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PhD students:
- Elke Schaper (SNSF-funded): website
- Large-scale detection tandem repeat sequences
- Evolution and selection of proteins with tandem repeats
- Adam Szalkowski (SNSF-funded): website
- Modeling evolution of intrinsically disordered proteins - see paper
- Statistical alignment for proteins with tandem repeats
- Daniel Dalquen (co-supervising with Prof G. Gonnet, ETH Zurich): website
- ALF: Artificial genome simulation - see paper
- Studying selection on codon usage with codon models
- Stefan Zoller (co-supervising with Prof G. Gonnet, ETH Zurich): website
- Phylogeny inference with codon models (Stefan is a coauthor of CodonPhyML)
- Modeling evolution of protein-coding regions with repeats
- Maja Greminger (co-supervising with Dr M. Krützen, the Anthropological Institute and Museum, UZH): website
- Genetic basis of adaptive evolution in orangutans (Pongo spp.): Demographic modeling will be incorporated into tests for selection in order to disentangle natural selection from stochastic processes such as genetic drift.
Visitors:
- Ziheng Yang : Professor, FRS at University College London, UK (ETH-funded sabbatical stay Feb-Aug 2011)
- Julia Sidorova : postdoctoral fellow at Universitat Autonoma de Barcelona, Spain (SNSF-funded research visit Apr-Jul 2012)
- Gabriel Rech : visiting PhD student, University of Salamanca, Spain (funded by the Spanish Ministry of Science, Sept-Dec 2012)
Master students:
- Xi Luo
- Tim Enke
- Alexander Mirsky
- Veronika Boskova
Alumni:
- 2009 - Slavica Dimitrieva (ETH medal for master thesis): studied synonymous rate variation in Pfam domains and families; developed PanditPlus database see paper (now PhD student at EPFL)
- 2009 - Anna Hanulova: to measure tree signal in a dataset, implemented an LRT of a fully resolved tree vs star-tree - see here (now a PhD student at the University of Bern)
- 2010 - Marcelo Zanetti (ETH medal for master thesis) developed CodonPhyML - a fast implementation of codon models for ML tree inference - now is a PhD student at ETHZ
- 2010 - Mingcong Wang: studied coevolution and selection on residues of Rubisco - see paper (now a PhD student at UZH).
- 2010 - Giedrius Pociuipa (ERASMUS student from the RWTH Aachen University, Germany): studied the genome evolution of thermophiles and radioresistant bacteria.
- 2011 - Louis du Plessis: studied synonymous rate variation in mammalian and E. coli genes (now a PhD student at ETHZ).
- 2012 - Maria Llanos: studied synonymous rate variation in Drosophila lb genes
- 2012 - Bo Wang: studied the influence of errors in tree topology on evolutionary parameter estimation
Collaborators:
- Andrey Kajava, CRBM-CNRS, UMI & UMII, Montpellier, France
- Nemo Peeters, Laboratory for interactions of plants and microorganisms, INRA-CNRS, Castanet-Tolosan, France
- Evgeniy Balakirev, Institute of Marine Biology, Vladivostok, Russia
- Carolin Kosiol, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
- Christophe Dessimoz, European Bioinformatics Institute (EBI), Hinxton, UK
- Olivier Gascuel, LIRMM, UMII, Montpellier, France
- Ziheng Yang, Biology department, UCL, UK
- Joe Bielawski, Dept of Biology and dept of Maths and Statistics, Dalhousie University, Halifax, Canada
- Maxim Kapralov, Dept of Plant Sciences, University of Oxford, UK
- Mattias Peter, Biochemistry department, ETH Zurich, Switzerland
- Homayoun Bagheri, Institute of Evolutionary Biology and Environmental Studies, University of Zurich , Switzerland
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