Alumni

Our former PhD students and postdocs


Biographies

Sarah Nadeau

Sarah Nadeau

Sarah completed her B.S. and M.S. in Biological Engineering at Cornell University before joining the group for her Ph.D. While in the cEvo group, Sarah developed a novel statistical tool to improve infectious disease genome-wide association studies. Then, she co-developed the data infrastructure for the Swiss SARS-CoV-2 Sequencing Consortium. Finally, Sarah performed several large-scale phylodynamic analyses focusing on evaluating public health measures to combat the COVID-19 pandemic. Sarah is currently exploring a career in public health research.

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Jana Huisman

Jana Huisman

Jana started her PhD in the cEvo group in 2017, jointly supervised by Tanja Stadler and Sebastian Bonhoeffer from the Theoretical Biology group (D-USYS). Her work focussed on the role of plasmids in the spread of antibiotic resistance. During the COVID-19 pandemic, she (co-)developed the method used to estimate the effective reproductive number (Re) of SARS-CoV-2 in Switzerland, and extended this to estimate Re from wastewater data. Jana received the ETH medal for her thesis, titled "Population dynamics of infectious agents: antibiotic resistance plasmids and SARS-CoV-2".

Jana is now a postdoc at MIT in the group of external pageJeff Gore, where she continues to study the effect of mobile genetic elements on the dynamics of bacterial populations.

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Claire Guinat

Claire Guinat

Claire graduated in Veterinary Medicine from the National Veterinary School of Toulouse (ENVT) in 2012. She completed her PhD in veterinary epidemiology at the Royal Veterinary College (RVC) and The Pirbright Institute in 2016. After her PhD, Claire completed a 4-year postdoc fellowship at ENVT. In 2020, she joined ETH Zurich as a Marie-Curie Individual Post-doctoral Research Fellow. Since 2022, she is now a research fellow at the National Research Institute for Agriculture, Food and Environment (INRAE). She is also member of the expertise committee on Animal Health and Welfare (Anses, 2022-2026) and on Avian Influenza and Vaccination (EFSA, 2022-2024).

Claire’s research focuses on investigating the transmission dynamics of zoonotic and animal infectious diseases with the view to improve our ability to predict and control future outbreaks. Her work combines pathogen genome sequences and case surveillance data to reconstruct epidemics and identify determinants of spread. Her research is highly inter-disciplinary, involving integrative approaches such as epidemiology, disease modelling, phylodynamics and ecology. She is currently involved in projects focusing on avian influenza, African swine fever, peste des petits ruminants and hepatitis E virus.

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Marc Manceau

Marc Manceau

Marc studied life sciences and applied mathematics/statistics at the Ecole Normale Supérieure in Paris. He then stayed in Paris to pursue a PhD, working on probabilistic models used to study biological evolution. Three more years in academia followed, with a postdoctoral position at ETH Zürich in the cEvo team, where he worked on mathematical modeling and data analysis in epidemiology.

Although mainly trained in academia, his current professional objective is to make the most of the theoretical mathematical/statistical knowledge gained in academia to solve more concrete problems. He is starting to work as a freelance (bio)statistician and is particularly interested in analyzing data or teaching statistics/data science for projects with added societal value, e.g. in agronomy, ecology, public health, medicine.

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Rachel Warnock

Enlarged view: Rachel Warnock

Rachel completed her PhD in palaeobiology at the University of Bristol in 2014. Following a postdoc at the Smithsonian Museum of Natural History, she joined cEvo as an ETH Postdoctoral Research Fellow in 2016. Her research explores the use of phylogenetic tools in palaeobiology. During her time in Basel she focused on a new phylodynamic model for the analysis of stratigraphic ranges (the duration between the first and last appearance a species in the fossil record) in the software DPPDiv and RevBayes. She also worked on the R package FossilSim for simulating fossil occurrence data. She is now a Professor of Systems Palaeobiology at Friedrich-Alexander University Erlangen-Nürnberg, where she will continue research and teaching in phylogenetics.

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Venelin Mitov

Enlarged view: Venelin Mitov

Venelin completed his B.Sc. in Computer Science at the University of Sofia in 2005. Following 6 years of employment as a software engineer, in 2011, he rejoined academia, enrolling in the M.Sc. program in Computational Biology and Bioinformatics at ETH Zürich.

