Category Archives: training

(Reopened) Postdoctoral Researcher in Bioinformatics for Rice genomics

[Update 8/2012 – this position has been filled]

Position Description
An NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the impact of a very recent burst in copy number of a transposable element in rice. This work will involve analysis of high throughput genomic sequencing using Illumina/Solexa technology to examine the genomes of hundreds of recombinant inbred lines of rice. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies, identify polymorphisms, and perform quantitative trait mapping. 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. Applications will be accepted until the position is filled and review will begin on July 15, 2012.  Salary and benefits are commensurate with NSF 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 and methods of studying population biology. 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 Donald Danforth Center, Cornell University, and USDA ARS Dale Bumpers National Rice Research Center.

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 the research project http://dynamiterice.org 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.

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Perl Wednesdays

We’ve started doing Perl training on Wednesdays for any IIGB and UCR students and postdocs (or curious faculty). This is starting at beginning with command line usage and will hopefully build to advanced bioinformatics. Sofia and Steven are leading these currently and hope it will be a good jumpstart to improving programming skills of our lab and others. Join the mailing list if you want to get updates on the meeting times and locations and will also try and post useful slide sets and problems here as well.

Congrats Jessica

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.

Lessons from the 1st Quarter

Well the 1st quarter is over and had a few observations about life of an assistant professor.

  1. Remember to check that you don’t need to turn in grades! I thought I could safely ignore emails about sending in grades, since I wasn’t teaching this quarter, but meant I forgot to turn in grades for grad students working in the lab. Whoops! Lesson learned.
  2. Spending money isn’t that hard, but researching how to spend it on equipment is time consuming.  The optimization of trying to find the best deal, planning for current and future experiments, and establishing new technologies took more time than I expected.  Planning how to best spend money longer term is also taking some time, I don’t know if there is any good formula to rely on because it depends on what future grant support is awarded. But I think that I am getting better at making the equipment decisions – but I am my own sysadmin for macs in the lab and also the new separate (from the shared bioinformatics cluster) linux machines I have for our web and specialized compute needs and find that very time consuming.
  3. Travel is good, but takes up time that can be spent writing, instructing, and my own research. While I can do much of my research from my laptop and an internet connect, I am distracted when away from lab and doing a disservice to the meeting I am attending if I am always working while on the road.  Better to divide my time better and focus on the meeting at hand. Course this means I should always have the talks finished before I get to the meeting and that has been difficult to guarantee.
  4. People are important. I can’t do all the research myself. Getting students and postdocs into the lab who can be trained on techniques and the background of the research questions is the most important thing to get the lab moving forward.  I am excited about the teaching and learning process but it is a process that needs a vision and schedule that I establish.  I’m still fine tuning that schedule and the approaches while keeping us aimed toward a vision of the kind of research we will do in the next 3-5 years.
  5. Time flies – take stock of how you spent it! Stopping and reflecting on what was accomplished is good to remind me and remind trainees that we have done things even if it feels like there is a mountain of work ahead.  As the gets better at this I’ll probably be able to give better feedback about dead-ends and keeping people on track earlier in the game.  We are still getting our timing together to have regular lab meetings and journal clubs that I expect to be the heart of the learning that happens in the lab at this point. I’m teaching programming, bioinformatics, phylogenetics & molecular evolution, and mycology at the outset and so am working to make these subjects more approachable with the right kind of background reading materials.  Probably will have to turn this into a review or primer someday as I feel like this synthesis of different fields is not something I can point anyone to just one or two resources for.

I’m still getting aquatinted with who to ask for help and where to go for advice, but I’ve been lucky to have generous junior and senior colleagues who have provided encouragement and advice.  Here’s to hoping next quarter I learn a little more about how to do things, focus on the grant writing, and make some tangible progress on the research projects that need some new data before this summer. A lot of papers are queued up from collaborative work that were submitted this month and I hope that means more focus on the two main project foci of the lab.  New folks will be joining us next quarter and I’m excited about the progress we have made and will be able to make as everyone comes up to speed.

Happy New Year!