Stajich Laboratory for Fungal Evolutionary Genomics

Blog

2021

Lab Retreat at UC James Research

The lab gathered in August at the UC Nature Reserves - James Reserve for our first retreat. It was a chance to reconnect, take some hikes and spot some natural diversity in the San Jacinto Mountains (originally Cahuilla lands). We got to explore the Reserve on some hikes We walked around Lake Fulmor just outside of the reserve. We took some water samp...

2020

Lichen collecting in Joshua Tree

We kicked off collecting samples for our California Conservation Genomics Project where we are sequencing the native California lichen Acarospora socialis. This work is the core of Julia Adam‘s Dissertation which is focusing on study of population genetic and phylogeographic patterns and how the fungal and bacteria microbiome is related to ecological context of this crustose lichen across an elevation gradient in multiple landscapes. The CCGP project will generate a reference gen...

2019

Derreck is PHinisheD

Congrats to Derreck Carter-House, Ph.D. Derreck defended his dissertation in December 2019 and turned in the final version this month. It was a fun day to hear his defense and we had several celebrations to mark his completion. Jason and Derreck celebrate him turning in his approved dissertation at Grad Division Derreck started a tradition of fanny packs in the lab so we honored him by wearing our ‘stajich-pack’ proudly

Video introduction to research in the lab

Jesús Peña introduces his research on sexual reproduction in the zygomycete fungi in the lab through a new video as part of the UCR Microbiology Graduate Ambassador. Have a watch and learn more about the research Jesús is working on.

Summer Goodbyes: Suki

The end of summer meant goodbye to our excellent REU student Saisuki Putumbaka. Suki was a member of the lab for two months and worked on fungal-bacteria interactions project as part of the UCR Research Experiences for Undergraduates organized through the Center for Plant Cell Biology. Under the guidance of Derreck she tested ideas about the bacteria harbored by a broad range of zygomycete fungi from our draft genome sequencing projects. She also learned how to take pictures of some of thes...

Congrats to Yan!

I am delighted to announce that Yan Wang a current postdoc in our group, will be a starting his next position as an Assistant Professor in the Department of Biology at the University of Toronto-Scarborough. Yan has spent the last two years in the lab working on Zygolife and Neocallomastigomycota fungi projects. We are super proud of all he has accomplished in his training and research. This includes multiple publications from his thesis work and several papers submitted from his current pro...

Spring papers news

We enjoyed a wonderful spring flower season here in Southern California (Harford Springs Riverside County Regional Park) Several publications were accepted and published in last few months and want to highlight the hard work from lab members and collaborators. Jinfeng lead article published on the localized burst of Rice Transposable Elements Ping and Pong in only a subset of the domesticated lineages and clues to what changed to drive their increased activity. Variation of mPing, Ping, ...

2018

Congrats Derreck on CCSTS fellowship

Congrats Derreck! He was selected by the California Council on Science and Technology (CCST) to give a presentation and represent Dept of Microbiology and Plant Pathology and UCR at the California Science Translators Showcase. He will be giving a talk about his research at the California State Capitol to legislators/state senators, agency managers, and senior policy leaders. He was chosen out of a pool of California PhD students, post-docs, and career scientists from all different STEM fields...

Fall lab news

Nat visited New Mexico State University several times this summer to complete work at the Jornada LTER site working with Nicole Pietrasiak (@drylandalgae) on the micro- and myco-biomes of biological crusts. Visits to Anza Borrego and Boyd Deep Canyon for Tania to scope out UCNRS research sites to explore desert rock varnish and rock or crust associated black fungi. Julia continued to develop her Joshua Tree research sites for lichen studies and has collected and sequenced new accessions for a...

Summer conference season

The lab is back from conferences this summer. The Cellular and Molecular Fungal Biology Gordon Research Conference in Holderness, NH and the 11th International Mycological Congress in Puerto Rico. Tania also gave her first talk  at the Black Yeast workshop held in Amsterdam as part of the ISHAM meeting.[gallery ids=”1986,1985,1988,1984,1989,1983,1987,1990,1991”]Many tweets were had … #FungalGRC2018 and #IMC11 or #IMC11pr. Posters and talks were given by everyone in the lab who attended and it...

Recent Lab Papers (2018)

There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, an ascomycete black yeast, complemented some reference genome work we published last year [1].  Former postdoc Ousmane Cissé publish...