Between the years 2014 and 2020, Venelin completed his PhD and postdoctoral studies in the cEvo group, under the supervision of Prof. Dr. Tanja Stadler. His main focus of research has been the evolution of biological traits, such as morphological characters of animal or plant species, protein expression levels of cells, virulence traits of patients suffering an infection, and others. A common feature of these systems is that biological units like species, cells or viruses are connected by phylogenetic trees representing their ancestry or transmission history. Venelin has developed novel phylogenetic comparative models and software for detecting patterns of trait evolution along such trees. In 2018, his Ph.D. thesis entitled “Phylogenetic Comparative Methods in the Era of Big Data” has been nominated for the ETH silver medal for an outstanding Ph.D. dissertation. Venelin pursues his work in this area in his spare time. Next to his research, Venelin has been involved as co-organizer of the first Taming the Beast summer school as well as a co-organizer of the Methods & Beers interdisciplinary seminar in Basel.

Starting from February 2020, Venelin joined the company IntiQuan, specializing in computer assisted drug design and development.  

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Jūlija Pečerska

Enlarged view: Jūlija Pečerska

Jūlija joined the cEvo group as a PhD student in 2014. In her time in the group she worked on estimating the transmission fitness costs of different drug resistances in multidrug-resistant tuberculosis strains. She also helped develop and teach the Computational Biology course at ETH and a series of Taming the Beast workshops around the world.

After successfully defending her PhD, Jūlija joined the Computational Genomics group at the Zürich University of Applied Sciences (ZHAW) as a postdoc. There she works on developing methods for efficient simultaneous multiple sequence alignment and phylogenetic tree inference.

Jūlija’s interests lie in epidemiology and computer science. She greatly enjoys both developing better methods for epidemiological inference as well as educating the community of scientists and scientists-to-be on how to use them.

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Nicola Müller

Enlarged view: Nicola Müller

Nicola started his PhD in the cEvo group in 2016. During that time, he worked on novel phylogenetic and phylodynamic tools to study epidemiological and macroevolutionary processes.

After finishing his PhD at the end of September 2019, he joined the lab of Trevor Bedford at the Fred Hutchinson Cancer Research Center in Seattle (USA) as an SNF Post-doc Mobility Fellow. There, he studies how reassortment influences the fitness of seasonal human influenza viruses.

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Carsten Magnus

Enlarged view: Carsten Magnus

Carsten studied mathematics in Münster, Germany, and moved to the field of theoretical biology in 2007 when he started a PhD with Roland Regoes at the ETH Zurich, Switzerland. After a short postdoctoral stay in Zurich, Carsten continued his research with Prof. Angela McLean in Oxford, UK, and with Prof. Alexandra Trkola in Zürich, Switzerland, funded by the SNF and DFG. From September 2015 till February 2019 Carsten was a member of the Computational Evolution group at the D-BSSE in Basel where he continued his research as a senior scientist, co-developed the Computational Biology lecture and co-founded the Methods & Beers seminar series. Carsten started working for F. Hoffmann-La Roche as a Senior Data Scientist in 2019. There he uses real world data to develop clinical decision support apps.

Carsten's main interests focus on the interaction of antibodies with the human immunodeficiency virus (HIV). He applies newly developed mathematical techniques to study different questions such as how many antibodies are needed to neutralize the virus or which route of cell infection leads to faster immune escape of the virus. In the cEvo group, Carsten was extending existing phylodynamic tools to study the within-host diversification of HIV.

Besides applying mathematical concepts to biological questions, Carsten is passionate about communicating science to a non-scientific audience. “Mit Mathematik gegen HIV” (fighting HIV with mathematics) was the title of one of the papers he was involved in featured in “20Minuten” and additionally he was recently awarded with a “Flash poster award” for explaining virological concepts with minions (the little yellow kids movie characters).

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Joëlle Barido-Sottani

Enlarged view: Joëlle Barido-Sottani

Joëlle joined the cEvo group as a PhD student in October 2014 and successfully defended in October 2018. She worked on developing and implementing a multi-state birth death model for inferring lineage-specific birth and death rates, which is currently available as an R package (ML.MSBD) and as a package for BEAST2 (MSBD). She also developed the R package FossilSim for simulating fossil and taxonomy data.

She started a postdoc with Tracy Heath at the Iowa State University in February 2019, during which she will contribute to the RevBayes project.

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Veronika Bošková

Enlarged view: Veronika Bošková

Veronika was a PhD student in the cEvo group from 2013 to 2017. She focused on development of Bayesian phylodynamic methods for analyses of large datasets with duplicate sequences. She also tested existing tree prior models to identify conditions under which they provide incorrect parameter estimates and to see how they influence the inference results in datasets from early epidemic. Lastly, she applied the phylodynamic models to real data of C. diphtheriae and Zika virus.

After a short PostDoc at ETH, Veronika is joining CIBIV group in Vienna as SNSF early PostDoc fellow starting in January 2019.
 

