Ioannis Mouratidis

Byte-exact, format-aware compression for FASTA, FASTQ, BED and VCF files

NYX provides fast, lossless compression for common omics data formats, achieving better compression ratios and speed than existing codecs.

Accelerating Inference in Genomic Foundation Models via Speculative Decoding

This paper introduces speculative decoding to accelerate genomic and proteomic sequence generation using foundation models without compromising prediction quality.

Safeguarding open-weight genomic foundation models through weight locking

The paper evaluates weight-locking techniques to prevent fine-tuning of genomic foundation models, finding that naive attacks fail but informed attacks can partially bypass the lock.

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

This paper presents two quantum algorithms for efficient k-mer detection in genomic data using Grover's amplitude amplification, showing potential for accelerating pattern matching in large datasets.

The cumulative impact of passenger mutations on cancer development

This study shows that passenger mutations can significantly impact cancer development by accumulating in tumor suppressor genes, leading to reduced expression and poorer prognosis.

Fundamental limitations of genomic language models for realistic sequence generation

This study evaluates genomic language models for synthetic genome generation, finding they fail to capture long-range genomic organization and evolutionary constraints.

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

The paper maps G-quadruplexes across the human genome and haplotypes, showing their enrichment in repetitive regions and association with genomic instability and PRDM9 binding.

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

ZSeeker detects potential Z-DNA-forming sequences in genomes with improved accuracy and accessibility through a Python package and web interface.

MPRAbase: A Massively Parallel Reporter Assay Database

MPRAbase is a curated database of MPRA experiments that provides access to 17.7 million regulatory elements tested across 35 cell types and 4 organisms.

invertiaDB: A Database of Inverted Repeats Across Organismal Genomes

invertiaDB is a database of inverted repeats across 118,070 organisms, providing a centralized resource for searching, visualizing, and downloading inverted repeat data.

Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups

The paper identifies peptide sequences unique to specific taxonomic groups, revealing their evolutionary and functional significance across species and their potential in human health applications.

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

The paper identifies ribosomal DNA arrays as the most H-DNA rich element in the human genome using the T2T assembly, showing 42.65-fold enrichment compared to chance.

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

The paper analyzes inverted repeats across 118,065 genomes to study their distribution, frequency, and functional roles in genomic instability and evolution.

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

Quadrupia identifies and characterizes G-quadruplex sequences across 108,449 genomes, revealing taxonomic patterns and experimentally validating key structures.

kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species

kmerDB provides a database of genomic and proteomic sequence information, including kmers, quasi-primes, and primes, for 45,785 genomes and 22,386 proteomes.

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

The paper calculates the rarity of short nucleic and peptide sequences across genomes and proteomes, finds dipeptide rarity in peptides but not dinucleotides, and develops predictive models for sequence frequency.

Frequentmers - a novel way to look at metagenomic Next Generation Sequencing data and an application in detecting liver cirrhosis

This paper introduces frequentmers, a metagenomic feature for early disease detection, and applies it to identify liver cirrhosis with high accuracy using stool samples.

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

The paper identifies nullomers and nullpeptides across species, showing they are under negative selection and could serve as DNA fingerprints or for phylogenetic analysis.