ZyGoLife visitors

Last week we hosted several visitors from our ZyGoLife collaborative team in sunny California. I wrote a few notes on Nicole Reynolds and Javier Tabima’s visit for the zygolife site on their extended research stay. We also got to host the Zygofornia Zygolife team meeting.  Here are some pictures I took from the desert and mountain visits. Zygolife team photo, minus Jason, in the UC James Reserve, San Jacinto Mountains, California Lost in a forest? Or finding fungi? i...

Desert Adventures, 2018

Nat and Jason headed out to the Mojave National Preserve to meet up with Erik Hom and his StudyUSA class from Univ of Mississippi. We started at the Sweeney Granite Mountains Desert Research Center which is one of 39 Natural Reserves in the University of California.  We were there to teach a bit about cryptogamic crusts, show the Kelso dunes off, and explore some more of the desert crust sampling sites that our collaborator Nicole Pietrasiak (@drylandalgae) and Paul De Ley have collected from...

2017

The Joshua Tree Album

Our lab trip to Joshua Tree NP and photo session before the start of the quarter resulted in our 2017 album cover lab photo. We also visited one of Julia’s field sites where she is working on a lichen biodiversity inventory and some comparison of the genetic diversity of the fungi and algae symbiont along an elevation gradient in the park.Derreck is excited to collect some dung samples that may recover some zygomycete isolates for the Zygolife project. The rest of pictures from the day a...

Welcome new graduate students Tania and Julia

Welcome to first year graduate students Julia Adams (Plant  Biology) and Tania Kurbessoian (Microbiology). Tania joins us after completing a MS in Microbiology at Cal State-Northridge. She will starting out work on projects relating to genomics and physiology of extremophilic fungi,  black yeasts and efforts to culture and describe diversity of desert fungi. Julia completed a BS at Wellesley and has worked on a variety of projects related to lichen fungi. She will focus on lichen fungi from d...

Congrats Nat on passing qualifying exam

Congrats to Nuttapon (Nat) who passed his qualifying exam this week and is now a PhD Candidate. Along with Derreck he is the second Plant Pathology graduate student in the lab and is working towards his PhD on microbial diversity of cryptogamic or biological soil crusts found in the desert. His primary research area is Joshua Tree National Park and desert areas in the UC Reserve System. Nat and Jason have benefited greatly from collaboration with New Mexico State Univ Professor Nicole Pietras...

Congrats to Derreck

Congratulations to Derreck who passed his qualifying exam this week! Derreck’s projects focus on interactions between the zygomycete (Mucoromycota and Zoopagomycota) fungi and bacteria, primarily from the genus Serratia.

Chytrid Opsin structure paper published

Great work by former graduate student Steven Ahrendt (@sahrendt0), visiting student and current Duke graduate student Edgar Medina (@WhippingFungi) on the publication of a manuscript describing a Type II Opsin found in the zoosporic fungi.  ”Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling” in PeerJ! Thanks also to co-author and collaborator Chia-en Chang in Chemistry Dept at UCR who helped me...

Serratia vs Fungi, The Movie

When Bacteria attack! Here’s a short movie Derreck made of Serratia marcescens (red) spreading across Rhizopus stolonifer in his investigation of antagonism between bacteria and fungi.

MycoMeth project

With Bob Schmitz at Univ of Georgia, We’re working on a project we call MycoMeth to examine evolution of methylation across Fungi. We would welcome contributions of ~2ug of DNA from diverse fungi that have a sequenced genome.  Please email Jason or Bob if you would like to contribute.

Asilomar and beyond

Just back from another fantastic Fungal Genetics Conference at Asilomar. An amazing number of helpful tweets under the #Fungal17 hashtag. Sarah Unruh (@sau916) and I are talking about how to best archive or building a storify this so it is easier to read. Always a fun meeting to see friends and nosh at the smorgasbord of fungal genetics, epigenetics, genomics, ecology, evolution, and chemistry that is going on. Jason got to give a Plenary talk and express the utility of sequencing fungal geno...

2016 Round Up - by the numbers

Quick post to sum up some of the news from 2016 and head into 2017. - Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016 Three graduate students survived another year in the lab: Sawyer, Nat, Derreck Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016. Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformat...

