Resources

Teaching
Tools
Media
Links

Teaching

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Studies

For the Study programs of the Uni Bern see the Studies section on our Uni Bern web-site.

Epistasis and fitness landscapes

Fitness landscape simulation for the tutorial at the ICTS Workshop Living Matter. Download the Mathematica notebook here:

adaptation on a fitness landscape [37 KB Mathematica notebook - text format]

A recording of the two accompanying lectures is available on the website of the workshop.

Tools

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empiricIST: a software that allows for accurate estimation of selection coefficients and credibility intervals from bulk competitions

empiricIST is an integrative framework for the analysis of bulk competition data, and includes separate programs for processing raw sequence data and correcting for sequencing errors, obtaining statistically meaningful estimates of selection coefficients in a fast and efficient manner, and for providing ready-to-use summary statistics of the MCMC analysis and its associated parameter estimates.

empiricIST GitHub repository

Also check out our manuscript on The fitness landscape of the codon space across environments to see an example of how empiricIST can be used. We used the selection coefficients estimates to quantify changes in the topology and the topography of the codon fitness landscape in different environments considering non-synonymous and synonymous mutations.

Interactive online tool to visualize the loss of a neutral Dobzhansky-Muller incompatibility in the presence of gene flow

Go directly to the tool by clicking below:

Interactive DMI web app

Interactive online tool for experimental design of high-throughput bulk competitions

Go directly to the tool by clicking below:

Optimize high-throughput bulk competitions

Or download and read the corresponding manuscript first: A statistical guide to the design of deep mutational scanning experiments – also available as free preprint.

Simulating and inferring selection

Exercise module for the 2018 Workshop on Population and Speciation Genomics in Český Krumlov.

Find the R notebook here:

simulating and inferring selection

Our GitLab repository contains the RStudio files and all other files necessary to get started with the exercise and comes with precompiled binaries for macOS and Linux and a setup script.

For more information and a pdf of the accompanying lecture see the website of the workshop or download the lecture slides here: Positive and negative selection [PDF, 6 MB].

Media

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Popular press/News releases

Novos fundos para estudar resistências antimicrobianas (FCG Newsletter in Portuguese, August/September 2017)
IGC Scientists receive new funding to study antimicrobial resistances (IGC press release, August 2017)
Evolutionary theory – a work in progress (International Innovation, June 2014)
Tamiflu-resistant influenza: parsing the genome for the culprits (News Mediacom, March 2014)
Von Fliegen und Menschen (Vetmedmagazin, January 2011)

Videos

Fitness landscapes and the predictability of evolution (Seminar at the KITP in Santa Barbara, August 2017)
Using statistics to prepare better experiments (IGC paper video in English, July 2016)
Usar estatística para desenhar experiências mais eficientes (IGC paper video in Portuguese, July 2016)
Shifting fitness landscapes in response to altered environments (Contributed talk at the ESEB congress in Lisbon, Portugal, August 2013)
Can reinforcement complete speciation? (Contributed talk at the Speciation 2010 conference in Laxenburg, Austria, December 2010)

Theoretical Ecology and Evolution

The Bank lab @ Universität Bern & the Gulbenkian Institute