Fundamental Limitations of Genomic Foundation Models for Sequence Generation
Oral presentation
Genomic Foundation Models
AI Evaluation
Event: AGBT General Meeting
Location: Orlando, FL, USA
Date: February 2026
Professional Summary
Research engineer focused on AI safety, alignment, and AIxBio security. I study how
capabilities and values emerge during model training and build scalable interventions to align
frontier models, drawing on deep expertise in biosecurity and biological foundation models.
38 publications (12 first or senior author) and 3 patents in large-scale data analysis and ML
for biology; co-founded an AI-driven cancer-diagnostics startup and authored grants securing
$4M+ in competitive funding.
Education
PhD in Bioinformatics
2023 – 2026
The Pennsylvania State University
M.Sc. in Artificial Intelligence
2020 – 2023
KU Leuven
B.Sc. in Mathematics
2013 – 2018
Aristotle University of Thessaloniki
Interests
AI Safety
AI Alignment
Evals
Interpretability
Biosecurity (AIxBio)
About Me
I’m a research engineer working on AI safety and alignment at Resolution, where I study how capabilities and values emerge during model training and help build scalable interventions to align frontier models.
I came to alignment from the frontier of AIxBio. Through a PhD in bioinformatics and years leading computational genomics teams, I built deep expertise in biological foundation models and biosecurity—red-teaming agentic AI scientists, evaluating the dual-use capabilities and adversarial robustness of genomic language models, studying data-poisoning and backdoor attacks, and developing tamper-resistant weight-locking for open-weight biological AI. That domain grounding is what I now bring to general questions of AI safety.
My path has run from mathematics to artificial intelligence to bioinformatics and back to AI safety, across four countries and many hats: from co-founding a cancer-diagnostics startup to building research infrastructure from scratch, and from publishing open-source bioinformatics tools to evaluating state-of-the-art systems like Evo 2. What drives my work is a conviction that as AI systems become increasingly capable, we need rigorous, empirical frameworks to evaluate and ensure their safety.
I’m passionate about mentorship and collaborative science. I’ve had the privilege of guiding researchers from their first steps in the field to their first lead-author publications, and I thrive in environments that balance rigorous research with rapid iteration.
When I’m not working, you’ll find me running or learning a new language.
Selected Publications
* first or co-first author✉ corresponding author (project supervision)
(2026).
BioVeil MATRIX: Uncovering and categorizing vulnerabilities of agentic biological AI scientists.
arXiv preprint arXiv:2605.00927.
(2026).
Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models.
arXiv preprint arXiv:2603.27465.
(2026).
Fundamental limitations of genomic language models for realistic sequence generation.
bioRxiv.
(2025).
Leveraging sequences missing from the human genome to diagnose cancer.
Communications Medicine.
(2025).
ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences.
Briefings in bioinformatics.
For an up-to-date list of publications, also see Google Scholar.
(2026).
Accelerating inference in genomic and proteomic foundation models via speculative decoding.
bioRxiv.
(2026).
Characterization of hairpin loops and cruciforms across 118,019 genomes spanning the tree of life.
Genome Biology and Evolution, 18(5), evag089.
(2026).
Doing more with less: Genomic quasi-G-primes differentiate septic from healthy
patients.
PloS One.
(2026).
Zimin patterns in genomes.
PLoS Computational Biology.
(2025).
Identification of the shortest species-specific oligonucleotide sequences.
Genome research.
(2025).
invertiaDB: a database of inverted repeats across organismal genomes.
Nucleic acids research.
(2025).
KmerCrypt: private k-mer search with homomorphic encryption.
Briefings in Bioinformatics.
(2025).
Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry.
bioRxiv.
(2025).
MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF
files.
BMC bioinformatics.
(2025).
MAFin: motif detection in multiple alignment files.
Bioinformatics.
(2025).
Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework.
arXiv preprint arXiv:2509.06234.
(2025).
