A5039988707- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Complex Network Analysis Techniques
- Data Visualization and Analytics
- Gene expression and cancer classification
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Biomedical Text Mining and Ontologies
- Machine Learning in Bioinformatics
- Analytical Chemistry and Chromatography
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- Cholinesterase and Neurodegenerative Diseases
- Genetic Neurodegenerative Diseases
- Single-cell and spatial transcriptomics
- Oral Health Pathology and Treatment
- Protein Degradation and Inhibitors
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Pharmacogenetics and Drug Metabolism
- Advanced Proteomics Techniques and Applications
- Oral and gingival health research
- Endoplasmic Reticulum Stress and Disease
- Cancer Genomics and Diagnostics
- Cell Image Analysis Techniques
Alexander Fleming Biomedical Sciences Research Center
2020-2024
European Bioinformatics Institute
2024
National and Kapodistrian University of Athens
2017-2023
Cyprus Institute of Neurology and Genetics
2019-2021
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities
Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases, or phenotypes. Despite the variety existing tools, most them can process single list per time, thus making more combinatorial analysis complicated and prone to errors. In this article, we present FLAME, web tool combining multiple lists prior analysis. Users upload several use interactive UpSet plots, as...
Abstract Summary ChemBioServer 2.0 is the advanced sequel of a web server for filtering, clustering and networking chemical compound libraries facilitating both drug discovery repurposing. It provides researchers ability to (i) browse visualize compounds along with their physicochemical toxicity properties, (ii) perform property-based filtering compounds, (iii) explore lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results achieve selectivity...
Huntington’s disease is a rare neurodegenerative caused by cytosine–adenine–guanine (CAG) trinucleotide expansion in the Huntingtin (HTT) gene. Although (HD) well studied, pathophysiological mechanisms, genes and metabolites involved HD remain poorly understood. Systems bioinformatics can reveal synergistic relationships among different omics levels enables integration of biological data. It allows for overall understanding pathways, HD. The purpose this study was to identify differentially...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is undeniably the most global health emergency since 1918 Influenza outbreak. Depending on its evolutionary trajectory, virus expected to establish itself as an endemic infectious disease exhibiting seasonal flare-ups. Therefore, despite unprecedented rally reach a vaccine that can offer widespread immunization, it equally important effective prevention and treatment regimens for 2019 (COVID-19). Contributing this...
Efficient integration and visualization of heterogeneous biomedical information in a single view is key challenge. In this study, we present Arena3Dweb, the first, fully interactive dependency-free, web application which allows multilayered graphs 3D space. With users can integrate multiple networks along with their intra- inter-layer connections. For clearer more informative views, choose between plethora layout algorithms apply them on set selected layers either individually or...
Functional enrichment is the process of identifying implicated functional terms from a given input list genes or proteins. In this article, we present Flame (v2.0), web tool which offers combinatorial approach through merging and visualizing results widely used applications while also allowing various flexible options. version, utilizes aGOtool, g: Profiler, WebGestalt, Enrichr pipelines presents their outputs separately in combination following visual analytics approach. For intuitive...
Abstract Idiopathic Pulmonary Fibrosis (IPF) is a rare disease of the respiratory system in which lungs stiffen and get scarred, resulting breathing weakness eventually leading to death. Drug repurposing process that provides evidence for existing drugs may also be effective different diseases. In this study, we present computational pipeline having as input number gene expression datasets from early advanced stages IPF output lists repurposed ranked with novel composite score. We have...
Abstract Extracting and processing information from documents is of great importance as lots experimental results findings are stored in local files. Therefore, extracting analyzing biomedical terms such files an automated way absolutely necessary. In this article, we present OnTheFly2.0, a web application for entities individual plain texts, office documents, PDF or images. OnTheFly2.0 can generate informative summaries popup windows containing knowledge related to the identified along with...
Finding, exploring and filtering frequent sentence-based associations between a disease biomedical entity, co-mentioned in disease-related PubMed literature, is challenge, as the volume of publications increases. Darling web application, which utilizes Name Entity Recognition to identify human-related terms articles, mentioned OMIM, DisGeNET Human Phenotype Ontology (HPO) records, generates an interactive entity association network. Nodes this network represent genes, proteins, chemicals,...
Abstract Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, supports directed as well up to nine different types of connections between pairs nodes with the use Bézier curves. It comes color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization VR mode and predefined layer layouts (zig-zag, star cube). This update also includes enhanced navigation controls...
ABSTRACT Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases or phenotypes. Despite the variety existing tools, most them can process single list per time, thus making more combinatorial analysis complicated and prone to errors. In this article, we present FLAME, web tool combining multiple lists prior analysis. Users upload several preference use...
Drug repurposing techniques allow existing drugs to be tested against diseases outside their initial spectrum, resulting in reduced cost and eliminating the long time-frames of new drug development. In silico further speeds up process either by proposing suitable invert transcriptomic profile a disease or indicating based on common targets structural similarity with other similar mode action. Such methods usually return number potential repurposed that need vitro, pre-clinical clinical...
Fibrotic diseases cover a spectrum of systemic and organ-specific maladies that affect large portion the population, currently without cure. The shared characteristic these feature is their uncontrollable fibrogenesis deemed responsible for accumulated damage in susceptible tissues. Idiopathic Pulmonary Fibrosis , an interstitial lung disease, one most common studied fibrotic still remains active research target. In this study we highlight unique (i) genes, (ii) biological pathways (iii)...
Abstract The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins reference genomes or Pfam domains. Each family accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem geolocation metadata, structure predictions, as well 3D models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 each at least members....
The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks annotations simultaneously. Precalculated (e.g., Gene Ontology, Pathway enrichment, community detection, or clustering results) can be uploaded visualized in network, either as colored pie-chart nodes color-filled areas 2D/3D Venn-diagram-like style. In the case where no exists, algorithms automated detection are offered. Users adjust...
Abstract NORMA is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks annotations simultaneously. Precalculated (e.g. Gene Ontology/Pathway enrichment or clustering results) can be uploaded visualized in either as colored pie-chart nodes color-filled convex hulls Venn-diagram-like style. In the case where no exists, algorithms automated community detection are offered. Users adjust views using standard layout allow slightly...
Abstract Motivation Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming costly task. Computational methodologies that propose pathway/mechanism communities reveal relationships can be great value as they help expedite process identifying how perturbations in single pathway affect other pathways. Results We present random-walks-based methodology called PathWalks, where walker crosses pathway-to-pathway network under...
ABSTRACT Extracting and processing information from documents is of great importance as lots experimental results findings are stored in local files. Therefore, extracting analysing biomedical terms such files an automated way absolutely necessary. In this article, we present OnTheFly 2.0 , a web application for entities individual plain texts, Office documents, PDF or images. can generate informative summaries popup windows containing knowledge related to the identified along with links...