neherlab@biozentrum
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pathogen evolution, genomics, and biophysics

Evolution of bacteria

  • horizontal transfer
  • pangenomes
  • drug resistance evolution
  • long-read sequencing

HIV evolution

  • intra-patient evolution
  • mutation and recombination
  • fitness landscapes
  • latent reservoir

Molecular epidemiology

  • real-time tracking
  • prediction
  • antigenic evolution
  • influenza
  • enterovirus

Theory

  • population genetics
  • rapid adaptation
  • phylogenetics
  • timetree inference

Links

Biozentrum Basel
Nextclade
pangenome.ch: bacterial pan-genomes
nextstrain.org: Real-time tracking of pathogen evolution
HIVEVO: Intra-patient evolution of HIV-1
github/neherlab
TreeTime webservice for phylodynamics analysis

We are a research group at the Biozentrum, University of Basel, Switzerland. We are broadly interested in evolution, ecology, and population genetics with a focus on rapidly evolving pathogens such as HIV, influenza virus, or pathogenic bacteria. These organisms have large population sizes, short generation times and are subject to strong selective pressure for example by immune responses or drug treatment. Understanding their evolutionary dynamics and adaptability is important to limit the spread of these pathogens. On the other hand, dense surveillance and the rapid evolution of many pathogens allow us to study fundamental questions in evolutionary biology and ecology. We are always looking for exceptional people who want to join us as students or post-docs. Get in touch with Richard Neher.

recent publications all publications

Evolution, geographic spreading, and demographic distribution of Enterovirus D68
Emma B. Hodcroft, Robert Dyrdak, Cristina Andres et al.
PLOS Pathogens, 18 e1010515. 10.1371/journal.ppat.1010515 pdf bibtex Fri 20 May 2022
PanGraph: scalable bacterial pan-genome graph construction
Nicholas Noll, Marco Molari and Richard Neher
bioRxiv, 2022.02.24.481757. 10.1101/2022.02.24.481757 bibtex Thu 24 February 2022
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates
Valentin Druelle and Richard Neher
bioRxiv, 2022.02.13.480259. 10.1101/2022.02.13.480259 bibtex Mon 14 February 2022

recent postsall posts

How accurate are branch length estimates in RNA virus phylogenies?
Thu 31 October 2019
Debating soft vs hard sweeps in RNA viruses is a waste of time
Sun 30 December 2018
Mugration models and homoplasy analysis in TreeTime
Thu 19 April 2018

available thesis projects

Master thesis: Reconstructing influenza spread and evolution jointly from all eight genome segments
Sat 04 February 2017
Master thesis: Real-time tracking of animal influenza viruses
Fri 03 February 2017
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