Article-Journal | Ioannis Mouratidishttps://ioannis-mouratidis.github.io/publication_types/article-journal/Article-JournalHugo Blox Builder (https://hugoblox.com)en-usThu, 01 Jan 2026 00:00:00 +0000https://ioannis-mouratidis.github.io/media/icon_hu_899445b689d8f445.pngArticle-Journalhttps://ioannis-mouratidis.github.io/publication_types/article-journal/Accelerating inference in genomic and proteomic foundation models via speculative decodinghttps://ioannis-mouratidis.github.io/publication/provatas-2026-accelerating/Thu, 01 Jan 2026 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/provatas-2026-accelerating/Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patientshttps://ioannis-mouratidis.github.io/publication/sha-2026-quasi/Thu, 01 Jan 2026 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/sha-2026-quasi/Fundamental limitations of genomic language models for realistic sequence generationhttps://ioannis-mouratidis.github.io/publication/tzanakakis-2026-fundamental/Thu, 01 Jan 2026 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/tzanakakis-2026-fundamental/Zimin patterns in genomeshttps://ioannis-mouratidis.github.io/publication/chantzi-2026-zimin/Thu, 01 Jan 2026 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2026-zimin/Identification of the shortest species-specific oligonucleotide sequenceshttps://ioannis-mouratidis.github.io/publications/species-specific-2025/Sat, 01 Feb 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/species-specific-2025/<p>This work provides a comprehensive catalog of minimal species-specific sequences with applications in diagnostics, environmental monitoring, and food authentication.</p>Identification of the shortest species-specific oligonucleotide sequenceshttps://ioannis-mouratidis.github.io/publication/mouratidis-2025-identification/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/mouratidis-2025-identification/invertiaDB: a database of inverted repeats across organismal genomeshttps://ioannis-mouratidis.github.io/publication/provatas-2025-invertiadb/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/provatas-2025-invertiadb/KmerCrypt: private k-mer search with homomorphic encryptionhttps://ioannis-mouratidis.github.io/publication/provatas-2025-kmercrypt/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/provatas-2025-kmercrypt/Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestryhttps://ioannis-mouratidis.github.io/publication/chantzi-2025-landscape/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2025-landscape/Leveraging sequences missing from the human genome to diagnose cancerhttps://ioannis-mouratidis.github.io/publication/georgakopoulos-2025-leveraging/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/georgakopoulos-2025-leveraging/Leveraging sequences missing from the human genome to diagnose cancerhttps://ioannis-mouratidis.github.io/publications/cancer-detection-2025/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/cancer-detection-2025/<p>This work demonstrates how sequences that are absent from the human genome can be leveraged as biomarkers for cancer detection, with potential applications in liquid biopsy-based diagnostics.</p>MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF fileshttps://ioannis-mouratidis.github.io/publication/patsakis-2025-mafcounter/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/patsakis-2025-mafcounter/MAFin: motif detection in multiple alignment fileshttps://ioannis-mouratidis.github.io/publication/patsakis-2025-mafin/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/patsakis-2025-mafin/Minimum-Cost Synthetic Genome Planning: An Algorithmic Frameworkhttps://ioannis-mouratidis.github.io/publication/patsakis-2025-minimum/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/patsakis-2025-minimum/MPRAbase a Massively Parallel Reporter Assay databasehttps://ioannis-mouratidis.github.io/publication/zhao-2025-mprabase/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/zhao-2025-mprabase/Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of lifehttps://ioannis-mouratidis.github.io/publication/chantzi-2025-quadrupia/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2025-quadrupia/Quantum implementation of multi-pattern string matching for k-mer detectionhttps://ioannis-mouratidis.github.io/publication/papalitsas-2025-quantum/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/papalitsas-2025-quantum/Real-world survival outcomes with first-line chemoimmunotherapy and biomarker analysis in extensive-stage small-cell lung cancerhttps://ioannis-mouratidis.github.io/publication/panagiotou-2025-real/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/panagiotou-2025-real/Ribosomal DNA arrays are the most H-DNA rich element in the human genomehttps://ioannis-mouratidis.github.io/publication/chantzi-2025-ribosomal/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2025-ribosomal/Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant