282 citations · 2.1k across the 32 of their papers we have counts for
24 papers · 1 filter
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…
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo +4
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolv…
Predicting evolution from the shape of genealogical trees
Richard A. Neher, Colin A. Russell, Boris I. Shraiman
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogica…
Inferring HIV escape rates from multi-locus genotype data
Taylor A. Kessinger, Alan S. Perelson, Richard A. Neher
Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major histocompatibility complex (MHC) molecules on the surface of virally infected cells and generate…
Coalescence, genetic diversity in sexual populations under selection
Richard A. Neher, Taylor A. Kessinger, Boris I. Shraiman
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly…
Interference limits resolution of selection pressures from linked neutral diversity
Benjamin H. Good, Aleksandra M. Walczak, Richard A. Neher +1
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in n…
Genetic draft, selective interference, and population genetics of rapid adaptation
Richard A. Neher
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based o…
Genealogies of rapidly adapting populations
Richard A. Neher, Oskar Hallatschek
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on…
FFPopSim: An efficient forward simulation package for the evolution of large populations
Fabio Zanini, Richard A. Neher
The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence o…
Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses
Vitaly V. Ganusov, Richard A. Neher, Alan S. Perelson
Human immunodeficiency virus (HIV-1 or simply HIV) induces a persistent infection, which in the absence of treatment leads to AIDS and death in almost all infected individuals. HIV…
Fluctuations of fitness distributions and the rate of Muller's ratchet
Richard A. Neher, Boris I. Shraiman
The accumulation of deleterious mutations is driven by rare fluctuations which lead to the loss of all mutation free individuals, a process known as Muller's ratchet. Even though M…
Estimating the Strength of Selective Sweeps from Deep Population Diversity Data
Philipp W. Messer, Richard A. Neher
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations t…
Emergence of clones in sexual populations
Richard A. Neher, Marija Vucelja, Marc Mézard +1
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the populat…
Rare beneficial mutations can halt Muller's ratchet
Sidhartha Goyal, Daniel J. Balick, Elizabeth R. Jerison +3
The vast majority of mutations are deleterious, and are eliminated by purifying selection. Yet in finite asexual populations, purifying selection cannot completely prevent the accu…
Rate of Adaptation in Large Sexual Populations
Richard A. Neher, Boris I. Shraiman, Daniel S. Fisher
Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can…
Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations
Richard A. Neher, Boris I. Shraiman
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci…
Statistical Genetics and Evolution of Quantitative Traits
Richard A. Neher, Boris I. Shraiman
The distribution and heritability of many traits depends on numerous loci in the genome. In general, the astronomical number of possible genotypes makes the system with large numbe…
Recombination rate and selection strength in HIV intra-patient evolution
Richard A. Neher, Thomas Leitner
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understan…
Competition between recombination and epistasis can cause a transition from allele to genotype selection
Richard A. Neher, Boris I. Shraiman
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex trait…