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.
We wished postdoc John Abramyan a farewell and happy trails last week. He was the first postdoc to join the lab and completed a projects relating to Bd, chytrid cell wall genes, and some a gene regulation bioinformatics project. He also was main force in getting the experimental portion of our lab started when the group was established. John is moving on to work on vertebrate evolutionary questions at the University of British Columbia in Vancouver, BC, CANADA. We’ll miss having him in the lab and wish him much luck in his next adventure.
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.
Sofia Robb joined the lab this week to begin work as a postdoc scholar on genomics and bioinformatics aspects of studying transposable elements in Rice. She will also participate in developing teaching modules for the Dynamic Genomes course in collaboration with the Wessler lab. Sofia recently completed her PhD from the University of Utah working on planaria in the Sanchez lab.
Edgar Medina has been visiting the lab for the last few months from the Universidad de los Andes, Bogotá, Colombia to work on Batrachochytrium genome evolution. This past Friday he completed his Master’s degree, defending his thesis via Skype. Was quite fun to see him adeptly switched between Spanish and English in the Q&A period while showing his slides that were remotely projected onto the screen back in Bogotá. It was a real pleasure to have him here for the few months and look forward to a chance to keep interacting on many of our projects. Way to go Edgar!
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.
Postdoctoral Research in Bioinformatics and Transposon Biology in Rice
University of California, Riverside
[Position filled as of 6/2011]
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.
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.
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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UCR undergraduate Jessica De Anda has been working in the lab this summer and Fall will be starting in the MARC U* STAR program at UCR. This program provides mentoring to students interested in pursuing a graduate degree in science and supports laboratory research during the school year and the summers. We’re excited she was selected to be part of this program and look forward to her continued work in the lab on aspects of transposon dynamics and evolution in fungi.
Congrats to grad student Divya Sain, who passed her prelim qualifying exam in September and is now a PhD candidate as she begins her 3rd year at UCR in the GGB program.
We bid farewell last weekend to our lab visitor, Nastassa Gioti, who is headed back to Sweden after 6 fun weeks in Riverside. We learned from her, and she got to dig into her genome datasets for Neurospora in the context of the comparative and genome annotation tools we have, so it was fun all around!
This also marked the second get together (but the first where we remembered to bring a camera). Since we gathered at a local mexican restaurant with whimsical and amazing sculptures and art from recycled material, it was fitting we document it with pictures.