2016

MSA 2016

Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting. We road tripped by car from Riverside through the central valley up to Berkeley. At the conference we had a great chance to meet with other mycologists, ecologists, and fungal enthusiasts. The meeting was fantastic from the Clark Kerr campus at UC Berkeley we had dorm life living so everyone was close by and could eat meals together. The talks and posters were really outstanding and such fun to talk ab...

Desert Crust collecting, Summer edition

On August 4th, 2016, Nat, Derreck, Sawyer, and Jericho went to Joshua Tree National Park to collect more Biological Soil Crusts samples. They were lucky to find some Lichen crusts which we could not find in our last sampling trip. Here are some pictures of our sampling team.[caption id=”attachment_1525” align=”aligncenter” width=”604”] Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho[/caption][caption id=”attachment_1526” align=”aligncenter” width=”900”] Our first collection of Li...

New funding, new papers, new data

We celebrated a few events in April and May. - A new NSF grant was funded and started in April on rumen fungi ”Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota”. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi. Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on tra...

French connection

Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.[caption id=”attachment_1490” align=”alignright” width=”604”] An ascus of Neurospora bio...

A desert foray

We started some explorations on fungi in desert crusts this week with a project in Joshua Tree National Park. Nuttapom received a Robert Lee Graduate Student research grant to explore impacts of visitor disturbance on biodiversity of desert crusts in JTNP.  Nat with the help of Claudia, Derreck, and Prof Mike Allen did a first exploration of a few sites.  We are happy to see some rain falling this week so there should be some changes to the crusts in some subsequent visits this week and weeke...

Migrating fungal biologists

We said bye to Marco Marconi, visiting student from the Wilkinson Lab in Madrid, in December. He worked on some data mining from the 1KFG project and brought some new R tools for looking for enrichment across the CAZY, Interpro, and Pfam differences in species. - We welcome Plant Pathology graduate student Derreck Carter-House to the lab in January - after spending time working on molecular biology projects in plants and plant-microbe interactions in another lab.  Jason went across to En...

2015

2014-15 lab publication wordle

Recent lab news

The past few months have passed quickly but wanted to share a few updates.Jason presented at the EMBO Eukaryotes meeting in Spain, Mexican Mycology Congress, Univ of Arizona, attended the Kavli Frontiers meeting, co-organized the Southern California Eukaryotic Pathogens meeting held again at UCR and taught graduate course on Programming and Data analyses.The past few months we hosted Yinka Odebode from University of Lagos from August to November. He was supported by the West African Research ...

Happy trails!

A quick note to say congrats and good luck to postdocs and students who finished up the summer.Graduate student Steven Ahrendt who graduated from the GGB program and is now a postdoc at the JGI / UC Berkeley.Postdoc Ousmane Cissé finished his fellowship from the Swiss National Science Foundation and moved on to the NIH on a fellowship to work on Pneumocystis.Postdoc Rod Olarte moved to the University of Minnesota on a NSF postdoctoral fellowship.Undergraduates Dillon McDonald and Christina Ur...

Congratulations Steven

Congrats to Steven Ahrendt who successfully defended his PhD Dissertation this week. Graduation ceremony (and pictures) to follow next weekend before he moves on to his postdoc position at UC Berkeley/LBNL/JGI at the end of the month.</images/wp_upload/2015/06/2015-06-03-14.17.11.jpg>

Dumpling party

We had a lab dumpling party at Yizhou’s house to celebrate his new job and my birthday, and a farewell to Edward Liaw. Fun evening for everyone to get together and eat homemade dumplings

Asilomar Fungal Genetics 2015

Another great meeting of Fungal Genetics at Asilomar Conference center. Much exciting science, fungal genetics as a field is being driven by genomics and technology but there are nice cycles of experiments coming back to test and validate hypotheses generated from these data. A few pictures of the UCR group all together at dinner.

Dim Sum outing

Members of the lab gathered for a Dim Sum outing in Rowland Heights on Monday’s MLK holiday.

2014

Congratulations Dr Yizhou Wang

The end of the quarter was a blur but I wanted to properly congratulate Yizhou Wang. Dr Wang successfully defended his PhD in December and submitted his dissertation “Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa”  in the Plant Biology graduate program. He is our newest graduate from the lab and we couldn’t be happier and proud for him. He was able to complete a concentration MS in Statistics at the same time and was able to master bioinfor...

Lab hike in Forest Falls

Rod, Ousmane, Nichole, Jinfeng, Jason and family went on a short hike to Big Falls in Forest Falls. A few pictures of the fun.

