Ilias Georgakopoulos‐Soares

Arena3D 3.0 is a web server for exploring, analyzing, and sharing multilayered biological networks in 3D with various layouts and visualization tools.

ArthroVerse compiles and annotates protein families from arthropod-associated microbiomes to explore functional diversity and host-microbe interactions.

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

This paper uses genomic foundation models to assess how somatic mutations disrupt cancer biology and clinical outcomes across multiple cancer types.

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.

ResLit couples BioMistral-7B screening with two-pass Qwen3-30B extraction to build an antimicrobial-resistance database of 3,120 genes and 13,593 mutations, evidence-tiered against CARD, ResFinder, and NCBI RGC.

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

The paper identifies a comprehensive catalog of potential CTCF-binding sites across the complete telomere-to-telomere human genome and characterizes their functional roles in repetitive regions.

The paper maps long-range correlations in the complete telomere-to-telomere human genome, revealing heterogeneous genomic structure and chromosome-specific scaling.

HSeeker identifies and scores H-DNA-forming sequences using a three-part algorithm, providing genomic coordinates and stability scores for further analysis.

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.

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.

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

The paper identifies non-coding G-quadruplex variants associated with plasma proteins and clinical traits, showing stronger signals when considering G4 stability impacts and integrating with protein-truncating variants.

WasteFams catalogs 3,887 non-redundant protein families from wastewater metagenomes and metatranscriptomes, providing structural, taxonomic, and functional annotations for microbial function discovery.

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

The paper introduces e2MPRA, a method that simultaneously measures regulatory activity and epigenomic features of CREs using lentivirus-based MPRA and targeted Cut&Tag or ATAC-seq.

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

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

ZSeekerDB catalogs Z-nucleic acid sequences across organismal genomes, enabling cross-species analysis of their distribution and evolutionary significance.

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

The paper analyzes STR distribution across 117,253 organisms, finding significant taxonomic variation and higher STR abundance in eukaryotic and viral genomes compared to bacteria and archaea.

metagRoot provides a database of 71,091 enriched protein families from plant root microbiomes, annotated with structural and functional information to aid in microbiome research.

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

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

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.

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

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.