Curriculum Vitae
See my researcher profile in: ORCID || Google Scholar || Microsoft Academic || ResearchGate || Publons || Academia.edu || PubMed || Scopus
Education
| 2014-2019 | PhD in Bioinformatics Section of Cell Biology & Biophysics, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Thesis Title: “Computational Studies of Protein-Protein Interactions in Transmembrane Proteins” Advisory Committee: Emer. Prof. Stavros Hamodrakas, Assist. Prof. Vassiliki Iconomidou, Prof. Pantelis Bagos |
| 2014-2015 | Masters in Bioinformatics (Msc) Bioinformatics Post-graduate Programme, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Thesis Title: “Computational Studies of G-protein coupled receptor (GPCR) oligomerization Interactions” Supervisor: Assist. Prof. Vassiliki Iconomidou |
| 2006-2013 | Diploma in Biology (Bsc) Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Thesis Title: “Studies of Interactions Between GPCRs, G-proteins and Effectors” Supervisor: Prof. Stavros Hamodraka |
Professional & Research Experience
| 2023-Now | Bioinformatics consultant (part-time) Ancilia Biosciences, New York City, NY, USA (https://www.anciliabio.com/) |
| 2020-Now | Post-Doctoral Researcher Bioinformatics & Integrative Biology Lab, B.S.R.C. “Alexander Fleming”, Athens, Greece |
| 2019-2020 | Biologist (Lab Assistant) Center of Molecular Biology, 401 General Military Hospital of Athens, Hellenic Armed Forces Obligatory National Service in the Hellenic Armed Forces |
| 2018 | Research Assistant Section of Cell Biology & Biophysics, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Participant in the Research Project entitled “Bioinformatics and Biophysics Analysis of the Amyloidogenicity of Leukocyte Chemotactic Factor 2 (LECT2)”, funded by Alnylam Pharmaceuticals |
| 2016-2018 | Secretariat & Technical Support Bioinformatics Post-graduate Programme / Masters in “Bioinformatics – Computational Biology”, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Secretarial and Technical Support for the Bioinformatics Post-graduate program, later renamed “Masters in Bioinformatics – Computational Biology” (http://bioinformatics.biol.uoa.gr/msc) |
| 2015-2019 | Research Assistant (PhD Candidate) Section of Cell Biology & Biophysics, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece PhD candidate researcher |
| 2015 | Research Assistant Section of Cell Biology & Biophysics, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Participant in the Research Project entitled “Development and screening of novel, rationally designed IAPP (Amylin) variant / analog-peptides as drugs for Diabetes Type II”, co-financed by the European Union (European Regional Development Fund – ERDF) and Greek national funds through the Operational Program “Competitiveness and Entrepreneurship” of the National Strategic Reference Framework (NSRF) |
| 2015 | Research Assistant Section of Cell Biology & Biophysics, Department of Biology, National & Kapodistrian University of Athens, Athens, Greece Participant in the Research Project entitled “Bioinformatics approaches for studying membrane proteins and their implications in disease”, co-financed by the European Union (European Regional Development Fund – ERDF) and Greek national funds through the Operational Program “Competitiveness and Entrepreneurship” of the National Strategic Reference Framework (NSRF) |
Skills & Expertise
Scientific Skills:
- Molecular Dynamics (MD) simulations: experience with protein, nucleic acid, carbohydrate and lipid simulations. Standard simulation schemes (Equilibrium MD), Steered Molecular Dynamics (SMD), Potential of Mean Force (PMF) calculations, Free Energy Calculations (Free Energy Perturbation, Thermodynamic Integration, Umbrella Sampling, MM-PBSA etc)
- Force Field development: experience with molecule parametrization for lipids, modified amino acids and small molecule compounds, fitting to QM data, validation with experimental data.
- Sequence Analysis: experience with Multiple Sequence Analysis creation, manipulation and optimization, training and validation of profile Hidden Markov Models (pHMMs), analysis and annotation of large genomic and proteomic data.
- Network Analysis: Creation, visualization and analysis of protein-protein interaction networks, application of network theory to the analysis of MD simulations (Dynamical Network Analysis)
Technical Expertise:
- Molecular Modeling & Molecular Simulations (QM, MM & MD): Experience with GROMACS, NAMD, Amber, GAUSSIAN
- Small molecule parametrization: experience with the CHARMM/CGenFF, AMBER/GAFF, MARTINI force fields.
- Programming Languages: Python, Perl, Tcl/Tk, PHP, JavaScript, SQL, Shell (sh/bash), awk, C, Java, R
- Computer Operating Systems: Experience with Linux [Ubuntu and Ubuntu-based distros, Debian, OpenSUSE, Red Hat, CentOS] (advanced), Microsoft Windows [from 98/SE/ME to Windows 10] (advanced), Apple macOS X (intermediate)
- Structural Bioinformatics Software: experience with PyMOL, Visual Molecular Dynamics (VMD), UCSF Chimera, Avogadro, APBS, DelPhi, AutoDock, MODELLER, Schrödinger Maestro etc.
- Sequence Analysis Software: ClustalX/ClustalO, T-Coffee, HMMER, JalView, BLAST/BLAST+ etc
- Network Analysis: Cytoscape, Cytoscape.js, NetworkX
- MicroArray Analysis: Affymetrix Expression Console, Expander, Bioconductor
- Statistics / Biostatistics: Stata, SPSS
- Database Management: MySQL, Microsoft Access, SQLite
- Web Design: HTML (HTML5), CSS (CSS3), JavaScript, PHP, JSP (Java Servlet Pages), R/Shiny (Shiny apps)
- Content Management Systems: Experience with WordPress, Joomla, TYPO3, Drupal, Adobe GoLive