Publications

* first or co-first author ✉ corresponding author (project supervision)
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
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.
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Akshatha Nayak, Candace Chan, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). The cumulative impact of passenger mutations on cancer development. bioRxiv.
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Eleftherios Bochalis, Michail Patsakis, Nikol Chantzi, Ioannis Mouratidis, Dionysios V Chartoumpekis, Ilias Georgakopoulos-Soares (2025). Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci. Protein Science.
DOI
Nikol Chantzi, Candace SY Chan, Michail Patsakis, Akshatha Nayak, Austin Montgomery, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). Ribosomal DNA arrays are the most H-DNA rich element in the human genome. NAR Genomics and Bioinformatics.
DOI
Emmanouil Panagiotou, Ioannis Athanasios Vathiotis, Austin Montgomery, Camille Moeckel, Mirsini Livanou, Michail Mastrogeorgiou, Athanasios Trimis, Ioannis Trontzas, Nikolaos Konstantinos Syrigos, Ioannis Mouratidis, et al. (2025). Real-world survival outcomes with first-line chemoimmunotherapy and biomarker analysis in extensive-stage small-cell lung cancer. Clinical and Translational Oncology.
DOI