Curriculum Vitae

EDUCATION

Ph.D. in Bioinformatics, National and Kapodistrian University of Athens (06/2022–present)
Thesis: “Design and development of bioinformatics tools for the effective and systematic distinction between true (biological) and artificial somatic variants in pathological conditions, focusing on low-frequency variants”
Supervisor: Andreas Agathangelidis
M.Sc. in Digital Media and Computational Intelligence, Aristotle University of Thessaloniki (09/2019–09/2021)
Thesis: “Applications of Deep Learning on gravitational waves”
Supervisor: Anastasios Tefas
Grade: 9.20/10 (90 ECTS)
B.Sc. in Physics, Aristotle University of Thessaloniki (10/2010–04/2019)
Thesis: “Study of the merging of a neutron star with a black hole and the role of the equation of state”
Supervisor: Charalampos Moustakidis
Grade: 6.64/10 (240 ECTS)

EMPLOYMENT & SCIENTIFIC EXPERIENCE

Research Associate, Bioinformatics Lab, CERTH, Thessaloniki, Greece (11/2021–present)
Group Lead: Fotis Psomopoulos
Duties: Research software development and ML applications, involvement in student supervision and teaching, EU proposal writing and participation in European-funded projects.
International Visiting Research Staff, University of Helsinki, Helsinki, Finland (duration 1 month)
Duties: Research visit through the AHEAD project under the Marie Skłodowska-Curie Actions (MSCA) Staff Exchanges programme. Involved scientific literature curation, publication metadata integration, development of interoperable metadata schemas for the AHEAD observatory and collaboration with researchers across biomedicine, AI, ethics, sociology, psychology and law to advance responsible AI in healthcare.
PhD Student, Department of Biology, National and Kapodistrian University of Athens (06/2022–present)
Duties: Development of synth4bench, an open source synthetic data generation and benchmarking pipeline for low frequency somatic variant calling.
Master Student, Department of Informatics, Aristotle University of Thessaloniki (09/2020–09/2021)
Duties: Software development for Deep Learning Methods in collaboration with the CIDL research group and the Gravitational Waves Group, AUTh.

My participation in research projects:

Duration Project Position Description Funder

01/2025–present SYNTHIA ML methods for generating and evaluating synthetic data HORIZON-JU-IHI-2023-05

06/2024–12/2024 EVERSE Tools and practices for research software quality assessment HORIZON-INFRA-2023-EOSC-01

09/2023–05/2024 SciLake Algorithms for large-scale biodata analysis HORIZON-INFRA-2021-EOSC-01-04

11/2021–08/2023 Gallantries Bioinformatics educational content development Erasmus+

09/2020–10/2021 G2NET ML for gravitational wave astronomy COSTAction CA17137

Duration	Project	Position Description	Funder
01/2025–present	SYNTHIA	ML methods for generating and evaluating synthetic data	HORIZON-JU-IHI-2023-05
06/2024–12/2024	EVERSE	Tools and practices for research software quality assessment	HORIZON-INFRA-2023-EOSC-01
09/2023–05/2024	SciLake	Algorithms for large-scale biodata analysis	HORIZON-INFRA-2021-EOSC-01-04
11/2021–08/2023	Gallantries	Bioinformatics educational content development	Erasmus+
09/2020–10/2021	G2NET	ML for gravitational wave astronomy	COSTAction CA17137

TEACHING EXPERIENCE

University Courses

Volunteer Instructor, Introduction to Python, Aristotle University of Thessaloniki (03/2021)
A six-hour crash course for 4th-year Physics students.

Workshops

Instructor, Artificial Intelligence and Machine Learning in Life Sciences: from foundations to applications, Centre for Genomic Regulation (CRG), Barcelona, Spain (14–18/09/2026)
A hands-on course covering machine learning, deep learning, foundation models, generative AI, reproducibility, DOME recommendations and the EU AI Act for life-science researchers.
Instructor, Artificial Intelligence and Machine Learning in Life Sciences, Centre de Vacances et Colloques Paul Langevin (CNRS), Aussois, France (19–23/05/2025)
An intensive course focused on ML and generative AI in the life sciences.
Helper, Exploratory analysis of biological data: Data Carpentry, EMBL Heidelberg & Virtual (22–26/01/2024)
A hands-on workshop teaching data analysis fundamentals.
Instructor, WES / WGS Data Analysis, IMGGE, Belgrade, Serbia (28/11–01/12/2022)
Taught CNV calling.

