Computational proteomics and signaling
We model proteomic, phosphoproteomic, cytokine, and secretome data to infer pathway activity, regulatory structure, and disease-relevant molecular states.
BioSysLab
National Technical University of Athens
Biomedical Systems Laboratory
Engineering, computation, and molecular measurement for translational biology and medicine.
BioSysLab develops measurement and computational frameworks for translational biology. The lab's core expertise is mathematical, computational, and data-driven modeling, integrating molecular measurements and clinical context with biomedical questions in cancer, chronic disease, drug response, and precision health.
20+
years in multiplex assays, proteomics, and systems biology
34
alumni trainees across postdoc, PhD, MS/Diploma, and undergraduate levels
NTUA
Biomedical systems, computation, and engineering
Research
Research directions
We study biological systems through mathematical models, machine learning & AI, network biology, and computational analysis of high-dimensional biomedical data. Wet-lab access and experimental/clinical collaborators support.
Biomarker modeling and translation
We combine plasma proteins, liquid-biopsy signals, clinical variables, and causal evidence into interpretable models for early detection, monitoring, and stratification.
AI for translational biology
We develop interpretable and generative models of disease trajectories, tumor resistance, drug response, and adaptive biomedical decision-making.
Mathematical disease dynamics
We study disease progression as dynamic state landscapes, using tools such as optimal transport, stochastic models, control theory, and trajectory inference.
People
Current members
Leonidas G. Alexopoulos
Professor, National Technical University of Athens
Prof. Alexopoulos leads BioSysLab at NTUA. He works at the interface of engineering, computation, proteomics, and medicine, with more than two decades of experience in multiplex assays and systems biology.
He has trained at Duke, MIT, and Harvard, co-founded the biotech spin-off Protavio, and co-founded the NTUA Master's program in Translational Engineering in Health and Medicine.
Nikolaos Meimetis
Postdoctoral Researcher
Nikolaos is a computational systems biologist and engineer with interests in translational oncology, tumor progression and treatment resistance, and interpretable models that connect molecular state to therapeutic decision-making.
He earned his PhD in Biological Engineering at MIT, followed by a postdoctoral appointment at MIT, after training in Mechanical Engineering at NTUA. His work also explores basic mechanisms of cellular state transitions, regulatory drivers, liquid-biopsy biomarkers, and open-source computational biology.
Polychronis Dellis
Laboratory Manager
Polychronis supports BioSysLab's laboratory operations and research infrastructure. He has academic experience as a Scientific Associate / Assistant Professor at TEI of Athens and is currently affiliated with the School of Pedagogical and Technological Education.
Alumni Former BioSysLab roles and student research contributions
- Asier Antoranz PhD student
- Jan Rozanc Research staff / postdoctoral alumnus
- Theodore Sakellaropoulos PhD student
- Dimitris Messinis Research staff / postdoctoral alumnus
- Dimitrios Tzeranis Postdoctoral researcher
- Michael Neidlin Postdoctoral researcher
- Louiza Gkouma MS/Diploma student
- Nafsika Chala MS/Diploma student
- Danae Zareifi PhD student
- Christos Fotis PhD student
- Savvina Gkouma MS/Diploma student
- Theocharis Iordanis MS/Diploma student
- Smaragda Dimitrakopoulou MS/Diploma student
- Melina Tourni MS/Diploma student
- Antonion Korcari MS/Diploma student
- Thomas Gkekas MS/Diploma student
- Nagia Kokkori MS/Diploma student
- Odysseas Chaliotis MS/Diploma student
- Panagiotis Terzopoulos MS/Diploma student
- Antonis Sardis MS/Diploma student
- Konstantinos Athanasopoulos MS/Diploma student
- Giorgos Alevizos MS/Diploma student
- Ioannis N. Melas PhD student
- Maria Chrysopoulou MS/Diploma student
- Konstantinos Ntagiantas MS/Diploma student
- George Kanakaris PhD student
- Orfeas Aidonopoulos MSc student
- Ilona Binenbaum MSc student
- Alexander Polesiouk Diploma thesis student
- Marina Botonaki Diploma thesis student
- Terry Tounta Diploma thesis student
- Maria Michalopoulou Diploma thesis student
Publications
Selected publications
-
FlowTransOP: Distributional Translation of Omics Signatures via Constrained Deep Flow Matching.
Meimetis, Magliacane, Hoang, Lauffenburger. bioRxiv, 2026.
-
Secretome and Pathway Analysis of Stress Induced Disc Degeneration In Vitro.
Kanelis, Nuesch, Snuggs, Le Maitre, Alexopoulos. JOR Spine, 2026.
-
Protein kinase D drives the secretion of invasion mediators in triple-negative breast cancer cell lines.
Gali et al. iScience, 2024.
-
Inference of drug off-target effects on cellular signaling using interactome-based deep learning.
Meimetis, Lauffenburger, Nilsson. iScience, 2024.
-
Conserved transcriptomic signatures and protein markers in cellular senescence models.
Skea et al. Research Square preprint, 2023.
-
AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis et al. npj Systems Biology and Applications, 2024.
-
Predicting single cell genotypes from single cell expression profiles in AML using deep learning.
Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2023.
-
A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease.
Zareifi, Chaliotis, Chala, Meimetis et al. iScience, 2022.
Courses
Teaching
Teaching connects computation, biological engineering, biomedical technology, and design for health applications.
Introduction to Biological Engineering
Also available in English for Erasmus students.
Biomedical Systems Design / Biodesign
Also available in English for Erasmus students.
Biomechanics / Biomedical Technology
Also available in English for Erasmus students.
Vacancies
Open positions
Open calls and informal inquiries will be posted here.
We welcome prospective students or collaborators with a strong fit in systems biology, computational biology, proteomics, or biomedical engineering to contact the lab with a concise research interest note and CV.
Contact
Find BioSysLab
BioSysLab is located at the National Technical University of Athens, Zografou campus.
Office
Department of Mechanical EngineeringBuilding E, Room 320
National Technical University of Athens
Heroon Polytechniou 9
15780 Zografou, Greece
Tel: +30 210 7721666
Email: leo@mail.ntua.gr
Laboratory
Department of Mechanical EngineeringBuilding M
Biomedical Systems Laboratory
National Technical University of Athens
Heroon Polytechniou 9
15780 Zografou, Greece
Tel: +30 210 7721516