445 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- University of California, Santa BarbaraUS6 papers
- Max Planck Institute for Intelligent SystemsDE5 papers
- Kavli Institute for Theoretical PhysicsUS4 papers
- Max Planck SocietyDE4 papers
- Karolinska InstitutetSE3 papers
- Karolinska University HospitalSE3 papers
- Stanford UniversityUS3 papers
- Centre National de la Recherche ScientifiqueFR2 papers
- Los Alamos National LaboratoryUS2 papers
- Stockholm South General HospitalSE2 papers
- University of CambridgeGB2 papers
- University of TübingenDE2 papers
17 papers · 1 filter
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…
Deleterious synonymous mutations hitchhike to high frequency in HIV-1 env evolution
Fabio Zanini, Richard A. Neher
Intrapatient HIV-1 evolution is dominated by selection on the protein level in the arms race with the adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies…
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…
LMM-Lasso: A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction
Barbara Rakitsch, Christoph Lippert, Oliver Stegle +1
Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fractio…
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…
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…