Protein foundation models increasingly support the generation of novel biological sequences, yet their reliance on large public datasets creates opportunities for adversarial manipulation of the material they learn from and retrieve. We investigate two data-only poisoning attacks against protein design systems, targeti...
Charalampos Koilakos, K. Provatas, Michail Patsakis et al.· 0 citations
BarcodesDB is presented, a comprehensive database of synthetic DNA barcodes systematically identified by scanning 403 199 complete organismal genome assemblies across the tree of life, together with 215 Gbp of raw metagenomic sequencing reads spanning marine, soil, polar and host-associated environments, providing maxi...
Michail Patsakis, K. Provatas, I. Mouratidis et al.· Bioinformatics Advances· 0 citations
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
Together, these analyses define the mutation-class, spatial, and genomic-context landscape associated with predicted Z-DNA-forming sequences across the human pangenome.
I. Georgakopoulos-Soares, Georgios Megalovasilis, Eleftherios Bochalis et al.· Research Square· 0 citations
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
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
High-gain gated-FFN rows are a recurrent architectural phenotype whose structural prominence acts as an enrichment signal, not a calibrated measure of functional criticality or a specification of causal organization.
Alexandros Tzanakakis, Aris Karatzikos, I. Georgakopoulos-Soares· 0 citations
It is argued for defense-in-depth governance that links capability thresholds to proportionate responsibilities across the biological AI ecosystem, reducing high-consequence risk while preserving beneficial use.
Candace S. Y. Chan, Aris Karatzikos, I. Georgakopoulos-Soares· 0 citations
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
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