Author

I. Georgakopoulos-Soares

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#gene editing Open access Oct 2026

Pan-Cancer APOBEC Mutagenesis, Immune Microenvironment, and Clinical Outcome: A Comprehensive Multi-Omics Analysis of All Ten Family Members Across 9653 TCGA Tumors

The apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) family comprises ten cytidine deaminases implicated in cancer mutagenesis, yet their broader biological significance remains incompletely understood. We performed an integrated pan-cancer analysis of all ten APOBEC family members across 9653 tumors f...

Sairos Ghniem, I. Georgakopoulos-Soares, A. Zaravinos · International Journal of Mol... · 0 citations

Open access Sep 2026

Z-DNA-associated genomic instability in the human pangenome

Abstract Z-DNA is a non-canonical, left-handed nucleic acid conformation implicated in gene regulation and genome instability. Long-read sequencing and telomere-to-telomere genome assemblies now enable analysis of repetitive regions that were absent or incompletely represented in earlier human references. Leveraging T2...

I. Georgakopoulos-Soares, Georgios Megalovasilis, Eleftherios Bochalis et al. · Research Square · 0 citations

Open access Oct 2026

Landscape and mutational dynamics of G-quadruplexes across the complete human genome

G-quadruplexes (G4s) are alternative DNA structures with diverse biological roles, but their examination in highly repetitive parts of the human genome has been hindered by the lack of reliable sequencing technologies. Recent long-read based genome assemblies have enabled their characterization in previously inac...

Nikol Chantzi, Shi Wei. Liew, Aurell Wijaya et al. · Genome Biology · 0 citations

Open access Jul 2026

Accelerating inference in genomic and proteomic foundation models via speculative decoding

Abstract Motivation Genomic and protein foundation models (GFMs and PFMs) have demonstrated strong performance in learning the language of DNA and proteins, but their use in large-scale sequence generation is limited by the latency of autoregressive decoding. Because every token triggers a forward pass of a large Trans...

K. Provatas, Aris Karatzikos, Charalampos Koilakos et al. · Bioinform. · 0 citations

Open access Aug 2026

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

TurboQuant-Bio, an open toolkit that compresses Evo 2’s weights and attention cache to four bits without calibration data, and serves both through fused kernels, proves near-lossless across perplexity spanning the tree of life, genomic classification, splice-site prediction, gene completion and clinically relevant vari...

Michail Patsakis, Alexandros Tzanakakis, I. Georgakopoulos-Soares · bioRxiv · 0 citations