Theoretical models of generalized quasispecies

Theoretical modeling of quasispecies has progressed in several directions. In this chapter, we review the works of Emmanuel Tannenbaum, who, together with Eugene Shakhnovich at Harvard University and later with colleagues and students at Ben-Gurion University in Beersheva, implemented one of the more useful approaches, by progressively setting up various formulations for the quasispecies model and solving them analytically. Our review will focus on these papers that have explored new models, assumed the relevant mathematical approximations, and proceeded to analytically solve for the steady-state solutions and run stochastic simulations. When applicable, these models were related to real-life problems and situations, including changing environments, presence of chemical mutagens, evolution of cancer and tumor cells, mutations in Escherichia coli, stem cells, chromosomal instability (CIN), propagation of antibiotic drug resistance, dynamics of bacteria with plasmids, DNA proofreading mechanisms, and more.