Summer 2024 Newsletter
Q3 (Summer) Newsletter
Welcome to our Summer 2024 newsletter. We've been busy! Find out what we've been up to!
Summer 2024 was busy for the group! Conference season was in full boom, with members travelling everywhere in between Canada and Europe. Posters and talks were presented and we connected or reconnected with collaborators across the world. We also held our retreat in Saanen where we had a variety of workshops, organized a barbecue and went on a hike. Some of us even ventured on a Via Ferrata. Take a look!
On Sept 16th, Adrian had the opportunity to present his wastewater modeling work and the R package “EpiSewer” during an online data analysis meeting of the US National Wastewater Surveillance System (NWSS). The presentation sparked interest in the package for potential application in state-level wastewater surveillance in the US.
Louis attended the 31st Dynamics & Evolution of Human Viruses conference, held in Squamish, Canada in June this year, where he caught up with old colleagues, made some new connections, and did a quick hike up the Chief after dinner.
Robert attended the 97th Annual Meeting of the German Society of Mammalian Biology (DGS 2024) in Munich, Germany from Sept 2nd to 6th at the Paläontologisches Museum München. He presented a talk about his master’s research on shrew jaw morphology and its anatomical diversity. His work was accepted by Proceedings of the Royal Society B for publication. He also visited Sebastian Höhna’s lab at LMU Munich.
Charlyne attended the 2024 European Summer Programme in Infectious Disease Analysis and Modelling (ESPIDAM) in Stockholm, Sweden from June 24th to 28th. She connected with fellow modellers, learning about consideration to make in epidemiological modelling. She also presented a poster titled Surveilling Genetic Diversity of Respiratory Viruses in Swiss Clinical Samples.
Etthel attended the 44th Annual Congress of the European Society of Mycobacteriology in Bruges, Belgium from June 23th to 26th. She was invited to give a talk on phylodynamics for TB, which inspired interesting discussions and new collaborations with TB experts.
Highlighted images from our activities
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Louis' hike up the Chief -
Gomphotherium, by Robert
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Etthel at the Congress of the European Society of Mycobacteriology
Papers we've published
Good news! These are some of the papers that we've worked on. Congratulations to Tanja, Louis, Chaoran, and many more!
Read more:
- external page Louis: High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
- external page Louis: Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks
- external page Chaoran, Louis and Tanja: V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
- external page Tanja: Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence
Ugne Stolz defended her thesis on June 19th titled Beyond the Binary: Generalised Trees for Phylodynamics. Find out more information here.
Sheena Conforti defended their thesis on August 30th titled Advancing environmental surveillance for antimicrobial resistance: molecular assays, wastewater monitoring and genomic analyses. Find out more information here.
Gabriele Marino joined as a PhD student in June 2024 after earning a Master’s degree in Computer Science. With diverse experiences in Computational Neuroscience, Legal AI, and Software Engineering, he discovered a passion for Bioinformatics while working as a Research Intern in Computational Biology in Paris. At ETH Zurich, his goal is to develop novel statistical learning approaches to address critical questions in public health and virus evolution. Outside of academia, he enjoys playing the piano and guitar, playing chess, hitting the gym, and engaging in running and swimming.
Ewan Ciuffi joined as a PhD student in September 2024 as part of the National Centre of Competence in Research (NCCR) Evolving Language, a multidisciplenary consortium across Switzerland with the goal of unravelling the evolutionary origins, history and function of language. In this capacity, he will work on developing novel Bayesian phylogenetic and phylodynamic methods to study the evolution of languages in collaboration with lingusists at the University of Zurich. Before this, he studied mathematics and statistics at the University of Bristol and Sorbonne Université.
Julia Pilarski joined us in September 2024 as a PhD student. She obtained her Master degree in Computational Biology and Bioinformatics at our department in 2023. After a successful internship at Roche, she returned to our group to implement and apply computational tools to learn more about cell development. In her leisure time, she loves exploring the Alps and the rest of the world. She is enthusiastic about new things, as much as she enjoys the calm of everyday life.
Noémie Lefrancq joined us in September 2024 as a postdoctoral fellow, funded by an ETH fellowship. Prior to coming to Basel, she obtained her PhD at the University of Cambridge, and her undergraduate degree from ENS Paris. She will be working on developing scalable phylodynamics methods to explore the mechanisms of pathogen spread. Outside of the lab, Noémie loves all things sports: rowing, running, cycling, skiing and more! She also enjoys exploring new cities and places.
We've said goodbye to ...
Sophie Seidel left us at the end of May 2024. Sophie worked on developing new tools for inferring timed cell phylogenies from single-cell lineage tracing data, with applications in developmental biology. Currently Sophie is doing a short-term postdoc with Prof. Niko Beerenwinkel, where she's exploring how mitochondrial mutations can be used as lineage markers in immunology. In 2025 she will move to Seattle to start a postdoc in the group of Prof. Jay Shendure at the University of Washington.