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.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.

open positions

Post-doctoral position in phylogenetics and microbial evolution
Fri 21 April 2023

recent publications all publications

PanGraph: scalable bacterial pan-genome graph construction
Nicholas Noll, Marco Molari, Liam Shaw and Richard Neher
Microbial Genomics, in press., 2022.02.24.481757. 10.1101/2022.02.24.481757 bibtex Mon 17 April 2023
Evolution of the SARS-CoV-2 mutational spectrum
Jesse D Bloom, Annabel C Beichman, Richard A Neher and Kelley Harris
Molecular Biology and Evolution, msad085. 10.1093/molbev/msad085 bibtex Mon 10 April 2023
A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Bernadeta Dadonaite, Katharine H. D. Crawford, Caelan E. Radford et al.
Cell, 0 10.1016/j.cell.2023.02.001 bibtex Fri 10 February 2023

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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