282 citations · 2.1k across the 32 of their papers we have counts for
32 papers
Eco-evolutionary dynamics of adapting pathogens and host immunity
Pierre Barrat-Charlaix, Richard A. Neher
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA v…
Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen
Le Yan, Richard Neher, Boris I Shraiman
Rapidly evolving pathogens like influenza viruses can persist by accumulating antigenic novelty fast enough to evade the adaptive immunity of the host population, yet without conti…
Progress and open problems in evolutionary dynamics
Richard A. Neher, Aleksandra M. Walczak
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate th…
Establishment and stability of the latent HIV-1 DNA reservoir
Johanna Brodin, Fabio Zanini, Lina Thebo +4
HIV-1 infection currently cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). To ch…
In-vivo mutation rates and fitness landscape of HIV-1
Fabio Zanini, Vadim Puller, Johanna Brodin +2
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequ…
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
Richard A. Neher, Trevor Bedford, Rodney S. Daniels +2
Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and re-infect previously infected individuals. Antigenic properties are largely det…