https://ioannis-mouratidis.github.io/tags/Genomics/GenomicsHugo Blox Builder (https://hugoblox.com)en-usWed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/media/icon_hu_899445b689d8f445.pnghttps://ioannis-mouratidis.github.io/tags/Genomics/https://ioannis-mouratidis.github.io/projects/compression-tool/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/projects/compression-tool/<h2 id="overview">Overview</h2> <p>A novel compression tool developed in C++ and Python specifically optimized for multiple genomic file formats. This tool significantly reduces storage requirements while dramatically improving compression speed compared to existing solutions.</p> <h2 id="performance">Performance</h2> <ul> <li><strong>10-20% smaller file sizes</strong> compared to standard genomic compression tools</li> <li><strong>50-70% faster compression times</strong> enabling real-time analysis</li> <li><strong>Multiple format support</strong>: Handles various genomic data formats</li> <li><strong>Lossless compression</strong>: Maintains data integrity for scientific applications</li> </ul> <h2 id="technical-approach">Technical Approach</h2> <p>The tool leverages domain-specific knowledge about genomic data structure to achieve superior compression ratios and speeds. Implementation in C++ provides low-level performance optimization while Python bindings enable easy integration into bioinformatics pipelines.</p> <h2 id="impact">Impact</h2> <p>This compression tool enables:</p> <ul> <li>Reduced storage costs for large-scale genomic projects</li> <li>Faster data transfer and backup operations</li> <li>Real-time compression for sequencing pipelines</li> <li>More efficient cloud-based genomic analysis</li> </ul> <h2 id="applications">Applications</h2> <ul> <li>Large-scale sequencing projects</li> <li>Genomic data archiving</li> <li>Cloud-based bioinformatics platforms</li> <li>Real-time sequencing data processing</li> </ul>https://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>https://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>https://ioannis-mouratidis.github.io/projects/kmerdb/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/projects/kmerdb/<h2 id="overview">Overview</h2> <p>kmerDB is a comprehensive database that consolidates genomic and proteomic k-mer sequence information across all species in Genbank and UniProt. This resource enables rapid species identification, comparative genomic studies, and evolutionary analysis.</p> <h2 id="features">Features</h2> <ul> <li><strong>Comprehensive Coverage</strong>: Encompasses k-mer data from all species in major sequence databases</li> <li><strong>Dual Coverage</strong>: Includes both genomic (DNA) and proteomic (amino acid) sequences</li> <li><strong>Fast Queries</strong>: Optimized data structures enable rapid k-mer lookups</li> <li><strong>Species Identification</strong>: Enables efficient molecular diagnostics and species authentication</li> <li><strong>100-fold Compression</strong>: Novel compression procedures reduce data storage requirements dramatically</li> </ul> <h2 id="technical-implementation">Technical Implementation</h2> <p>The database was built using advanced compression algorithms achieving 100-fold data reduction while maintaining query performance. This enables storage and analysis of k-mer information from the entire tree of life.</p> <h2 id="applications">Applications</h2> <ul> <li>Species identification and authentication</li> <li>Comparative genomics</li> <li>Evolutionary studies</li> <li>Molecular diagnostics</li> <li>Environmental monitoring</li> <li>Food authentication</li> </ul> <h2 id="publications">Publications</h2> <p>Mouratidis, I., Baltoumas, F. A., Chantzi, N., et al. (2024). kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species. <em>Computational and Structural Biotechnology Journal, 23</em>.</p>https://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>