Publications

* first or co-first author ✉ corresponding author (project supervision)
Christos Papalitsas, Ioannis Mouratidis, Michail Patsakis, Evangelos Stogiannos, Ilias Georgakopoulos-Soares, Grigorios Koulouras (2025). Quantum implementation of multi-pattern string matching for k-mer detection. bioRxiv.
DOI
Nikol Chantzi, Akshatha Nayak, Fotis A Baltoumas, Eleni Aplakidou, Shiau Wei Liew, Jesslyn Elvaretta Galuh, Michail Patsakis, Austin Montgomery, Camille Moeckel, Ioannis Mouratidis, et al. (2025). Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. Genome research.
DOI
Jingjing Zhao, Fotis A Baltoumas, Maxwell A Konnaris, Ioannis Mouratidis, Zhe Liu, Jasmine Sims, Vikram Agarwal, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares, Nadav Ahituv (2025). MPRAbase a Massively Parallel Reporter Assay database. Genome Research.
DOI
Michail Patsakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework. arXiv preprint arXiv:2509.06234.
arXiv
Michail Patsakis, Kimonas Provatas, Fotis A Baltoumas, Nikol Chantzi, Ioannis Mouratidis, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares (2025). MAFin: motif detection in multiple alignment files. Bioinformatics.
DOI
Michail Patsakis, Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files. BMC bioinformatics.
DOI ✉
Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Candace SY Chan, Michail Patsakis, Akshatha Nayak, Rachael Bradley, Mayank Mahajan, Jasmine Sims, Dianne Laboy Cintron, et al. (2025). Leveraging sequences missing from the human genome to diagnose cancer. Communications Medicine.
DOI *
Nikol Chantzi, Shiau Wei Liew, Aurell Wijaya, Candace Chan, Ioannis Mouratidis, Emilyane de Oliveira Santana Amaral, Yasin Uzun, Martin Hemberg, Karen M Vasquez, Chun Kit Kwok, et al. (2025). Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry. bioRxiv.
DOI
Kimonas Provatas, Ioannis Mouratidis, Ilias Georgakopoulos-Soares (2025). KmerCrypt: private k-mer search with homomorphic encryption. Briefings in Bioinformatics.
DOI
Kimonas Provatas, Nikol Chantzi, Nafsika Amptazi, Michail Patsakis, Akshatha Nayak, Ioannis Mouratidis, Apostolos Zaravinos, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares (2025). invertiaDB: a database of inverted repeats across organismal genomes. Nucleic acids research.
DOI