RNDr. Jan Brabec, Ph.D.

Job Position: Associated scientist - Laboratory of Genomics and Diversity of Protists

Contact details

E-mail: brabcak@paru.cas.cz
Room: nová budova 5. patro

Description

Research focus

Phylogenomics and genomic adaptations to parasitism of parabasalid protists.

Phylogenomics and evolution of parasitism of parasitic flatworms (Neodermata) and thorny-headed worms (Acanthocephala).

Molecular taxonomy of fish cestodes. 

Molecular ecology and population genomics of metazoan parasites of fish. 

Historical DNA sequencing of museum's wet collection specimens (museomics).

Molecular identification and differential diagnostics of helminth parasites. 

 

Ongoing research projects

Origin of parasitism in Neodermata

One of the research lines of a multi-lab project granted to Tomáš Scholz to which I contribute transcriptomic data and analyses of parasitic flatworms, in collaboration with Roman Kuchta. The early phylogeny of parasitic flatworms (including the widely known cestodes and trematodes) remains to be resolved satisfactorily and we address this issue through de novo characterisation of genomes and transcriptomes of selected representatives of the basal neodermatan lineages, bioinformatic analyses of the genomic data and interpreting individual morphological/ultrastructural traits in the light of this data.
 

Parasite radiations: Domino effect of host radiations?

A project from my previous postdoctoral position at the Muséum d'histoire naturelle de Genève (supervised by Dr Isabel Blasco-Costa) where I was responsible for carrying out the entire workflow of data generation and participate on data analyses. We are currently busy analyzing the rich dataset, testing various evolutionary ecology hypotheses concerning metazoan fish parasites with complex life cycles. While scientists still known very little about how adaptive radiations of host species affect the associated parasite communities, we try to understand if parasite taxa tend to diversify as a consequence of rapid host speciation, which traits predispose parasites to diversification and what processes generating variability underpin novel adaptations among distinct parasite population leading to speciation. These questions are key to our understanding of the speciation process in parasites and the evolution towards host specificity. 

 

Phylogenomics of formalin-fixed museum flatworms

A joint project of Dr Isabel Blasco-Costa (Muséum d'histoire naturelle de Genève) and myself that strives to test the utility of exome-capture methodologies for capturing highly damaged DNA of formalin-fixed museum specimens. Museum specimens are often the only available representatives for a given group of organisms ever collected, challenging to be recollected from nature again, and whose molecular records are often missing from current phylogenetic or systematic treatments. The aim of this project is to establish an efficient protocol and assess the power of the phylogenomic markers obtained in resolving the interrelationships of these organisms.

Curriculum vitae

Employment history

2020–now Research assistant, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences

2019–2020 Postdoctoral fellow, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences. Project: AQUAPARA-OMICS: Aquatic parasitism meets biomics – addressing key biological questions using novel datasets and modern analytical tools (Grant Agency of the Czech Republic)

2017–2019 Postdoctoral fellow, Natural History Museum of Geneva, Switzerland.
Project: Parasite radiations: Domino effect of host radiations? (Swiss National Science Foundation)

2012–2017 Postdoctoral fellow, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences. Project: Molecular diagnostics, historical biogeography and genetic structuring of the populations of model platyhelminth parasites

 

Education

2006–2012 PhD, Parasitology, Faculty of Science, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Molecular systematics and evolution of basal cestode lineages

2004–2006 MSc, Parasitology, Faculty of Biological Sciences, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Paraphyly of pseudophyllidean tapeworms: testing a phylogenetic hypothesis using sequence data (18S & 28S rDNA)

2001–2004 BSc, Biomedical Laboratory Techniques, Faculty of Biological Sciences, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Molecular phylogeny of tapeworms of the order Pseudophyllidea

 

Research visits

Dr Tim Littlewood, Life Sciences Department, The Natural History Museum, London, UK, 2013, 2014

Dr Peter Olson, Department of Zoology, The Natural History Museum, London, UK, 2005, 2010

Prof Klaus Brehm, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany, 2006, 2008

 

Publications

More publications