Evolutionary genomics of pathogens

Laboratory of Evolutionary Genetics @UNINE

We are a diverse group of people combining skills in evolutionary biology, microbiology, bioinformatics and genomics. But we are also passionate about conservation genetics and many other topics.

We are at the University of Neuchâtel (Switzerland) and run the Laboratory of Evolutionary Genetics.


Daniel Croll

Principal investigator, Assistant Professor

Daniel Daniel Croll is an assistant professor in Evolutionary Genetics and Vice-Director of the Institute of Biology at the University of Neuchâtel, Switzerland since 2017. He completed his PhD in 2009 at the University of Lausanne, followed by a postdoctoral position at the ETH Zurich with Prof. Bruce A McDonald. Daniel received a Swiss National Science Foundation Advanced Postdoctoral Fellowship to join the lab of Prof. James Kronstad at the University of British Columbia in Vancouver from 2013-14. Daniel was a junior group leader and lecturer at the ETH Zurich from 2015-16. Daniel has a broad range of interests from population genetics, microbiology, bioinformatics and conservation genomics.

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Thomas Badet

Postdoctoral fellow

Thomas Evolution of genomes and gene expression

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Alice Feurtey

Postdoctoral fellow / Junior group leader [co-supervised with Bruce McDonald, ETH Zürich]

Alice Population genomics of Zymoseptoria tritici

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Sabina Tralamazza

Postdoctoral fellow

Sabina Metabolome evolution

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Ursula Oggenfuss

PhD student

Ursula The biology of transposable elements

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Nikhil Kumar Singh

PhD student

Nikhil The genetic basis of host-pathogen interactions

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Leen Abraham

PhD student

Leen Transcriptional control of host-pathogen interactions

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Anik Dutta

PhD student [co-supervised with Bruce McDonald, ETH Zürich]

Anik My PhD research is focused on the wheat-Zymoseptoria tritici pathosystem. I focus on the mechanisms of maintaining genetic variation in pathogen life-history traits in nature. I combine high throughput phenotyping with genomics to elucidate the adaptive patterns and evolutionary trajectories of the pathogen in heterogeneous environments. I look for trade-offs among life-history traits and their role in constraining adaptation.

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Luzia Stalder

PhD student

Luzia Microbiome interactions

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Vinciane Monod

PhD student [co-supervised with Katia Gindro and Valérie Hofstetter, Agroscope]

Vinciane Monod Grapevine diseases

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Hadjer Bellah

PhD student (Swiss Government Excellence Fellowship)

Hadjer Plant pathogen interactions

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Sarai Reyes

PhD student

Sarai Next-generation framework for the detection of genetically modified organisms

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Guido Puccetti

PhD student

Guido Phenomics of Zymoseptoria tritici

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Vinciane Mossion

PhD student

Vinciane Mossion Transcriptomics and phylogenetics of ferns

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Gholam-Hossein Jowkar

PhD student [co-supervised with Maria Anisimova, ZHAW Wädenswil]

Gholam Algorithm development for phylogenetic reconstructions

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MSc students

Laetitia Holzer, Sara Hurschler, Elizabete Ferreira, Nicolas Seiler, Hanna Glad, Fanny Gagliardi


Lab technicians

Ophélie Gning

Cristela Bondo Mateus (apprentice)


Visitors/interns

Hanna Glad, UNIFR


Alumni

Lea Stauber (PhD student 2017-2021)

Simone Fouché (PhD student & postdoc 2015-2020)

Maëlle Wanner (intern/stagiaire 2020)

Estelle Fleury (MSc student 2019-2020)

Emilie Chanclud (SNSF & Marie Curie postdoctoral fellow 2018-2020)

Sami Sayer (visiting PhD student 2019-2020)

Stéphanie Ruaud (MSc student 2018-2020)

Camille Kessler (MSc student 2018-2019)

Norfarhan Mohd-Assad (PhD student 2013-2018, Farhan is now a Senior Lecturer at Universiti Kebangsaan in Malaysia)

Luzia Stalder (MSc student 2017, Luzia is now doing her PhD with us)

Tiziana Vonlanthen (MSc student 2016-17, Tiziana works now at the Agroscope Reckenholz as a scientific assistant)

Fanny Gagliardi (intern, Biology student UniNE 2018)

Dr. Clémence Plissonneau​ (postdoctoral fellow, recipient of an INRA Young Scientist grant, Clémence currently is responsible for bioinformatics at Gautier Semences).

Dr. Fanny Hartmann (PhD student 2013-2017, Fanny is currently a Postdoctoral Fellow at Université de Paris-Sud).

Juliana Benevenuto (6-month PhD scholarship from the São Paulo Research Foundation in 2016, Juliana is currently a postdoctoral fellow at Florida State University)

Dr. Ethan Stewart (ETH Zurich, co-supervised PhD student with Bruce McDonald 2011-2016). Ethan is currently a Postdoctoral Fellow at Cornell University.

Christoph Eschenbrenner (Universität Kiel, Germany, visit for genome assembly techniques 2016) ​ Dr. Thierry Marcel (INRA BIOGER, COST SUSTAIN short term scientific mission 2016)

Sandra Wenger (BSc student 2015-2016)

Alessandra Stürchler (MSc research project 2015-2016) ​ Dr. Mark Lendenmann (co-supervised PhD student with Bruce McDonald 2015-2016)

Dr. Jana Drabešová (PhD student internship 2011)