fabien burki
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Welcome

Fabien is AE for MPE

7/4/2019

 
Fabien recently became Associate Editor for Molecular Phylogenetics and Evolution, handling protist papers. The goal is to increase the protist-focused paper in this journal, so please send your manuscript along!

New papers

27/1/2019

 
Boum boum, 2 new papers from the lab were recently published:
  1. A Quick Guide in Current Biology on the ascetosporean parasites (29(1):R7-R8)
  2. The description of TSAR, a new very very large group of eukaryotes, in Molecular Biology and Evolution (right now in advance access format)

Lab turnover

11/10/2018

 
We recently said bye to Jürgen, who went back to Germany after a successful 2 years in the lab. Sad, but we welcomed a new member last week: Anders Alfjorden, who is doing a PhD on various aspects of Ascetosporean parasites.

Paper accepted

26/5/2018

 
Good news! A collaborative work between Simon Whelan, Iker and Fabien has just been accepted for publication in Bioinformatics. PREQUAL is the name of a neat new tool that implements a full probabilistic approach to detect and deal with stretches of non-homologous characters in sets of unaligned sequences. This will be very useful to prepare phylogenomic datasets. Stay tune for the paper.

Finally, a lab photo

25/5/2018

 
Picture

New lab member

25/5/2018

 
This is a long due post, but in January we welcomed the newest member of the lab, Ioana. She's a postdoc working on the genomics of Ascetosporea, and developing microfluidics to improve the genome sequencing of protists.

New book chapter

11/11/2017

 
​Fabien is happy to be part of the newest volume (84) of Advances in Botanical Research, on Secondary Endosymbioses. Title of his chapter is: The Convoluted Evolution of Eukaryotes With Complex Plastids. Check it out here.
Picture

New funding

11/11/2017

 
With 2 successful research grants in a week, we are getting ready to look into the evolution of ascetosporean parasites (Rhizaria), currently a black box on the map of microbial eukaryote parasites.

Warmest thanks to our funding agencies VR and Formas for their support.

Postdoc position available: comparative genomics of poorly known protist parasites

9/8/2017

 
Apply online

Brief description:
 Study the evolution and specific adaptations to parasitism in Ascetosporea, an emerging threat in marine environments that has remained beyond reach of modern molecular tools. Ascetosporea is a collection of poorly characterized microbial eukaryote parasites of marine invertebrates. It is best-known for including deadly pathogens of oysters and mussels, costing millions of dollars to the growing aquaculture industry. To date, however, Ascetosporea is absent from models describing the evolution of parasites because comparative genomic data is lacking. This is due to multiple factors, including minute cell size, obligate intracellular lifestyle, lack of suitable host cell lines, and techniques for in vitro culture. Here, we propose to overcome these challenges by using micromanipulation and single-cell genomic/transcriptomic methods. We will sequence de novo the genome and transcriptome of several uncultured parasites encompassing the diversity of Ascetosporea, as well as their closest free-living outgroups. With these data, we will broadly look at the evolution of parasitism in Ascetosporea, i.e. identify pre-parasitic conditions, ancestral parasitic innovations, and lineage-specific adaptations using comparative genomics.

​Full description here:
scilife_postdoctoral_fellow.pdf
File Size: 30 kb
File Type: pdf
Download File

Master project available to work on plastid metagenomics

7/6/2017

 
project_plastidmetagenome.pdf
File Size: 378 kb
File Type: pdf
Download File

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  • news
  • papers
  • Research
  • People
    • Fabien (asst prof)
    • Anders (PhD student)
    • Mahwash (PhD student)
    • Max (PhD student)
    • Charlie (MSc student)
    • Ioana (postdoc)
    • Miguel (postdoc)
    • Megan (postdoc)
  • Teaching
  • Tweets
  • contact