Winter 2025 Newsletter
Q1 (Winter) Newsletter
Welcome to the first newsletter edition of 2025. We've been busy! Find out what we've been up to!
Winter 2025 was busy for the group, despite the holidays! Members attended multiple meetings and conferences between Germany, Austria and the UK. Members were also involved in teaching activities and seminars.
We had the pleasure of going skiing twice: in Andermatt and in Flumserberg, where we enjoyed beautiful blue skies!
We're looking forward to upcoming events in 2025 and you can look forward to more content. We included a new section about visitors to our lab. If you would like to see some new content, let us know! Feel free to contact us with your suggestions!
Read on to find out what we've been up to this Winter!
In January, Noémie was invited to speak at the external page Population Genetics group 58 in Sheffield, UK. She presented her PhD work in a talk entitled "Uncovering the spatial spread and fitness dynamics of Bordetella pertussis". The meeting was a great opportunity to connect with researchers in the field of population genetics, learn about the diversity of questions tackled and the approaches used.
On December 9th–13th, Bethany and Robert travelled to Erlangen, Germany to attend the external page 68th Annual Meeting of the Palaeontological Association. Bethany was invited to give a symposium talk entitled “Inferring extinction rates from phylogenies”. Robert presented a poster on modelling punctuated evolution in Bayesian total-evidence dating with penguins. They both helped the RevBayes workshop entitled “Fossil sampling biases and phylogenetics”.
Ewan and Tim attended the external page 2025 NCCR Evolving Language Winter School in Champéry from the 3rd through to the 7th of February. This is the main annual meeting of the NCCR and hosted a large variety of lectures and workshops on diverse topics such as the evolutionary dynamics of language, computational modelling of natural language, and the biological mechanisms facilitating language in humans.
On February 12th, Louis, Antoine, Noémie, Robert, Chaoran, Etthel, Daniele and Tanja all attended the PhyloSIB meeting at the University of Lausanne. PhyloSIB is organised by the Swiss Institute of Bioinformatics (SIB) and brings together all Swiss groups working on phylogenetics and adjacent fields. This year Louis was part of the scientific organising committee and the day was filled with exciting talks from all over Switzerland, including talks by Antoine and Daniele!
During the week of February 25th through 28th, Tim attended a planning meeting in Tutzing (half an hour south of Munich), Germany for a MSC-DN application he and several other researchers are putting together. If successful, this application would establish a network of research groups and doctoral students focused on unifying the currently fragmented computational phylogenetics research community.
Robert was accepted to the Evolutionary Biology in Guarda Summer School. He will spend a week in Guarda in June to learn about brainstorming research ideas and writing up a grant proposal without the Internet.
Daniele gave a seminar titled “New models for evolutionary and conservation biology using artificial intelligence” at the Wasser Cluster Institute in Lunz, Austria.
On March 11th Louis attended the Margaret Dayhoff Centenary at the University of Bern. Dr. Margaret Dayhoff was one of the pioneers of bioinformatics and created the first sequence database, the Atlas of Protein Sequence and Structure (first published in 1965 as a book), the precursor of databases like GenBank and SwissProt. Besides looking back on the life of Dr. Dayhoff, the day contained talks from successful women in science as well as panel discussions on careers and the future of Swiss bioinformatics.
Highlighted images from our activities
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PhyloSIB 2025 (photo by Christophe Dessimoz) -
Part of our cEvo ski trip! -
Tim and Ewan at the 2025 NCCR Evolving Language Winter School in Champéry
Papers we've published
Good news! These are some of the papers that we've worked on. Congratulations to all the authors!
Read more:
- external page Sheena: Strengthening Policy Relevance of Wastewater-Based Surveillance for Antimicrobial Resistance
- external page Noémie: Learning the fitness dynamics of pathogens from phylogenies
- external page Daniele: Ecological change and conflict reduction led to a social circulatory system in ants
- external page Daniele: Eco-Evolutionary Dynamics of Plant–Soil Feedbacks Explain the Spread Potential of a Plant Invader Under Climate Warming and Biocontrol Herbivory
- Tanja: Artificial intelligence for modelling infectious disease epidemics
- external page Louis: Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia
- external page Louis: Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy
- external page Chaoran: From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics
- external page Antoine: A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites
- external page Etthel: Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages
- external page Etthel: Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex
Adrian Lison defended his thesis on on January 21st titled "Statistical methods for real-time infectious disease surveillance: Monitoring transmission using clinical, behavioural, and environmental data" . Find out more information here.
Jonas Mason joined us in March 2025 as a semester project student as part of his Master's studies. He previously completed his Bachelor's in Biology also at ETH, and he will be working on the evolutionary dynamics of Bordetella pertussis in France in light of the COVID-19 pandemic together with Noémie Lefrancq. Outside of the lab, he enjoys anything outdoorsy and playing football. He loves woodworking, even if not all of his projects always turn out quite as planned.
Laura Tomás joined our team as a post-doctoral fellow in March 2025. She developed her background in bioinformatics through her studies in Salamanca and Barcelona, before completing her PhD in cancer evolution at the University of Vigo. At cEvo, her research will focus on integrating single-cell lineage tracing with transcriptomic data. Outside the lab, she enjoys playing board games, reading detective novels, and cooking—although when a dish turns out well, she can never quite manage to recreate it the same way!
Tobias Dieselhorst joined our group as a PhD student in March 2025. He previously studied physics at the Universities of Jena, Granada and Cologne. During his master's thesis at the Institute for Biological Physics in Cologne, he became fascinated by the interdisciplinary applications of phylodynamics. At cEvo, he will work on the mathematical properties of evolutionary processes and their application to novel phylodynamic inference schemes. Outside of his studies, Tobias is passionate about jazz, plays the saxophone and loves sports that take place in and on the water.
Daniele Silvestro joined us in January 2025. He is a computational biologist with a PhD from Goethe University (Frankfurt) and previous experience at Universities of Gothenburg, Fribourg and Lausanne. He will develop new methods using AI and Bayesian models applied to evolutionary and conservation biology. Outside of the lab, he enjoys hanging out with his kids and fossil hunting.
Jana Dinger joined us in March 2025 as a Master’s thesis student. She previously completed her bachelor’s degree in Mathematics at ETH. Jana will be working on identifiability in age-dependent phylogenetic trees with Nicola Mulberry and Julia Pilarski. Outside of the lab, she enjoys all types of travel adventures, from day trips and hikes to backpacking vacations. She is also currently learning Spanish—though with only mediocre success so far.
Visitors
These are the visitors that took some time off their busy schedules to discuss or present their research.
Alyssa Henderson from external page EAWAG visited us on 05/02/2025 to discuss her project on selection and metabolism among heterotrophic bacteria. She is interested to use modeling and phylogenetic tools to understand more about the diversity of amino acid composition in these communities.
On March 5th, 2025, Léo Perrier, a postdoctoral researcher in the NCCR Evolving Language at the University of Neuchâtel, visited us to discuss his work on bioacoustics in the context of language evolution and learn more about phylogenetics. He presented his PhD project, which explored the characteristics of animal vocalisations with a focus on rodents. He is interested in studying the evolutionary dynamics of animal calls through a phylogenetic framework.
Awards, Prizes & Grants
This is a recap of the awards, grants, and prizes that we've received or have been nominated for. Read on to find out more details!
Jérémy Andréoletti and Antoine Zwaans received a external page Publisher's Award for Excellence in Systematic Research for their work the formulation and implementation of the Occurrence Birth-Death Process (OBDP) in software RevBayes.