PROJECT
SUPERVISORS
Project Supervisor
Theodora Katsila
Background
I carried out my doctoral research at the Biomedical Research Foundation of the Academy of Athens, earning a PhD in Chemistry from the University of Patras. Following postdoctoral training at the Vall d’Hebron Institute of Oncology in Barcelona, I returned to Greece, where I have held research and teaching positions at the University of Patras and the Hellenic Open University, and currently serve as a Research Associate Professor and Group Leader at the Institute of Chemical Biology of the National Hellenic Research Foundation. My team brings together in silico, in vitro, and in vivo approaches (the “IN3” tri-modal innovation engine) to accelerate progress in translational precision medicine, exploring how drugs, advanced materials, and smart systems can be repurposed, using proteoform analysis to uncover both digital and molecular biomarkers.
Over the course of my career, I have built pioneering computational and experimental pipelines designed to shorten the path from laboratory discovery to clinical application. This work has resulted in extensive publications and scientific contributions, as well as corporate research funding and co-invented patents that amplify the reach of our discoveries. In 2023, I was honored with the Rosalind Franklin Society Special Award in Science and featured as one of the Humans of HUPO. These recognitions reflect my commitment to advancing proteomics and AI-driven translational biomarkers to bring precision medicine closer to clinical reality.
Minos-Timotheos Matsoukas
I earned my PhD in Medicinal Chemistry from the University of Patras and completed postdoctoral training in computational chemistry at the Autonomous University of Barcelona, currently serving an Assistant Professor at the University of West Attica in Athens, where I lead the Computational Drug Design and AI research group. My expertise lies at the intersection of computational chemistry and biology, with a focus on machine learning and artificial intelligence for drug discovery. In particular, I specialize in virtual screening of chemical libraries to identify novel bioactive compounds and in studying the dynamics of transmembrane proteins through structural biology data. Alongside my academic work, I have been actively involved in the pharmaceutical industry through innovative startups and collaborations, serving as a project manager and scientific advisor in drug discovery programs. My vision is to help transform drug discovery by harnessing AI and big data, accelerating the design of new therapeutics and bringing them closer to clinical and commercial applications.
Research
Our research program is centered on translational precision medicine and healthcare innovation. We integrate in silico, in vitro, and in vivo methodologies into one framework (IN3) to fast-track discoveries from concept to societal impact. We leverage computational modelling, AI, and multi-omics to understand druggability and safety, harness molecular and digital biomarkers, and repurpose drugs and materials for disruptive applications.
A hallmark of our research is the use of extracellular vesicles and particles, exploiting 3D cell culture models to profile them and identifying druggable key players and candidate biomarkers for disease monitoring. By coupling high-resolution mass spectrometry and imaging, we can best capture mechanistic insights. Overall, our lab operates at the interface of computational drug design and experimental validation, developing pipelines that rapidly model, test, and validate novel solutions upon de-risking.
Publications
Charou D, Rogdakis T, Latorrata A, Valcarcel M, Papadogiannis V, Athanasiou C, Tsengenes A, Papadopoulou MA, Lypitkas D, Lavigne MD, Katsila T, Wade RC, Cader MZ, Calogeropoulou T, Gravanis A, Charalampopoulos I (2024). Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer's disease. Stem Cell Research & Therapy, 15(1): 200.
https://doi.org/10.1186/s13287-024-03818-w
Poulaki A, Katsila T, Hatziyannis ES, Stergiou IE, Kapsogeorgou E, Hatzis S, Vassilopoulos G, Voulgarelis M, Giannouli S (2024). Metabolic Reprogramming in Myelodysplastic Syndromes. Blood, 144 (suppl 1): 6694.
https://doi.org/10.1182/blood-2024-211216
Swen J.J., van der Wouden C.H., Manson L.E., Abdullah-Koolmees H., Blagec K., Blagus T., … Ubiquitous Pharmacogenomics Consortium (2023). A 12-gene pharmacogenetic panel to prevent adverse drug reactions: an open-label, multicentre, controlled, cluster-randomised crossover implementation study. The Lancet, 401(10374):347.
https://doi.org/10.1016/S0140-6736(22)01841-4
Ouzounis S, Panagiotopoulos V, Bafiti V, Zoumpoulakis P, Cavouras D, Kalatzis I, Matsoukas MT, Katsila T (2023). A Robust Machine Learning Framework Built Upon Molecular Representations Predicts CYP450 Inhibition: Toward Precision in Drug Repurposing. OMICS, 27(7):305.
https://doi.org/10.1089/omi.2023.0075
Katsila T, Spyroulias GA, Patrinos GP, Matsoukas M-T (2016). Computational approaches in target identification and drug discovery. Computational and Structural Biotechnology Journal, 14:177.
https://doi.org/10.1016/j.csbj.2016.04.004