New Zygomycete evolution project in lab

A new NSF funded project on Zygomycete fungi was recently funded. The press release from UCR and NSF provide some more information on the scope of the project and the goals of the new Genealogy of Life initiative at the NSF.We’ll be sharing news, data and protocols, and progress on the project website ZyGoLife.org and @zygolife  and looking to recruit one graduate student and some undergraduates to work on the projects in our lab focused on genomics and phylogenomic studies of these diverse l...

IMC10 - Bangkok, Thailand

I had the great opportunity to attend the International Mycological Congress 10 in Bangkok, Thailand during this summer. It was filled with talks from mycologists studying cell biology, genetics, evolution, symbioses, ecology, production of secondary metabolites, and many other aspects of mycology from across the world. It was a great chance to hear about new work in many different experimental systems.  I chaired a session on Population Genomics and GWAS in Fungi and got to hear some great p...

Mucoromycotina cell wall paper published

Congrats to Divya and Jason as our paper with collaborators Hugo Melida and Vincent Bulone:  Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches  is now available at Environmental Microbiology. We discovered in this work that two Mucoromycotina species have novel fucose sugar composition in their cell walls which is not found in other Fungi. We also identify expansions and unique subfamilies of Chitin synthase genes. Figure...

MSA 2014 fungi-fun

Steven and Jason attended the Mycological Society of America’s 2014 conference in East Lansing, MI. This included  coming in a day early enough for some of us to go on the foray on Sunday after we attended the Microbiology of the Built Environment conference in Boulder, CO.MSA2104 was a great chance to catch up with friends and colleagues and hear some excellent talks on the current state of research in the fields of systematics & taxonomy; ecology & pathology; genetics & molecula...

Cryptococcus literature curation paper

We published a paper on the manual curation of the literature for the Cryptococcus complex of species (C. neoformans _var neoformans_, C. neoformans var grubii, and  C. gattii) this includes associated gene names with systematic locus names, something that was not easy to lookup without reading the published literature. In all more than 600 loci had gene names associated with them and include updated Gene Ontology associations, gene product names and descriptions and a table of orthology rela...

2013

Congrats Divya!

We congratulate Divya on defending her dissertation on “Discovery of fungal cell wall components using evolutionary and functional genomics”.  Her last revisions and formatting is taking place and she should be the first minted PhD from the Stajich lab before Christmas.  We are happy and proud of her accomplishment to complete this important milestone!   

Welcome Ousmane Cisse

We are happy to welcome Dr Ousmane Cisse to the lab to work on evolution of multicellularity in Fungi. He will primarily focus on comparative genomics and evolution of filamentous fungal growth in the fungal kingdom, examining the genome of Neolecta and taking advantage of data from the 1000 fungal genomes project and other data sets. He joins us after completing his PhD at the University of Lausanne in Switzerland. He focused on comparative genomics of several Taphrinamycotina fungi and will...

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 ...

Undergrad summer research

Today was the presentations from UCR RISE summer program and undergraduate student Na Jeong showed her work on studying the inhibitory properties of the H. polyrhiza species of chytrid on several Ascomycete fungi. She was mentored by Steven Ahrendt in the lab who first made this observation. Here is Na presenting her work and with Jason and Steven.

Lab BBQ at Lake Perris

We headed over to Lake Perris for a lab BBQ and fun afternoon in the sun.  Here’s a few pictures of the group all together.

back from Asilomar

Congrats to the lab for a great Fungal Genetics meeting. Everyone was participating in the meeting, presenting their work, and hearing about the new things coming out in other research laboratories. Was exhausting pace with 8AM to 10 PM (or later) every day but I think the fun and science excitement overshadowed the tiredness.  Congratulations to Steven who won a poster prize and to Jason for his election to the Fungal Genetics Policy Committee.  FungiDB was demoed in a workshop and poster se...

Steven passes his quals

We had a little celebration to recognize Steven passing his qualifying exam this week.

2012

Stajich Lab Wordles for 2012

Wordle/Tagxedo graphs from Pubmed2Wordle on all papers published from the lab And here is the abstract wordle for the 2012 papers  

Welcome back Anastasia!

