Publications

* first or co-first author ✉ corresponding author (project supervision)
Kimon Antonios Provatas, Avery Self, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2026). BioVeil MATRIX: Uncovering and categorizing vulnerabilities of agentic biological AI scientists. arXiv preprint arXiv:2605.00927.
DOI ✉
Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2026). Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models. arXiv preprint arXiv:2603.27465.
DOI ✉
Nikol Chantzi, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2026). Zimin patterns in genomes. PLoS Computational Biology.
DOI
Alexandros Tzanakakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2026). Fundamental limitations of genomic language models for realistic sequence generation. bioRxiv.
DOI ✉
Congzhou M Sha, Michail Patsakis, Ioannis Mouratidis, Xiang Wei, Taewhan Chung, Justin Kovac, Ilias Georgakopoulos-Soares (2026). Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients. PloS One.
DOI
Nikol Chantzi, Camille Moeckel, Candace S Y Chan, Akshatha Nayak, Guliang Wang, Ioannis Mouratidis, Dionysios Chartoumpekis, Karen M Vasquez, Ilias Georgakopoulos-Soares (2026). Characterization of hairpin loops and cruciforms across 118,019 genomes spanning the tree of life. Genome Biology and Evolution, 18(5), evag089.
DOI
Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Michail Patsakis, Alexandros Tzanakakis, Akshatha Nayak, Ioannis Mouratidis, Evangelos I Avgoulas, Ilias Georgakopoulos-Soares (2026). Accelerating inference in genomic and proteomic foundation models via speculative decoding. bioRxiv.
DOI
Guliang Wang, Ioannis Mouratidis, Kimonas Provatas, Nikol Chantzi, Michail Patsakis, Ilias Georgakopoulos-Soares, Karen M Vasquez (2025). ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences. Briefings in bioinformatics.
DOI *
Candace SY Chan, Ioannis Mouratidis, Austin Montgomery, Georgios Christos Tsiatsianis, Nikol Chantzi, Martin Hemberg, Nadav Ahituv, Ilias Georgakopoulos-Soares (2025). The topography of nullomer-emerging mutations and their relevance to human disease. Computational and Structural Biotechnology Journal.
DOI
Akshatha Nayak, Candace Chan, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). The cumulative impact of passenger mutations on cancer development. bioRxiv.
DOI