Michail Patsakis

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.

Calibration-free compression brings Evo 2 to its full million-token context on a single GPU

The paper introduces TurboQuant-Bio, a toolkit that compresses Evo 2's weights and attention cache to four bits without calibration data, enabling genome-scale analysis on single GPUs.

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.

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.

Characterization of Z-DNA dynamics across the tree of life

The paper characterizes Z-DNA dynamics across different lineages using ZSeeker, finding lineage-specific enrichment and depletion patterns in cellular and viral genomes.

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.

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.

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.