Browsing by Author "Lipman, David J."
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item On the Prediction of Local Patterns in Cellular Automata.(1986) Wilbur, W.J.; Lipman, David J.; Shamma, S.A.; ISRThe class of deterministic one-dimensional cellular automata studied recently by Wolfram are considered. We represent a state of an automaton as a probability distribution of patterns of a fixed size. In this way information is lost but it is possible to approximate the stepwise action of the automaton by the iteration of an analytic mapping of the set of probability distributions to itself. Such nonlinear analytic mappings generally have nontrivial attractors and in the most interesting cases (Wolfram Class III) these are single points. The point attractors under appropriate circumstances provide good approximations to the frequencies of local patterns generated by the discrete rules from which they were derived. Two appropriate settings for such approximations are transient patterns generated from random starts and patterns generated in a noisy environment. In the case with noise, improvement is found by correction of the analytic mappings for the effects of noise. Examples of both types of approximations are considered.Item Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses(PLoS Biology, 2005) Holmes, Edward C.; Ghedin, Elodie; Miller, Naomi; Taylor, Jill; Bao, Yiming; St. George, Kirsten; Grenfell, Bryan T.; Salzberg, Steven L.; Fraser, Claire M.; Lipman, David J.; Taubenberger, Jeffery K.Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002–2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003–2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.