neherlab@biozentrum
  • Home
  • Outreach
  • Publications
  • Software
  • Talks
  • Teaching
  • Team

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
  • SARS-CoV-2
  • influenza
  • enterovirus

Theory

  • population genetics
  • rapid adaptation
  • phylogenetics
  • timetree inference

Links

Biozentrum Basel
Nextclade
pangenome.org: 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 and Viral Properties of the SARS-CoV-2 BA.3.2 Subvariant
Zesuliwe Jule, Cornelius Romer, Taskeen Hossen et al.
medRxiv, 10.1101/2025.10.28.25338622 bibtex Tue 28 October 2025
Synteny and linkage decay in bacteriophage pangenomes
Jemma M. Fendley, Marco Molari, Richard A. Neher and Boris I. Shraiman
bioRxiv, 10.1101/2025.08.12.669904 bibtex Wed 13 August 2025
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment
Jordan T Ort, Samuel S Shepard, Sonja A Zolnoski et al.
Virus Evolution, 11 veaf058. 10.1093/ve/veaf058 bibtex Mon 04 August 2025

recent postsall posts

Waves driven by immune evasive variants: How large and how often?
Sun 18 June 2023
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

available thesis projects

CBB MSc students: please get in touch with Richard Neher for available projects

  • Imprint
  • Powered by Pelican. Theme based on: Elegant by Talha Mansoor