Tag Archives: computational

Postdoc: Comparative genomics and bioinformatics

Postdoc position in comparative genomics and bioinformatics

Applications are invited for a bioinformatics postdoctoral position in ?the research group of Laszlo G Nagy (Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary). We are now looking to hire new people with a background in bioinformatics, phylogenetics or fungal evolution. The Lab offers excellent training opportunities in fungal comparative genomics, cutting edge projects, abundant funding, an inspiring atmosphere and extensive collaborator network.

The primary focus of the lab is understanding the general principles of convergent evolution and fungal multicellularity through comparative genomics, transcriptomics and single-cell transcriptomics of multicellular fruiting bodies in Basidiomycetes. Fruiting bodies represent some of the most complex morphological structures found in fungi, yet, their developmental and evolutionary origins are hardly known. Complex fruiting bodies have evolved independently several times in the Basidiomycetes, offering an excellent model system to study the genetic mechanisms of convergent evolution.

The successful Candidate has:

  • PhD in bioinformatics, evolutionary biology, mycology or other relevant field
  • Experience in genomics, Perl and/or Python scripting
  • Good team player traits
  • Experience in working with fungi is a plus

Contact and application – The starting date of the project is September 2015. The position will last for one year with the possibility of extension up to 4 years. If interested, send a motivation letter along with your CV to Laszlo Nagy (lnagy@brc.hu).

Dr. Laszlo Nagy
Fungal Evolution & Genomics Lab
Synthetic and Systems Biology Unit, Institute of Biochemistry
Biological Research Center, HAS


Lichen genome projects and the power shift prompted by next-gen sequencing

Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues.

This isn’t the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has taken a while to get going because of some logistical problems getting the DNA (and any problems are amplified because it takes a long time to get new material since lichens grow very slow).

The transfer of the power for researchers to be able to quick exploratory whole-genome sequencing with next-gen and eventually, high quality genome sequences from next-gen sequencing is predicted to transform how this kind of science gets done. It means we’ll probably just sequence a mutant strain instead of trying to map the mutation – this is happening already in anecdotal stories in worms and in our work in mushrooms. N.B. this is done after a mutagenized strain has been cleaned up a bit to insure we’re looking for one or only a few mutations based on some crosses – but that is part of standard genetic approaches anyways.

This fast,cheap,whole-genome-sequencing is also the stuff of personal genomics, but for basic research it will also mean that a first pass exploring gene repertoire of an organism will be a multi-week instead of multi-year project. I just hope we’re training enough people who can efficiently extract the information from all this data with solid bioinformatics, computational, data-oriented programming, and statistical skills to support all the labs that will want to take this approach. You’ll need a life-vest to swim in the big data pool for a while until more tools are developed that can be deployed by non-experts.