Two postdoctoral research positions are available in the laboratory of Dr. Thomas Richards at the University of Exeter, UK.
The project focuses on using environmental sequence data, including meta- genomics and transcriptomics, combined with single cell genomic data to investigate the biology and evolutionary significance of unculturable protist and fungal microbes from marine environments including deep-sea sediments.
One post is focused entirely on bioinformatic based analysis while the second post can include both bioinformatic and laboratory work. However, both applicants should be interested in working with second-generation sequence datasets and feel confident with post genomic analysis including for example: phylogenetic tree reconstruction and metabolic pathway reconstruction.
For more details please see:
This is a Gordon and Betty Moore Foundation funded project and is part of an international collaboration including associated laboratories at the University of British Colombia, University of Maryland Center for Environmental Science, Monterey Bay Aquarium Research Institute and the Department of Energy Joint Genome Institute and should include the opportunity for travel
To ask questions or apply please e-mail your CV and contact information for three referees to email@example.com . Materials must be received by the 13th November but late applications will be considered until the position is filled.
2012 was certainly a banner year in genome sequence production and publications. The cost of generating the data keeps dropping and the automation for assembly and annotation continues to improve making it possible for a range of groups to publish genomes.
I made a NCBI PubMed Collection of these here Fungal Genomes 2012
Some notable fungal genome publications include
There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes
(Now I might have missed a few in my attempt to get this done before holidays overtake me – if so, please post comments or tweets and I’ll be sure to amend the list on pubmed and here.)
A new trend for fungal genome papers can be seen now in the Genome Announcements of Eukaryotic Cell which aim to get the genome data out quickly with a citateable reference. These are short descriptions which I expect will become more popular ways to insure data made public can also be cited. I only counted about 5 published in 2012 but I expect to see a lot more of these in the 2013 either at EC or other journals. I’m sure there will still be some tension between providers making data public as soon as possible and the sponsoring authors’ desire to have first crack at analyzing and publish interpretations and comparison of the genome(s). The bacterial community has been doing this for Genome Reports in the SIGS journal and the Journal of Bacteriology so will see what happens as these small eukaryotic genomes become even easier to produce.
I look forward to exciting year with more of the 1000 Fungal genomes and other JGI projects start to roll out more genomes. I also predict there will be many more resequencing datasets published as functional and population genomics. It will also probably be a countdown for what are the last Sanger sequenced genomes and how the many flavors of next generation sequencing will be optimized for generation. I am hopeful work on automation of annotation and comparisons will be even easier for more people to use and that we start to provide a shared repository of gene predictions. I’ve just launched the latter and look forward to engaging more people to contribute to this.
We held a workshop last for some of the people using and developing tools and databases for fungal molecular ecology in Fungi in (beautiful) Boulder, CO last week as part of our efforts in the Microbiome of the Built Environment. I am working with my co-organizer and participants to prepare a meeting summary and some descriptions of concrete plans forward. We expect this to make it easier to analyze Fungal ITS sequences in tools like QIIME and provide linkage with resources built around phylogenetic analyses of Fungi. An longer meeting summary will be posted in the coming week after we have all the presentations gathered and the details of the meeting written out.