Jacopo Marchi

TL;DR: It is proposed that two concurrent cycles responsible for division and initiation of DNA replication set the time of cell division, which allows us to select a nearly constant added size per origin between subsequent initiations as the most likely mechanism setting initiation of replication.

TL;DR: In this article, the authors present a mathematical theory of coevolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections.

TL;DR: It is shown that the coding space of a given protein family—the total number of sequences in that family—can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occuring amino acid sequences, and that correlations between amino acid usage at different positions significantly impact that diversity.

TL;DR: An evolutionary model for viruses in the presence of immune host systems with finite memory is used to obtain a phase diagram of evolutionary patterns in a two-dimensional antigenic space and finds that, for small effective mutation rates and mutation jump ranges, a single lineage is the only stable solution.

TL;DR: It is shown that the coding space of a given protein family —the total number of sequences in that family— can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occuring amino acid sequences.