locihttps://ioannis-mouratidis.github.io/publication/bochalis-2025-taxonomic/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/bochalis-2025-taxonomic/The cumulative impact of passenger mutations on cancer developmenthttps://ioannis-mouratidis.github.io/publication/nayak-2025-cumulative/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/nayak-2025-cumulative/The topography of nullomer-emerging mutations and their relevance to human diseasehttps://ioannis-mouratidis.github.io/publication/chan-2025-topography/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chan-2025-topography/ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequenceshttps://ioannis-mouratidis.github.io/publication/wang-2025-zseeker/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/wang-2025-zseeker/ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequenceshttps://ioannis-mouratidis.github.io/publications/zseeker-2025/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/zseeker-2025/<p>ZSeeker provides researchers with a fast and accurate tool for identifying Z-DNA forming sequences across entire genomes, facilitating studies of genome regulation and stability.</p>A review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomeshttps://ioannis-mouratidis.github.io/publication/mareboina-2024-review/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/mareboina-2024-review/A survey of k-mer methods and applications in bioinformaticshttps://ioannis-mouratidis.github.io/publication/moeckel-2024-survey/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/moeckel-2024-survey/Advances in computational and experimental approaches for deciphering transcriptional regulatory networkshttps://ioannis-mouratidis.github.io/publication/moeckel-2024-advances/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/moeckel-2024-advances/Characterization of hairpin loops and cruciforms across 118,065 genomes spanning the tree of lifehttps://ioannis-mouratidis.github.io/publication/chantzi-2024-characterization/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2024-characterization/kmerDB: a database encompassing the set of genomic and proteomic sequence information for each specieshttps://ioannis-mouratidis.github.io/publication/mouratidis-2024-kmerdb/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/mouratidis-2024-kmerdb/kmerDB: A database encompassing the set of genomic and proteomic sequence information for each specieshttps://ioannis-mouratidis.github.io/publications/kmerdb-2024/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/kmerdb-2024/<p>kmerDB provides the research community with a powerful tool for k-mer based species identification, comparative genomics, and evolutionary studies.</p>Microsatellites explorer: A database of short tandem repeats across genomeshttps://ioannis-mouratidis.github.io/publication/provatas-2024-microsatellites/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/provatas-2024-microsatellites/Peptide absent sequences emerging in human cancershttps://ioannis-mouratidis.github.io/publication/tsiatsianis-2024-peptide/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/tsiatsianis-2024-peptide/The determinants of the rarity of nucleic and peptide short sequences in naturehttps://ioannis-mouratidis.github.io/publication/chantzi-2024-determinants/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/chantzi-2024-determinants/Utilizing nullomers in cell-free RNA for early cancer detectionhttps://ioannis-mouratidis.github.io/publication/montgomery-2024-utilizing/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/montgomery-2024-utilizing/Eligibility for screening with low-dose CT in a real-world cohort of patients with lung cancer in Greece: A brief reporthttps://ioannis-mouratidis.github.io/publication/livanou-2023-eligibility/Sun, 01 Jan 2023 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/livanou-2023-eligibility/Frequentmers-a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosishttps://ioannis-mouratidis.github.io/publication/mouratidis-2023-frequentmers/Sun, 01 Jan 2023 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/mouratidis-2023-frequentmers/Quasi-prime peptides: identification of the shortest peptide sequences unique to a specieshttps://ioannis-mouratidis.github.io/publication/mouratidis-2023-quasi/Sun, 01 Jan 2023 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/mouratidis-2023-quasi/Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolutionhttps://ioannis-mouratidis.github.io/publication/georgakopoulos-2021-absent/Fri, 01 Jan 2021 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/georgakopoulos-2021-absent/Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequenceshttps://ioannis-mouratidis.github.io/publication/georgakopoulos-2021-asymmetron/Fri, 01 Jan 2021 00:00:00 +0000https://ioannis-mouratidis.github.io/publication/georgakopoulos-2021-asymmetron/