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Alexandra Gavryushkina

Enlarged view: Alexandra Gavryushkina

Sasha started as a postdoctoral fellow in Tanja's group in September 2016. Her broad research interests lie in developing computational methods to study evolution. While working in Tanja's group she was extending the fossilized-birth death model to better incorporate available fossil data. This model has proved to be very useful for inferring dated species phylogenies and past diversification parameters. She also looked at the problem of reconstructing dated phylogenies of HIV broadly neutralizing antibodies.

Since March 2018 Sasha joined Paul Gardner's group at University of Otago (New Zealand) as a postdoctoral fellow.

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Hesam Montazeri

Enlarged view: Hesam Montazeri

Hesam was a postdoctoral researcher from January 2017 - August 2017 in the Computational Evolution group. He is mainly interested in developing novel probabilistic graphical models to study complex biomedical problems. His research interests particularly include HIV drug resistance development, phylogenetic analysis of transmission and contact networks in HIV, and recently on identification of novel cancer genes from large-scale RNA interference experiments. His research in the Stadler group focused on the spread of infectious diseases on contact networks. He examined the relationship between three network/trees in molecular epidemiology, namely contact network, transmission, and phylogenetic trees. He in depth investigated whether contact networks leave footprints on phylogenies. Hesam will be an assistant professor in University of Tehran from November 2018.

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David A. Rasmussen

Enlarged view: David Rasmussen

David was an ETH Postdoctoral Research Fellow in the Stadler group from 2014 to 2017. His postdoctoral work focused on extending phylodynamic methods to include different forms of population structure, including contact structure in social/sexual networks. These phylodynamic methods were then used to analyze the transmission dynamics of HIV in southern Africa. David will be starting his own group at North Carolina State University in January of 2018.

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Chi Zhang

Enlarged view: Chi Zhang

Chi joined ETH in September 2015 as a postdoc. His research interest is applying Bayesian statistics in molecular evolution and genomics, to infer evolutionary histories, divergence times, and diversification patterns, and evaluating the properties and performance of the methods using biological data and simulations.

His main project working with Tanja, Huw, and Alexei, was developing a Bayesian approach to jointly infer species networks and gene trees from multi-locus sequence data. Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. The method is available within the BEAST 2 add-on SpeciesNetwork, and provides a general framework for Bayesian inference of reticulate evolution.

Since September 2017, he is an associate professor in Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences.

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Denise Kühnert

Enlarged view: Denise Kühnert

Denise joined ETH in 2013, as a joint postdoc between Sebastian Bonhoeffer Theoretical Biology group and cEvo. She received an ETH Zurich postdoctoral fellowship.

Her main scientific goal is a broader understanding of infectious disease dynamics.

In one of her main projects at ETH she developed a multi-type birth-death model and applied it to investigate the transmission dynamics between risk groups in the Latvian HIV epidemic as well as global Influenza H3N2. In this model each data sample is denoted with a type (e.g. a risk group or geographic location) with different epidemiological parameters for each type (although they may be shared too). This allows, for example, explicit modelling of the exposed period, which had a strong impact on the disease dynamics of the 2014 Ebola outbreak in Sierra Leone. Her implementations are freely available within BEAST2, the standard software package in phylogenetics.

Since February 2017 she is a Marie-Heim Vögtlin fellow at the University Hospital Zurich.

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Louis du Plessis

Louis du Plessis

Louis started his PhD in 2011 and graduated in July 2016. His thesis is concerned with the question of how genome sequencing data may be used to shed light on infectious disease dynamics and investigates this question from several different angles.

Provided that a sufficient amount of genetic variation accummulates in a pathogen population over the course of an outbreak, this signature can be extracted with phylodynamic inference methods. Focussing on the 2013-2016 West African Ebola virus (EBOV) epidemic he investigated the potential of real-time phylodynamics and showed that it is possible to robustly infer the dynamics of epidemic spread from pathogen genetic data while an outbreak is still ongoing. He further investigated the likelihood-surface of a more realistic model that explicitly accounts for saturation effects due to the declining number of susceptible individuals. Using a number of simulations he showed that it is possible to infer epidemiological parameters under this model and that these inferences are robust to mild sampling violations.

A fitness landscape is a mapping from genotypes to fitness values that determines the course of adapatation, as selection drives populations toward fitness peaks. In another part of his thesis Louis investigated the ability of simple regression models to reconstruct a fitness landscape from a sparse sample of pathogen genotypes for which fitness measurements are available. Since we lack a real fitness landscape, he simulated quasi-empirical RNA fitness landscapes of comparable complexity and showed that while it is generally impossible to accurately reconstruct the complete fitness landscape it is possible to achieve a remarkably good description of the local landscape provided that an appropriate sampleing scheme is used.

Since August 2016 he is employed as a postdoctoral researcher at the Department of Zoology at the University of Oxford.

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