Projects

Autonomous and robust cell therapies

One of the most remarkable features of living organisms is their ability to adapt to uncertain and noisy environments. Over billions of years, evolution has equipped cells with sophisticated regulatory mechanisms that enable this property, known as homeostasis. When these mechanisms fail, the consequences can be severe, leading to diseases such as cancer and autoimmunity. Current therapies, ranging from drugs to cell-based interventions, struggle to produce consistent outcomes across diverse patient populations. In many cases, achieving reliable therapeutic responses remains a major challenge.

My work lies at the intersection of synthetic biology and control theory, an emerging field known as cybergenetics, which aims to engineer living cells with built-in control systems. These systems can sense, decide, and act to restore disrupted biological regulation.

During my PhD with the Khammash group at ETH Zurich, I focus on designing cell-based therapies that function as living feedback controllers. I have developed high-throughput genomic integration methods and an optogenetic digital twin platform to enable the rational engineering of these systems in mammalian cells (preprint, 2026). I am applying these approaches to engineer advanced controller topologies and deploy them for robust immune regulation.

Previously, during my MSc, I contributed to the modeling and experimental realization of proportional-integral feedback circuits for robust and precise regulation in mammalian cells (PNAS, 2022).

Bacterial biosensors for living diagnostics

Engineering live cells to reliably sense and respond to signals of the extracellular milieu constitutes one of the major goals of synthetic biology. Examples of such cellular systems are engineered bacteria that can act as sentinels or living diagnostics.

The gastrointestinal tract represents one of the most complex environments to deploy such biosensors, due to the vast number of microbial communities and their metabolites that are present. Yet, metabolites of this microbial ecosystem, such as short-chain fatty acids, are closely linked to host health and disease, making them compelling targets for in situ monitoring.

During my MSc thesis in the Platt group at ETH Zurich, I used directed evolution to develop biosensors for short-chain fatty acids. I identified improved variants and characterised their performance with high-throughput time course assays and deep learning-based structural modeling.

Cell-free biology & construction of a minimal cell

The in vitro assembly of a minimal cell from its fundamental biochemical components is one of the central challenges in synthetic biology. It represents a bottom-up approach to understanding life by rebuilding its core functions from scratch.

After being selected for the Summer Research Program in the Maerkl group at EPFL, I worked on establishing an orthogonal cell-free DNA replication system. I identified, cloned and purified all essential protein components of the RSF1010 replication machinery and tested them in in vitro replication assays. I also had my first crack at microfluidics, assessing the binding affinities of these proteins using high-throughput microfluidic platforms.

Biocomputing & iGEM competition

During 2016, I founded and co-led Greece's first university synthetic biology team for the iGEM competition.

Our project focused on engineering RNAi-based logic circuits as colorectal cancer therapeutics (poster →). I also developed a hierarchical cloning workflow for mammalian genetic circuit assembly, validated constructs in transfection assays, performed mathematical modeling and engineered an E. coli-based delivery system leveraging quorum sensing for cell-density-dependent invasion into cancer cells.

The multidisciplinary team brought together 11 fearless and amazing peers from 7 departments across 2 universities. Our work was awarded a Gold Medal and nominated for Best Therapeutics Project, and catalyzed a synthetic biology ecosystem in Greece, from a single team in 2017 to 45+ iGEM teams nationwide today.

iGEM Greece team photo iGEM Greece at the Jamboree
Cumulative Greek iGEM Higher-Ed Teams over Time

SKAI Naftemporiki neaflorina.gr esos.gr

Neural stem cell biology

Understanding and harnessing neural stem and progenitor cells is key to advancing both fundamental research and regenerative medicine. As an Amgen Scholar in the Franklin lab at the University of Cambridge, I refined a novel isolation protocol of endogenous neural stem cells from the postnatal brain of live rats and set up cell culture assays to characterize cell identity. This method (Stem Cell Reports, 2021) paves the way for longitudinal animal studies as well as autologous transplantations.

Amgen Scholars Cambridge 2016
From the Amgen Scholars Programme, University of Cambridge

Aging

Human mesenchymal stem cells (MSCs) are widely used in cell-based therapies, but their clinical application can be limited by replicative senescence during in vitro expansion. In the Koliakos lab at AUTh, I helped assess the anti-aging and antioxidative properties of MSCs overexpressing the proteasome catalytic β5 subunit. I performed catalase and superoxide dismutase activity assays using Wharton’s jelly-derived MSCs.

Space biology & aerospace engineering

Since 1961, nearly 700 humans have traveled to space, providing valuable insights into the physiological effects of spaceflight. However, our understanding of these effects at the cellular and molecular level, where many originate, remains limited. Characterizing molecular perturbations, such as transcriptional and proteomic changes, is essential for developing countermeasures, synthetic biology tools, and life support systems for long-duration missions.

With few exceptions, such as Apollo 17 and NASA’s BioSentinel mission, most biological experiments have been confined to low Earth orbit, primarily on the International Space Station. These platforms are limited by high costs, restricted access, and reliance on sample return, which can compromise biological fidelity. Even landmark studies, such as NASA’s multi-omics astronaut analysis, were constrained by small sample sizes and logistical complexity.

Nanosatellites offer a scalable and cost-effective alternative. Since 2002, nearly 3,000 have been launched globally, yet fewer than a dozen (<0.4%) have focused on space biology. While these missions demonstrated the feasibility of biological payloads in space, they were largely limited to organism-level survival studies and low-resolution measurements.

To date, no autonomous platform exists for in situ, high-throughput interrogation of biology in space. Moreover, current nanosatellite platforms are not modular or reconfigurable, requiring bottom-up engineering for each new payload. This creates a high barrier to entry, excluding a broad community of biologists, bioengineers, and biochemists from designing and deploying experiments in space.

To address this gap, I work on developing a fully autonomous and modular space platform for high-throughput biological experimentation in space, as the science lead of the AcubeSAT mission of the SpaceDot team at AUTh. The mission is one of 3 in Europe (and the first in Greece) to be selected for the European Space Agency's Fly Your Satellite! 3 program.

I have been involved across the full lifecycle of the system, from concept to flight qualification, contributing to the design, testing and integration of a miniaturized laboratory combining biology, microfluidics, imaging, sensing, and onboard experiment control. I led the science/payload subsystem (∼30 members over time) to achieve multiple milestones, including successful full environmental qualification (vibration, thermal-vacuum, leak testing), characterisation of yeast response to radiation exposure, and system design maturation and compliance with ESA requirements. All of our work is open-source →.

AcubeSAT satellite AcubeSAT team

ERTnews Parallaxi ΑΜΝΑ ΜΑΚΕΔΟΝΙΑ · and more →

Misc

Other than the above, I have tinkered with a lot of random things over the years. These include: