5 papers
Poisoning the corpora of protein design systems during pre-training and retrieval
Charalampos Koilakos, Kimon-Antonios Provatas, Michail Patsakis +3
Protein foundation models increasingly support the generation of novel biological sequences, yet their reliance on large public datasets creates opportunities for adversarial manip…
Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework
Michail Patsakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares
As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithm…
Investigating DNA words and their distributions across the tree of life
Charalampos Koilakos, Kimonas Provatas, Michail Patsakis +2
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural la…
MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files
Michail Patsakis, Kimonas Provatas, Ioannis Mouratidis +1
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These al…
MAFin: Motif Detection in Multiple Alignment Files
Michail Patsakis, Kimonas Provatas, Fotis A. Baltoumas +4
Motivation: Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in the field of comparative genomics and proteo…