Dr Sofia Robb, who completed her PhD at the University of Utah, joined the lab in August 2011 and has been working on the NSF funded Rice transposable element project in collaboration with Susan Wessler’s lab. She has [...]]]> Several postdocs have joined the group in the last few months, though I’ve been remiss to make an announcement.

Dr Sofia Robb, who completed her PhD at the University of Utah, joined the lab in August 2011 and has been working on the NSF funded Rice transposable element project in collaboration with Susan Wessler’s lab. She has already developed a new tool for identification of TEs from high throughput sequencing which we are employing on several varieties of rice and expanding it to be a more general purpose tool. Sofia is also co-developing teaching modules for the Dynamic Genomes course.

Dr Brad Cavinder, who completed his PhD at Michigan State University, joined the lab in January 2012 and is working on transposable elements in mosquitoes as part of the WM Keck funded project to identify and utilize active TEs as molecular tools in mosquitoes.

A third new member of the lab, Peng Liu who completed her PhD at the Chinese Academy of Sciences, will start in February to work on molecular characterization of some pathogenesis factors in the amphibian pathogen Batrachochytrium dendrobatidis.

Jason and Yizhou at [...]]]> Congrats to graduate student Yizhou Wang who passed his qualifying exam today. We’re proud to have him through this hurdle and to continue working on his research into genome defense and silencing of transposable elements in Neurospora crassa.

Jason and Yizhou at Asilomar 2011

Some press releases on the project below and we will coordinate it through several websites including a [...]]]> 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.

• International Team to Sequence Genomes of Fungi
• International team to sequence genomes of fungi
• Forest Service Part of Team Sequencing 1,000 Fungal Genomes

Daniel Borcherding and Ragu Ramamurthy join us to work full time on the FungiDB project to support genomic data integration, website improvements, and supporting the system move from beta into production mode.  We look forward to new improvements in the system and establishing a release cycle [...]]]> Welcome to two new programmers to the team working on FungiDB.

Daniel Borcherding and Ragu Ramamurthy join us to work full time on the FungiDB project to support genomic data integration, website improvements, and supporting the system move from beta into production mode.  We look forward to new improvements in the system and establishing a release cycle for the website and DB.

We will be working on discovery of active transposable element discovery in three mosquitos thanks to a grant that began this year from the W. M. Keck Foundation.  We will be using Illumina based resequencing of populations of mosquitos, RNA-Seq to study expression of genes and TEs to determine differences between active and silenced elements, bioinformatics to identify [...]]]>  

We will be working on discovery of active transposable element discovery in three mosquitos thanks to a grant that began this year from the W. M. Keck Foundation.  We will be using Illumina based resequencing of populations of mosquitos, RNA-Seq to study expression of genes and TEs to determine differences between active and silenced elements, bioinformatics to identify and characterize transposable elements in the genomes of 3 mosquitos, and experimentally test for activity of the transposases that are thought to match the target TEs.  The grant is highlighted in a campus press release and will be a collaboration between our lab and the labs of Dr Susan Wessler, and Dr Peter Atkinson. Should be a fun exploration and will help inform other TE work in the laboratory as well.

Position Description An NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the evolutionary dynamics of transposable elements in the rice genome and their contribution to phenotypic variation. This postdoctoral scientist will be involved in research [...]]]> Postdoctoral Research in Bioinformatics and Transposon Biology in Rice
University of California, Riverside

Position Description
An NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the evolutionary dynamics of transposable elements in the rice genome and their contribution to phenotypic variation. This postdoctoral scientist will be involved in research using bioinformatics, next generation sequencing of multiple rice strains, and RNA-Seq based transcriptional profiling. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies from next generation sequencing data produced by Illumina/Solexa technology. Background information on the biology underlying the project can be found in: K. Naito et al, Nature 2009 461: 131; K. Naito et al, PNAS 2006 103: 17620; N. Jiang et al, Nature 2003 421: 163.

The successful candidate will be expected to contribute and lead data analysis for the project. There will be opportunities for molecular biology, if desired, as part of validation of analyses. In addition, data and software from this project will be used to develop teaching materials as part of the HHMI funded Dynamic Genomes course at UC Riverside providing an opportunity to participate in teaching in an innovative topic-focused course for undergraduates. Applications will be accepted until the position is filled and review will begin on February 15, 2011.  Salary and benefits are commensurate with NIH guidelines and the University of California Postdoctoral Union agreement. Special consideration will be given to candidates with exceptional bioinformatics and genome evolution experience.

Qualifications
Minimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in programming is necessary along with an understanding of the mechanisms underlying genome evolution. Experience with next generation sequence data is highly desirable. Ability to communicate clearly, work independently, and interact collaboratively is essential.

The researcher will also work closely with co-PIs and collaborators at the Boyce-Thompson Institute and Cornell University.

To Apply
Contact Jason Stajich (jason.stajich@ucr.edu) or Susan Wessler (susan.wessler@ucr.edu) with a current CV and names of three references.

More information can be found online about the Stajich lab http://lab.stajich.org Wessler lab http://wesslerlab.ucr.edu and UC Riverside http://www.ucr.edu.

Information about UCR
In the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.

UCR is ranked 43rd among top public universities (US News and World Report 2010).

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