Fungal Evolutionary Genomics

Celebrate sunny citrus http://t.co/P0d376Zx 2 weeks ago
Elementary school science fair judging today - some of these kids will have a future in science I hope. http://t.co/1YzCWR3F 2 weeks ago
UCR's Cheryl Hayashi TED talk on The magnificence of spider silk http://t.co/FgfAnIOm 2011-12-14
“@UCR_ScienceNews: Jason Stajich of #UCRiverside joins international team in identifying genetic traits in #fungi http://t.co/1ESc0YmW” 2011-11-09
Lab paper on FungiDB: an integrated functional genomics database for fungi s.fungidb.org/ukjx2i 2011-11-09
Our new class in Fall 2012: GEN 220 (Computational Analysis of High Throughput Biological Data) is formal version of workshop dng this qrtr 2011-10-26
I'm going to talk at UCR SoCal Parasitology mtg abt our research including @fungidb. Will try to make fungi interesting to parasitologists! 2011-10-26
More updates...

Posting tweet...

Welcome new postdocs

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.

Congrats to Yizhou

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

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.

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.

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

Lab farewell for postdoc John Abramyan

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.

John (Left) enjoyed a farewell dinner with the lab

Welcome new FungiDB programmers

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.

Welcome Sofia

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.

Congrats to Edgar!

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!

FungiDB Programmer position

A programmer position is available in the lab to work on FungiDB. The duties include performing data loading into relational database system, development and improvement of scripts for data importing & downloading, and website development. This project is part of a collaborative project with members of the EuPathDB team.

More information and online application to the position is available at the UCR job listing.