We welcome back Anastasia Gioti to the lab visiting from Sweden by way of Greece. She has been to the lab for a a couple of two-month visits over the past three years working on genomics of Neurospora mating systems. Now she has returned this month as a visiting scholar to stay through the winter to continue our collaboration on evolution of mating systems, focusing on the genomic consequences of transitions in homothallic and heterothallic fungi. She gets to have a nice SoCal instead of a Sw...

Lake Arrowhead talk videos

Talks from the Sloan Foundation sponsored session at Lake Arrowhead meeting on Microbiology of the Built Environment are now posted on Microbe.net (which was jokingly pronounced as micro-beignet by some) including my talk on fungi in the Built environment.  Go take a look if you want to see an overview of some of the ways researchers are studying microbes in the built environment.  The Microbe.net team also recorded an interview with me about our work on the MicroBE data coordinating center a...

Andrii's sendoff

Andrii has returned to Durham after a short stint in the lab to pick up some new skills and teach us more about culturing and major questions in Entomophthorales fungi.  He did a nice writeup on his establishment of a copepod colony which we will use for our future attempt to get Coelomomyces colonies in the lab.He has posted his farewell talk that spans a few of the projects he has been working on his website too -take a look here.

Jason on the Microbe.net blog

Check out a video of Jason answering questions about our project to build a database supporting identification of Fungi in the Microbiome of the Built Environment supported by the Sloan Foundation.

Welcome new team members

Welcome to Edward Liaw who will start working on FungiDB for the genome.  Edward joins us after finishing a MS in Bioinformatics at UC Santa Cruz.Also a welcome to Greg Gu who is joining us after working as a specialist in Plant Pathology. Greg is transitioning to bioinformatics to work on fungal identification from environmental sequencing using bioinformatics approaches and will support our work to build a database for ITS sequences as part of the Sloan project’s Microbiome of the Built Env...

Divya awarded Guru Gobind Singh Fellowship

Congratulations to Divya who was awarded the Guru Gobind Singh Fellowship for 2012-13! This fellowship is awarded to one graduate student in the UC system who is a student of an Indian or Pakistani university and committed to returning to her country of origin after receiving her doctoral degree at a UC campus. This is a great honor and we’re all proud of Divya for applying for and receiving the award.  An article in UCR Today describes her work and the award.

Welcome Andrii

A warm Southern California welcome to Andrii Gryganskyi who is here visiting the lab for several months to work on genomics of Entomophthorales fungi and some other insect-associated fungi from the basal linages.  We’re excited to learn from his expertise in phylogenetics and culturing of these strains in the lab. We are helping to assemble and annotate several genomes in progress he has worked on as postdoc at Duke University to better understand relationships and genomic changes that have o...

Divya wins fellowship

Congratulations to PhD candidate Divya Sain, who just learned she will be awarded a Guru Gobind Singh Fellowship for 2012-2013.  In 1988 the University of California established an endowment to support graduate fellowships (named for Guru Gobind Singh, the Sikh religious leader) to be awarded to graduates of universities in a specific area of India and Pakistan for the purpose of pursuing graduate study at the University of California.Way to go Divya!

(Reopened) Postdoctoral Researcher in Bioinformatics for Rice genomics

[Update 8/2012 - this position has been filled]Position DescriptionAn 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 ...

Duke Mycology

A wonderful symposium reunion of alumni and current Duke and the RTP area Mycology and pathogenesis labs is being held April 5 & 6 at Duke University. The talks have so far been an interesting collection of model pathogen systems, drug development, and host-pathogen interactions. Tomorrow myself,  Tim James, and others will hit the evolutionary biology of fungi a bit focusing on chytrid pathogens.  Feeling a lot of pride in the training program here at Duke and some nostalgia for days pas...

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...

2011

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.[caption id=”attachment_701” align=”aligncenter” width=”300” caption=”Jason and Yizhou at Asilomar 2011”][/caption]

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.- International Team to Sequence Genomes of Fungi International team to se...

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 problem...

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 ...

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 _Bd_to confirm gene expression of the members of the family by RT-PCR before we choose a subset to work on further.[caption id=”attachment_638” align=”aligncenter” width=”614...

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 forwa...

FungiDB Programmer position

[This position filled as of Aug 2011]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.

Welcome Steven!

A warm welcome to graduate student Steven Ahrendt to lab. Steven is working on questions relating structural evolution of light sensing proteins in fungi, metagenomics, and bioinformatics. He will be co-advised by Assistant Professor Chia-en Angelina Chang.

