A5053848151- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Osteoarthritis Treatment and Mechanisms
- Gene Regulatory Network Analysis
- Cytokine Signaling Pathways and Interactions
- Inflammatory mediators and NSAID effects
- Melanoma and MAPK Pathways
- Cell Image Analysis Techniques
- Advanced Proteomics Techniques and Applications
- Single-cell and spatial transcriptomics
- Tendon Structure and Treatment
- Chemokine receptors and signaling
- Lower Extremity Biomechanics and Pathologies
- Spine and Intervertebral Disc Pathology
- Metabolomics and Mass Spectrometry Studies
- Cardiovascular Disease and Adiposity
- Genetics, Bioinformatics, and Biomedical Research
- Drug-Induced Hepatotoxicity and Protection
- Microbial Metabolic Engineering and Bioproduction
- Pharmacogenetics and Drug Metabolism
- Cell Adhesion Molecules Research
- Multiple Sclerosis Research Studies
- Advanced Biosensing Techniques and Applications
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
National Technical University of Athens
2016-2025
National Centre of Scientific Research "Demokritos"
2017-2025
University of Sheffield
2024
National and Kapodistrian University of Athens
2018-2022
Science and Technology Park of Crete
2018-2021
Earthquake Planning and Protection Organization
2019
Theageneio General Hospital
2019
Ospedale Antonio Cardarelli
2019
Athens Medical Center
2017
Philip Morris International (United States)
2014
Background Systems biology has embraced computational modeling in response to the quantitative nature and increasing scale of contemporary data sets. The onslaught is accelerating as molecular profiling technology evolves. Dialogue for Reverse Engineering Assessments Methods (DREAM) a community effort catalyze discussion about design, application, assessment systems models through annual reverse-engineering challenges. Methodology Principal Findings We describe our assessments four...
A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using pharmacogenomics database of 1,001 cell lines, we trained deep neural networks for prediction drug and assessed their performance multiple cohorts. We demonstrate that outperform the current state machine learning frameworks. provide proof concept use network-based frameworks aid precision oncology strategies.
In articular cartilage, chondrocytes are surrounded by a pericellular matrix (PCM), which together with the chondrocyte have been termed “chondron.” While precise function of PCM is not known there has considerable speculation that it plays role in regulating biomechanical environment chondrocyte. this study, we measured Young’s modulus from normal and osteoarthritic cartilage using micropipette aspiration technique, coupled newly developed axisymmetric elastic layered half-space model...
The epidermal growth factor receptor (EGFR) signaling pathway is probably the best-studied system in mammalian cells, and it also has become a popular example for employing mathematical modeling to cellular networks. Dynamic models have highest explanatory predictive potential; however, lack of kinetic information restricts current EGFR smaller sub-networks. This work aims provide large-scale qualitative model that comprises main side routes EGFR/ErbB still enables one derive important...
Abstract Objective Chondrocytes, the sole cell type in articular cartilage, maintain extracellular matrix (ECM) through a homeostatic balance of anabolic and catabolic activities that are influenced by genetic factors, soluble mediators, biophysical factors such as mechanical stress. Chondrocytes encapsulated narrow tissue region termed “pericellular matrix” (PCM), which normal cartilage is defined exclusive presence VI collagen. Because PCM completely surrounds each cell, it has been...
Abstract Substantial effort in recent years has been devoted to constructing and analyzing large-scale gene protein networks on the basis of “omic” data literature mining. These interaction graphs provide valuable insight into topologies complex biological but are rarely context specific cannot be used predict responses cell signaling proteins ligands or drugs. Conversely, traditional approaches narrow scope easily make use network-level data. Here, we combine network analysis functional...
Understanding the mechanisms of cell function and drug action is a major endeavor in pharmaceutical industry. Drug effects are governed by intrinsic properties (i.e., selectivity potency) specific signaling transduction network host normal vs. diseased cells). Here, we describe an unbiased, phosphoproteomic-based approach to identify monitoring drug-induced topology alterations. With our proposed method, investigated under diverse stimulations network. Starting with generic pathway made...
Computational analyses of systematic measurements on the states and activities signaling proteins (as captured by phosphoproteomic data, for example) have potential to uncover uncharacterized protein-protein interactions identify subset that are important cellular response specific biological stimuli. However, inferring mechanistically plausible protein networks (PSNs) from phosphoproteomics data is a difficult task, owing in part lack sufficiently comprehensive experimental measurements,...
Abstract Despite decades of intensive search for compounds that modulate the activity particular protein targets, a large proportion human kinome remains as yet undrugged. Effective approaches are therefore required to map massive space unexplored compound–kinase interactions novel and potent activities. Here, we carry out crowdsourced benchmarking predictive algorithms kinase inhibitor potencies across multiple families tested on unpublished bioactivity data. We find top-performing...
ABSTRACT Background This study investigates the native presence and potential anabolic effects of interleukin (IL)‐4 IL‐10 in human intervertebral disc (IVD). Methods Human nucleus pulposus (NP) cells cultured 3D from trauma degenerate IVDs NP explants were stimulated with 10 ng/mL IL‐4, IL‐10, or each combination 1 IL‐1β stimulation. The role IL‐4 IVD was evaluated using immunohistochemistry, gene expression, Luminex multiplex immunoassay proteomics (73 secreted) phosphoproteomics (21...
The aim of the current study was introduction and standardization two experimental conditions for dynamic pupillometry. Pupillometry is a method that can provide valuable data concerning functioning autonomous nervous system. system recording pupil reaction developed in Laboratory Clinical Neurophysiology 1st Department Neurology Aristotle University Thessaloniki, co‐operation with Fluid Mechanics Thessaloniki. This fully automated. It includes an infra‐red video camera, which has capacity...
Systematic study of cell signaling networks increasingly involves high throughput proteomics, transcriptional profiling, and automated literature mining with the aim assembling large scale interaction networks. In contrast, functional analysis usually focuses on a much smaller sets proteins eschews computation but directly cellular responses to environment perturbation. We sought combine these two traditions by collecting response measures reasonably then attempting infer differences in...
Motivation: Inferring how humans respond to external cues such as drugs, chemicals, viruses or hormones is an essential question in biomedicine. Very often, however, this cannot be addressed because it not possible perform experiments humans. A reasonable alternative consists of generating responses animal models and ‘translating’ those results The limitations translation, are far from clear, systematic assessments its actual potential urgently needed. sbv IMPROVER (systems biology...
Abstract Solid stress is a biomechanical abnormality of the tumor microenvironment that plays crucial role in progression. When it applied to cancer cells, solid hinders their proliferation rate and promotes cell invasion metastatic potential. However, underlying mechanisms how implicated metastasis not yet fully understood. Here, we used two pancreatic lines an established vitro system study effect stress-induced signal transduction on migration as well mechanism involved. Our results show...