Ioannis Mouratidis

Fundamental Limitations of Genomic Foundation Models for Sequence Generation

Sun, 01 Feb 2026 00:00:00 +0000

Accelerating inference in genomic and proteomic foundation models via speculative decoding

Thu, 01 Jan 2026 00:00:00 +0000

Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients

Thu, 01 Jan 2026 00:00:00 +0000

Fundamental limitations of genomic language models for realistic sequence generation

Thu, 01 Jan 2026 00:00:00 +0000

Zimin patterns in genomes

Thu, 01 Jan 2026 00:00:00 +0000

Leveraging sequences missing from the human genome to diagnose cancer

Mon, 01 Dec 2025 00:00:00 +0000

Oral presentation on leveraging sequences absent from the human genome for cancer diagnosis.

Identification of the shortest species-specific oligonucleotide sequences

Sat, 01 Mar 2025 00:00:00 +0000

Poster pitch and poster presentation on identifying the shortest species-specific oligonucleotide sequences. Conference attended by approximately 300 participants.

Identification of the shortest species-specific oligonucleotide sequences

Sat, 01 Feb 2025 00:00:00 +0000

This work provides a comprehensive catalog of minimal species-specific sequences with applications in diagnostics, environmental monitoring, and food authentication.

Nucleic quasi-primes: identification of the shortest unique oligonucleotide sequences in a species

Sat, 01 Feb 2025 00:00:00 +0000

Oral presentation on nucleic quasi-primes and the identification of shortest unique oligonucleotide sequences. Presented at AGBT General Meeting with approximately 250 attendees.

Genomic Data Compression Tool

Wed, 01 Jan 2025 00:00:00 +0000

Overview

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.

Performance

10-20% smaller file sizes compared to standard genomic compression tools
50-70% faster compression times enabling real-time analysis
Multiple format support: Handles various genomic data formats
Lossless compression: Maintains data integrity for scientific applications

Technical Approach

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.

Impact

This compression tool enables:

Reduced storage costs for large-scale genomic projects
Faster data transfer and backup operations
Real-time compression for sequencing pipelines
More efficient cloud-based genomic analysis

Applications

Large-scale sequencing projects
Genomic data archiving
Cloud-based bioinformatics platforms
Real-time sequencing data processing

Identification of the shortest species-specific oligonucleotide sequences

Wed, 01 Jan 2025 00:00:00 +0000

invertiaDB: a database of inverted repeats across organismal genomes

Wed, 01 Jan 2025 00:00:00 +0000

KmerCrypt: private k-mer search with homomorphic encryption

Wed, 01 Jan 2025 00:00:00 +0000

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

Wed, 01 Jan 2025 00:00:00 +0000

Leveraging sequences missing from the human genome to diagnose cancer

Wed, 01 Jan 2025 00:00:00 +0000

Leveraging sequences missing from the human genome to diagnose cancer

Wed, 01 Jan 2025 00:00:00 +0000

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.

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files

Wed, 01 Jan 2025 00:00:00 +0000

MAFin: motif detection in multiple alignment files

Wed, 01 Jan 2025 00:00:00 +0000

Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework

Wed, 01 Jan 2025 00:00:00 +0000

MPRAbase a Massively Parallel Reporter Assay database

Wed, 01 Jan 2025 00:00:00 +0000

Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life

Wed, 01 Jan 2025 00:00:00 +0000

Quantum implementation of multi-pattern string matching for k-mer detection

Wed, 01 Jan 2025 00:00:00 +0000

Real-world survival outcomes with first-line chemoimmunotherapy and biomarker analysis in extensive-stage small-cell lung cancer

Wed, 01 Jan 2025 00:00:00 +0000

Ribosomal DNA arrays are the most H-DNA rich element in the human genome

Wed, 01 Jan 2025 00:00:00 +0000

Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci

Wed, 01 Jan 2025 00:00:00 +0000

The cumulative impact of passenger mutations on cancer development

Wed, 01 Jan 2025 00:00:00 +0000

The topography of nullomer-emerging mutations and their relevance to human disease

Wed, 01 Jan 2025 00:00:00 +0000

Zseeker

Wed, 01 Jan 2025 00:00:00 +0000

Overview

Zseeker is an open-source Python tool designed for optimized detection of Z-DNA forming sequences in large genomic datasets. Z-DNA is an alternative left-handed DNA structure implicated in gene regulation, genome instability, and various biological processes.

Features

High Performance: Optimized algorithms enable analysis of entire genomes
Accuracy: Improved detection accuracy compared to previous methods
Scalability: Designed to handle large-scale genomic datasets
Easy to Use: Simple Python interface with clear documentation
Open Source: Freely available for academic and commercial use

Technical Details

Zseeker implements advanced algorithms for identifying sequences capable of forming Z-DNA structures based on sequence composition and thermodynamic properties. The tool is optimized for both speed and accuracy, making it suitable for genome-wide analyses.