MPRAbase a Massively Parallel Reporter Assay database.
Genome Research.
(2025).
Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.
Genome research.
(2025).
Real-world survival outcomes with first-line chemoimmunotherapy and biomarker analysis in extensive-stage small-cell lung cancer.
Clinical and Translational Oncology.
(2025).
Ribosomal DNA arrays are the most H-DNA rich element in the human genome.
NAR Genomics and Bioinformatics.
(2025).
Taxonomic quasi-primes: peptides charting lineage-specific adaptations and
disease-relevant loci.
Protein Science.
(2025).
The cumulative impact of passenger mutations on cancer development.
bioRxiv.
(2025).
The topography of nullomer-emerging mutations and their relevance to human disease.
Computational and Structural Biotechnology Journal.
(2024).
A review on cell-free RNA profiling: Insights into metabolic diseases and
predictive value for bariatric surgery outcomes.
Molecular metabolism.
(2024).
A survey of k-mer methods and applications in bioinformatics.
Computational and Structural Biotechnology Journal.
(2024).
Advances in computational and experimental approaches for deciphering transcriptional
regulatory networks.
BioEssays.
(2024).
kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species.
Computational and structural biotechnology journal.
(2024).
Microsatellites explorer: A database of short tandem repeats across genomes.
Computational and Structural Biotechnology Journal.
(2024).
Peptide absent sequences emerging in human cancers.
European Journal of Cancer.
(2024).
The determinants of the rarity of nucleic and peptide short sequences in nature.
NAR Genomics and Bioinformatics.
(2024).
Utilizing nullomers in cell-free RNA for early cancer detection.
Cancer gene therapy.
(2023).
Eligibility for screening with low-dose CT in a real-world cohort of patients
with lung cancer in Greece: A brief report.
Lung Cancer.
(2023).
Frequentmers-a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.
BMC genomics.
(2023).
Quasi-prime peptides: identification of the shortest peptide sequences unique
to a species.
NAR Genomics and Bioinformatics.
(2021).
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides
across functional categories and evolution.
Genome Biology.
(2021).
Asymmetron: a toolkit for the identification of strand asymmetry patterns
in biological sequences.
Nucleic acids research.
Patents
- Georgakopoulos-Soares, I., Mouratidis, I., & Provatas, K. (2025). System and Method for Extracting Neomers. U.S. Provisional Patent.
- Ahituv, N., Yizhar-Barnea, O., Georgakopoulos-Soares, I., Mouratidis, I., & Hemberg, M. (2023). Systems for mutation caller and methods of using the same. WO2024103003A3.
- Ahituv, N., Yizhar-Barnea, O., Georgakopoulos-Soares, I., Mouratidis, I., & Hemberg, M. (2022). Compositions comprising nullomers and methods of using the same for cancer detection and diagnosis. WO2022235718A3.
Presentations
Leveraging sequences missing from the human genome to diagnose cancer
Oral presentation
Cancer Detection
Event: Center for Molecular Carcinogenesis and Toxicology Symposium
Location: Austin, TX, USA
Date: December 2025
Attendance: ~50 attendees
Identification of the shortest species-specific oligonucleotide sequences
Poster pitch and poster presentation
Computational Biology
Quasi-Primes
Event: Revolutionizing Next-Generation Sequencing
Location: Antwerp, Belgium
Date: March 2025
Attendance: ~300 attendees
Nucleic quasi-primes: identification of the shortest unique oligonucleotide sequences in a species
Oral presentation
Computational Biology
Quasi-Primes
Event: AGBT General Meeting
Location: Marco Island, FL, USA
Date: February 2025
Attendance: ~250 attendees
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species
Poster presentation
Computational Biology
Database
Event: Biology of Genomes
Location: Cold Spring Harbor, NY, USA
Date: May 2024
Contact
Location: Austin, Texas
Reach me on LinkedIn. I’m always open to discussing AI safety and alignment research, including AIxBio safety.