Ioannis Mouratidis 🧬

Ioannis Mouratidis

(he/him)

Senior Research Engineer/Scientist Associate

University of Texas at Austin

Professional Summary

Machine learning and genomics researcher with 35 publications (10 first or senior author). Co-founded AI-driven cancer biomarker startup, authored grants securing $4M+ in competitive funding and currently lead a 5-member team with a focus in developing novel computational methods and testing the capabilities and safety profiles of biological foundation models.

Education

PhD in Bioinformatics and Genomics

Aug 2023 – Jan 2026

The Pennsylvania State University

M.Sc. in Artificial Intelligence

Sep 2020 – Jul 2023

KU Leuven

B.Sc. in Mathematics

Oct 2013 – Mar 2018

Aristotle University of Thessaloniki

Interests

AI Evals AI Safety Genomic Language Models Algorithms and Datastructures Pipeline Optimization AI x Bio
About Me

I’m a computational biologist working at the intersection of AI and genomics, with a particular focus on understanding and ensuring the safety of foundation models in biology.

My academic journey has taken me from mathematics to artificial intelligence, then to bioinformatics, and now back to AI with a focus on safety and foundation models in biology. Along the way, I’ve lived and worked in four different countries and worn many hats: from co-founding a cancer diagnostics startup to building research infrastructure from scratch, and from developing open-source bioinformatics tools to training genomic language models.

What drives my work is a conviction that as AI systems become increasingly capable, we need robust frameworks to evaluate their safety. Whether I’m assessing data poisoning vulnerabilities in genomic models or benchmarking the capabilities of state-of-the-art systems like Evo 2, I’m focused on ensuring these powerful tools advance science responsibly.

I’m passionate about mentorship and collaborative science. I’ve had the privilege of guiding researchers from their first steps in bioinformatics to their first publications, and I thrive in environments that balance rigorous research with the rapid iteration of startup culture.

When I’m not analyzing petabytes of genomic data, you’ll find me jogging in Austin or learning new languages.

Publications

* first or co-first author✉ corresponding author (project supervision)

(2026). Accelerating inference in genomic and proteomic foundation models via speculative decoding. bioRxiv.
DOI
(2026). Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients. PloS One.
DOI
(2026). Fundamental limitations of genomic language models for realistic sequence generation. bioRxiv.
DOI
(2026). Zimin patterns in genomes. PLoS Computational Biology.
DOI
(2025). Identification of the shortest species-specific oligonucleotide sequences. Genome research.
DOI *
Presentations

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

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

Email: ioannis.mouratidis [at] austin.utexas.edu

Location: Austin, Texas

I’m always open to discussing research collaborations, consulting opportunities, or mentoring in bioinformatics and machine learning.