Student Supervision

Support in the supervision of M.Sc. thesis: Generative methods in bioinformatics: the use case of synthetic genomics data, “Applied Bioinformatics & Data Analysis”, Democritus University of Thrace.
Support in the supervision of 2 student internships.

FELLOWSHIPS AND AWARDS

Travel grant from the ECCB association to present the poster Synthetic Data Evaluation Metrics in Life Sciences: An ELIXIR Scoping Review at ECCB2026, Geneva, Switzerland (31/08–04/09/2026).
Travel grant from the ISCB to present the poster Benchmarking Somatic Variant Callers: A Tale Unfolding In The Synthetic Genomics Feature Space at ECCB2024, Turku, Finland (16–20/09/2024).
Participation grant to attend BioHackathon Europe 2023 as co-lead for Project 2, Barcelona, Spain (31/10–01/11/2023), with travel and accommodation expenses covered by ELIXIR.

ACADEMIC SERVICES

Ad hoc Reviewer

Elsevier: Expert Systems With Applications, Neurocomputing, Swarm and Evolutionary Computation, Computer Methods and Programs in Biomedicine
IEEE: Data Descriptions
Oxford University Press: Bioinformatics Advances
Springer Nature: BMC Bioinformatics

Conference & Event Organization

MSCA AHEAD Project General Assembly, CERTH, Thessaloniki, Greece (19–20/05/2026)
EOSC-EVERSE Project Kick-off Meeting, Holiday Inn Hotel, Thessaloniki, Greece (11–15/03/2024)
17th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB23), Holiday Inn Hotel, Thessaloniki, Greece (10–12/10/2023)

Research Community Contributions

Co-lead in Generative AI (GenAI) Task Force (05/2026–present)
Contribute to the coordination and development of the Generative AI Task within the ELIXIR AI Ecosystem Focus Group, supporting community discussions and strategic initiatives on the use of generative AI in the life sciences.
Co-lead of Project 8: Advancing Research Software Quality across ELIXIR: Sustainable, Reproducible, and Interoperable Life-Science Software in BioHackathon Europe 2026.
Co-lead of Project 2: Assessing quality and privacy metrics of synthetic health data for benchmarking: the variant callers use case in BioHackathon Europe 2023.

MEMBERSHIPS

Member, International Society for Computational Biology (ISCB) (2023–present)

SELECTED PUBLICATIONS

S.-C. Fragkouli, N. Pechlivanis, A. Anastasiadou, G. Karakatsoulis, A. Orfanou, P. Kollia, A. Agathangelidis, and F. Psomopoulos (2026). Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms. Frontiers in Bioinformatics, 6.
S.-C. Fragkouli, S. Iqbal, L. Crossman, B. Gravel, N. Masued, M. Onders, D. Haseja, A. Stikkelman, A. Valencia, T. Lenaerts, F. Psomopoulos, P. Ó Broin, N. Queralt-Rosinach, and D. Cirillo (2026). An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences. NAR Genomics and Bioinformatics, 8(1), lqag012.
G. Farrell, E. Adamidi, R. Andrade Buono, et al. (including S.-C. Fragkouli) (2026). Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences. Nature Methods.
O. A. Attafi, D. Clementel, K. Kyritsis, E. Capriotti, G. Farrell, S.-C. Fragkouli, et al. (2024). DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology. GigaScience, 13, giae094.
S.-C. Fragkouli, P. Nousi, N. Passalis, P. Iosif, N. Stergioulas, and A. Tefas (2023). Deep residual error and bag-of-tricks learning for gravitational wave surrogate modeling. Applied Soft Computing, article 110746.

Full publication list here.