Asilomar memories

I can safely say everyone had a good time at Fungal Genetics at the Asilomar Conference Grounds earlier this month. So much fun it too us a week to catch up on sleep and dig out from work left undone. Here are a few pictures from poster presentations. We didn’t get everyone’s picture captured in the chaotic swirl of the poster session unfortunately. I’m really proud of how well everyone did and the apparent interest in our projects.I also launched our fungidb.org database website at the meet...

Snow on the mtns

Snow on the mountains while the temps are in the 70s here. A wet winter means there are lush hillsides…for now, until the dry season starts in another month.

W.M. Keck Foundation grant for discovery of active transposable elements in mosquitos

 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 transposa...

Postdoc in Bioinformatics and Transposon Biology in Rice

Postdoctoral Research in Bioinformatics and Transposon Biology in RiceUniversity of California, Riverside[Position filled as of 6/2011]Position DescriptionAn 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...

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 DescriptionA 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 c...

2010

2010 Publications Wordle

Here’s our 2010 publications wordle made with pubmed2wordle using this query that includes paper co-authored by Jason, Divya, and John with this search. [h/t to Kevin’s blog for showing this easy app - had done this previously with a cmdline bioperl script]

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.

Outings

Some pictures from a recent lab lunch to help celebrate Divya passing her qualifying exam.[gallery] 

transcriptomes, bioinformatics, and light regulated genes

A few papers from our work are now appearing. This includes several collaborative papers that have been in progress for several years, so I’m happy to see them published.- See the latest issue of PLoS Genetics for our work on analysis of the transcriptome during meiosis in _C. cinerea _in collaboration with several labs at UNC-CH, Indiana University, and SEMO. A chapter on bioinformatics protocols for using the Gbrowse_synteny tools The final version of our paper from a collaboration wit...

Congrats Divya!

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.[gallery]

Some published papers this last month

We had a productive period over the last year and finally saw set of papers representing this work come out in the last month. This represents great collaborations with several different groups.  In addition to the Coprinus genome, we were involved in the publication of two other genome sequences thus summer. One a basidiomycete mushroom and one for an oomycete and pathogen of plants, both with a host of collaborating labs. Two papers on Neurospora also appeared as part of collaborations with...

Our work on the cover

Our work on the mushroom genome of Coprinopsis cinerea is featured on the cover of this week’s PNAS.  Check out the blog post and the article.

A sendoff for the lab visitor

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...

A whirlwind spring

Spring is flying along. We’ve been presenting some of our work at conferences and getting ready for a full summer of meetings and Divya preparing for her qualifying exam.A few papers have come out or are now accepted. One I’ll highlight here is the publication of the Sordaria macrospora genome.  This was a fun collaboration with groups in Germany, France, Oregon State, and Edinburgh where we sequenced Sordaria with 454 and Illumina sequence and assembled the genome using de novo assembler and...

Fusarium mobile chromosomes

Congrats to graduate student Divya Sain a co-author on a paper published in Nature on mobile chromosomes in Fusarium, stemming from her work her work during a rotation in the Borkovich laboratory.The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.

Back from Ireland

I am back from a short trip to Ireland where I gave a seminar at National University of Ireland, Maynooth and spend some time with folks interested in evolution or fungi like David Fitzpatrick, James McInerney, Davide Pisani. I also learned about a new spinoff company from one of the faculty producing media that will help Bee immune systems. In my chats with some of the faculty I found out that I had lots in common with Sean Doyle on Aspergillus and some basidiomycete genomics questions and a...

PLoS Pathogens Pearl published

PLoS Pathogens has a short review format called Pearls.  We were invited to write a short summary on Batrachochytrium which was published in the January issue.Rosenblum, E., Voyles, J., Poorten, T., & Stajich, J. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6 (1) DOI: 10.1371/journal.ppat.1000550

Lab news for January

A quick January update.  Jason was appointed to a two year term as Councilor for Genetics/Molecular Biology for the Mycological Society of America, began a term on the editorial board of Eukaryotic Cell, and was also profiled in the GSA reporter. Finishing grants and working towards completing manuscripts from postdoc-land while we are computing results on from genome and RNA-Seq datasets. Working to getting our laboratory production up and running to generate more of our data.Currently the l...

Down to San Diego

Although I’m not going to be at PAG this year, I’ll be in San Diego for  the BioPerl and part of the GMOD meeting on Wed and Thursday.

