Category Archives: projects

Papers from the lab this month

We’re excited that several manuscripts were published in the last month.

One presents the first genome from the Cryptomycota, Rozella allomycis, in a manuscript published in Current Biology along with a nice companion piece from Mark van der Giezen about the work. Steven and Divya participating in this project in collaboration with Tim James at Michigan and Nico Corradi in Montreal. Some of the scripts used for this project are available as well here on github and other associated genome data are available here. We are working to get this into the next FungiDB release as well.

A manuscript from Andrii Gryganskyi who was a lab visitor last summer was published on the Entomopthorales fungus Entomophthora muscae.

A review on the application of genomics to mycology was published in Mycologia celebrating the new era of mycology and the first genome sequences published in this journal.

Work from Anastasia Gioti, who was a lab visitor for several months this year and has visited several times in the past years, wrapped up genome comparisons of Neurospora species which have transitioning from outcrossing (heterothallic) to self-fertile (homothallic) lifestyles. Our manuscript was made available in Evolution this summer and will be published in the Fall.

A paper on the population genomics of amphibian killing chytrid fungus B. dendrobatidis that culminated several years of work and large collection of researchers was published in PNAS at the beginning of the summer.

This one goes to 1000…

Our community sequencing project at the JGI was awarded which will allow a consortium of researchers to sequence 1000 fungal genomes through the DOE’s Joint Genome Institute. The intention is to sample two species from every major lineage of Fungi.

Some press releases on the project below and we will coordinate it through several websites including a forum for discussion about potential species beyond the target list.

Summer student project wrapup

This week the summer student programs ended and Carlos Rojas, Ramy Wissa and Lorena Rivera all gave presentations and posters on their work.  We really enjoyed having them around for the summer and look forward to their possible continuation in the Fall.

Carlos worked with postdoc John Abramyan on the CBM18 gene family in Bdto confirm gene expression of the members of the family by RT-PCR before we choose a subset to work on further.

Carlos Rojas explaining his poster on CBM18

Lorena and Ramy worked with graduate student Divya Sain on a screen of Neurosporastrains with candidate cell wall genes knocked out.  They completed a screen of 115 mutants x 3 replicates = a lot of petri dishes for their first time in the laboratory. Below is a picture of Ramy and Lorena with their peers from the MARCU program.

The 2011 MARCU* students gather before their presentations

Open Postdoc position for Fungal genome data integration

[Update May 5, 2011 — This position is on hold to focus on hiring a programmer to work on data development and loading]

There is an open position in the lab to support development of FungiDB, a database for fungal genome data integration.

Postdoctoral fellow supporting fungal genome database development

Position Description

A postdoc position is available in the laboratory of Dr. Jason Stajich to support the development of FungiDB, a database for fungal genomic and functional data.   Strong candidates will be proficient in the Perl programming language; modern biology in general and bioinformatics in particular; show a demonstrated ability to quickly pick up new biology and computer science concepts; be comfortable using relational databases; and possess core Unix skills to do these tasks efficiently.  Experience using Perl for genome sequence data processing a plus.

You’ll also have a relentless attention to detail, the ability to work independently on challenging problems with no direct easy solution.  You will use these skills to help organize, analyze, and display a vast amount of disparate biological data and interact with the fungal community. There will be opportunities for self-directed research utilizing this collection of genomics and comparative database and tools.

Application evaluation will begin Feb 1, 2011 until the position is filled. Salary and benefits will be commensurate with experience and University of California Postdoctoral Union agreement.


Minimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in Perl programming is required.  Demonstrated experience in web or bioinformatics software development is a plus. The ability to work with a small, distributed team is essential including exceptional written and verbal communication skills.

To Apply

Contact Jason Stajich with a CV and the names of three references letter writers.

Information available on UC Riverside and the Stajich lab.

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A primer on the Fungi

Our primer on the Fungi is available (currently free) on the Current Biology website.  A version with extra refs inserted is available in pre-print format here. In this primer we provide a broad overview of the major evolutionary defined groups within Fungal kingdom. Our intention is make the kingdom a little less mysterious for non-mycologists and introduce some open areas of research that require integrating evolutionary, morphological, and molecular research. This was joint work with Mary BerbeeMeredith BlackwellDavid HibbettTim JamesJoey Spatafora, & John Taylor.

Also thanks to several people for access to images: Jeffrey RollinsSabine HuhndorfDavid McLaughlin & lab, George L BarronGreg Jedd and Michelle Momany.