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Predicting influenza H3N2 vaccine efficacy from evolution of the dominant epitope
Melia E. Bonomo, Michael W. Deem
We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes.…
The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas
Melia E. Bonomo, Michael W. Deem
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria…
The standard genetic code facilitates exploration of the space of functional nucleotide sequences
Shubham Tripathi, Michael W. Deem
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the…
How the other half lives: CRISPR-Cas's influence on bacteriophages
Melia E. Bonomo, Michael W. Deem
CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invadi…
Nonclassical phase diagram for virus bacterial co-evolution mediated by CRISPR
Pu Han, Michael W. Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing prote…
Modular knowledge systems accelerate human migration in asymmetric random environments
Dong Wang, Michael W. Deem
Migration is a key mechanism for expansion of communities. In spatially heterogeneous environments, rapidly gaining knowledge about the local environment is key to the evolutionary…