Paulina N. Smaruj

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

The paper uses AkitaV2 to analyze CTCF-binding site sequences and predict their role in genome folding, identifying key sequence determinants and grammatical rules for insulation strength and pattern formation.

The paper identifies VNTR motifs linked to gene expression using a repeat-pangenome graph, showing motif variation explains more associations than VNTR length.