Use Cases

Genome-wide Z-DNA mapping
Regulatory element identification
Genome stability studies
Comparative genomics of non-B DNA structures
Disease-associated variant analysis

Publications

Wang, G., Mouratidis, I., Provatas, K., et al. (2025). ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences. Briefings in Bioinformatics, 26(3).

ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences

Wed, 01 Jan 2025 00:00:00 +0000

ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences

Wed, 01 Jan 2025 00:00:00 +0000

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.

kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species

Wed, 01 May 2024 00:00:00 +0000

Poster presentation on kmerDB, a comprehensive database of genomic and proteomic k-mer information for all species.

Leveraging sequences missing from the human genome to diagnose cancer

Thu, 01 Feb 2024 00:00:00 +0000

Invited talk on leveraging nullomers for cancer diagnosis. Presented at the Beat Childhood Cancer Research Consortium Annual Meeting with approximately 150 attendees.

A review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomes

Mon, 01 Jan 2024 00:00:00 +0000

A survey of k-mer methods and applications in bioinformatics

Mon, 01 Jan 2024 00:00:00 +0000

Advances in computational and experimental approaches for deciphering transcriptional regulatory networks

Mon, 01 Jan 2024 00:00:00 +0000

Characterization of hairpin loops and cruciforms across 118,065 genomes spanning the tree of life

Mon, 01 Jan 2024 00:00:00 +0000

kmerDB

Mon, 01 Jan 2024 00:00:00 +0000

Overview

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.

Features

Comprehensive Coverage: Encompasses k-mer data from all species in major sequence databases
Dual Coverage: Includes both genomic (DNA) and proteomic (amino acid) sequences
Fast Queries: Optimized data structures enable rapid k-mer lookups
Species Identification: Enables efficient molecular diagnostics and species authentication
100-fold Compression: Novel compression procedures reduce data storage requirements dramatically

Technical Implementation

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.

Applications

Species identification and authentication
Comparative genomics
Evolutionary studies
Molecular diagnostics
Environmental monitoring
Food authentication

Publications

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. Computational and Structural Biotechnology Journal, 23.

kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species

Mon, 01 Jan 2024 00:00:00 +0000

kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species

Mon, 01 Jan 2024 00:00:00 +0000

kmerDB provides the research community with a powerful tool for k-mer based species identification, comparative genomics, and evolutionary studies.

Microsatellites explorer: A database of short tandem repeats across genomes

Mon, 01 Jan 2024 00:00:00 +0000

Peptide absent sequences emerging in human cancers

Mon, 01 Jan 2024 00:00:00 +0000

The determinants of the rarity of nucleic and peptide short sequences in nature

Mon, 01 Jan 2024 00:00:00 +0000

Utilizing nullomers in cell-free RNA for early cancer detection

Mon, 01 Jan 2024 00:00:00 +0000

Quasi-primes: identifying the shortest species-specific sequences

Wed, 01 Nov 2023 00:00:00 +0000

Seminar on identifying the shortest species-specific sequences using quasi-prime concepts. Presented at the Center for Computational Biology and Bioinformatics with approximately 40 attendees.

Experience

Tue, 24 Oct 2023 00:00:00 +0000

Leveraging sequences missing from the human genome to diagnose cancer

Sun, 01 Oct 2023 00:00:00 +0000

Oral presentation on leveraging sequences absent from the human genome for cancer diagnosis. Presented at Cancer Research Day with approximately 150 attendees.

Eligibility for screening with low-dose CT in a real-world cohort of patients with lung cancer in Greece: A brief report

Sun, 01 Jan 2023 00:00:00 +0000

Frequentmers-a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis

Sun, 01 Jan 2023 00:00:00 +0000

Quasi-prime peptides: identification of the shortest peptide sequences unique to a species

Sun, 01 Jan 2023 00:00:00 +0000

Neomer Diagnostics

Sat, 01 Jan 2022 00:00:00 +0000

Overview

Co-founded Neomer Diagnostics in 2022 as Chief Technical Officer to translate patented nullomer research into a clinical cancer detection platform. The company developed machine learning pipelines for detecting cancer from liquid biopsies.

Role & Achievements

As CTO, I:

Developed ML pipeline in Bash, Julia, Python, and Slurm for cancer detection from liquid biopsies
Achieved AUC ranging from 0.89 to 0.94 in lung and ovarian cancers
Established regulatory roadmap for clinical validation and FDA approval
Secured $850K in translational research funding
Led technical team and coordinated with clinical partners

Technology

The platform leveraged sequences absent from the human genome (nullomers) as biomarkers for cancer detection. Machine learning models were trained on cell-free DNA and RNA data from liquid biopsies to distinguish cancer patients from healthy controls.

Clinical Applications

Early cancer detection
Cancer screening in high-risk populations
Monitoring treatment response
Detecting minimal residual disease

Funding & Recognition

Secured $850K in translational research funding
Patent portfolio covering nullomer-based diagnostics
Partnerships with clinical institutions

Period

January 2022 - May 2023

Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

Fri, 01 Jan 2021 00:00:00 +0000

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

Fri, 01 Jan 2021 00:00:00 +0000