Mani Larijani

ExTRaCT is a gene search pipeline that identifies APOBEC3 Z-domains in novel bat genomes with high accuracy and efficiency.

The paper uses molecular dynamics to analyze catalytic pocket dynamics of AID/APOBEC3 enzymes, finding that A3G-CD2 is predominantly open while most AID/APOBECs are closed or indeterminate, with specific residues influencing pocket states and catalytic activity.

The paper develops a mutation simulator to assess genome robustness under COSMIC mutational signatures, finding higher resilience in human and bat genomes to APOBEC-related mutations.

The paper predicts how APOBEC3A/B mutations affect immunopeptidome immunogenicity across HLA alleles and links these changes to tumor survival and CTL activation.

The paper analyzes APOBEC3-driven mutagenesis in monkeypox virus genomes, finding over-representation of TC hotspots and under-representation of GC hotspots, suggesting potential for future human APOBEC3-mediated evolution.