLIP methodology focuses on sequence clusters containing T-to-C conversions. Here, we demonstrate first time that non-T-to-C clusters, frequently observed in PAR-CLIP experiments, exhibit functional miRNA-binding events strong RNA accessibility. This discovery is based an...
Differential RNA localization and local protein synthesis regulate synapse function plasticity in neurons. MicroRNAs are a conserved class of regulatory RNAs that control mRNA stability translation tissues. They abundant the brain but extent into which they involved synaptic regulation is poorly known. Herein, computational analysis coding 3′UTR regions 242 presynaptic 304 postsynaptic proteins revealed 91% them predicted to be microRNA targets. Analysis longest isoform transcripts showed...
Abstract Aβ peptide that accumulates in Alzheimer’s disease brain, derives from proteolytic processing of the amyloid precursor protein (APP) exists three main isoforms derived by alternative splicing. The isoform APP695, lacking exons 7 and 8, is predominately expressed neurons abnormal neuronal splicing APP has been observed brain patients with disease. Herein, we demonstrate expression members ELAVL family (nELAVLs) correlate APP695 levels vitro vivo . Moreover, provide evidence nELAVLs...
Liver fibrosis progression in chronic liver disease leads to cirrhosis, failure, or hepatocellular carcinoma and often ends transplantation. Even with an increased understanding of fibrogenesis many attempts generate therapeutics specifically targeting fibrosis, there is no approved treatment for fibrosis. To further understand characterize the driving mechanisms we developed a high-throughput genome-wide CRISPR/Cas9 screening platform identify hepatic stellate cell (HSC)-derived mediators...
Abstract AKT-phosphorylated IWS1 regulates alternative RNA splicing via a pathway that is active in lung cancer. RNA-seq studies adenocarcinoma cells lacking phosphorylated IWS1, identified exon 2-deficient U2AF2 splice variant. Here, we show 2 inclusion the mRNA cell cycle-dependent process regulated by LEDGF/SRSF1 complexes, whose assembly controlled phosphorylation-dependent deposition of histone H3K36me3 marks body target genes. The encodes Serine-Arginine-Rich (RS) domain-deficient...