2009

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. 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...

BioPerl on TWiT.tv

  Chris Fields and I spoke about BioPerl past and present and tried to convince computer science types that biology is in fact interesting on TWiT.tv FLOSS. Check out the podcast for Episode 96.

Slides from Nov talks

A talk today in the CS department on open problems in bioinformatics and hope to entice some computer scientists to work on more of the problems here. Here are the slides in PDF and on SlideShare. I also had a chance to present some work at UCLA in their Bioinformatics series SlideShare are available.

Back from EMBO Comparative Genomics mtg

Back from an excellent meeting in St Feliu du Guixols for the EMBO Comparative Genomics of Eukaryotic Microorganisms. Not a strictly fungi focused meeting, but lots of genome comparisons of yeasts and molds were presented.  It will be held again in 2 years so mark your calendars as it is a great scientific exchange and a beautiful location.

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 ...

Abstracts wordle

Making some signs for the doors to offices.  Here’s a Wordle plot from abstracts of last 7 years of papers. Tip the hat to M. Dunham for the idea to make it part of the lab signs.      

Moving into new Genomics Building

Well, the doors have been opened and things are moving into the new Genomics building. Since we are so new, no things to really move into the lab as they will come from vendors directly. I got into my new office with furniture installed and everything. We have ordered some of the big equipment for the lab and started getting supplies. Will be some adjustment as we all learn the new space for the labs on the same floor as we start sharing space, supplies, and also ideas and collaborations.  An...

You've got keys...

To the newly finished Genomics building on campus.  Our (well only me still ) move date in mid-September or when the office furniture is installed. Yah!  Freezers, fridges, ordered.  A few lab compute servers are being placed.  Slowly getting things up and running.

MSA 2009 presentation

My presentation from BSA/MSA 2009 on early fungal evolution inferred from the chytrid genome is available here.  The conference was great for the time I could be there and the interaction with mycologists and botanists at the meeting seemed to be really helpful (I caught a few botany talks) and catching up with new and old friends is a great bonus at these meetings.

MSAing next week

I will be at the Botany & Mycology conference (mainly to see the MSA members) and present a talk on Tuesday morning of the meeting. Hope to run into some old friends and meet new people at the meeting which will see Botanists and Mycologists mixing (oh my).  I get to stop by Univ of Utah a few days early and give a quick talk and visit with some friends at the Eccles institute at the U and maybe will get to see a few more Salt Lake City sites.

Mushrooms on the journey

Went from CA to OR to ID, MT, and WY for work (Bioinformatics symposium at Oregon State) and a little vacation.  Here are a couple of mushrooms and lichens seen along the way.

Amanita in Pt Reyes

Saw this beauty while on our hike in Pt Reyes before the Miller Institute Annual Symposium

Twitter Weekly Updates for 2009-04-27

RT @NikonSmallWorld: 1 week to enter the competition! Submit yr best photomicrographs at http://www.nikonsmallworld.com #microscope #science # Save the Frogs day is April 29th http://savethefrogs.com/day/ #

Summer plans

Word on the street is we will be moving into the new Genomics building at the end of the summer.

Twitter Weekly Updates for 2009-04-20

RT @hyphaltip: Lichen named for Pres Obama by UCR herbarium curator Kerry Knudsen http://is.gd/sMwk #

Twitter Weekly Updates for 2009-04-13

git archiving code from my thesis http://github.com/hyphaltip/thesis/tree/master #

Twitter Weekly Updates for 2009-04-06

Adding some OrthoMCL processing scripts to github to convert FASTA processed genome-pair search results for proper input http://is.gd/qOoM #

JGI User meeting

Live blogging JGI User meeting where the talks range from application of sequencing to problems in biofuels, comparative genomics and evolution, and the discussion of new sequencing technologies.Here are some links from Day 1. We’ll probably have the rest of the days’ coverage in the Friend Feed Room.- Friend Feed Room Jonathan Eisen’s page with some aggregated links for coverage A few of the posts I wrote are on another site, Mike Mendez, Cameron Currie on Ant farming of fungi Joe...

Twitter Weekly Updates for 2009-03-16

Setting up lab pages #

See you at Asilomar

I will be at Asilomar for the Fungal Genetics 2009 meeting presenting some work on the transcriptional landscape in Neurospora and collaborative work on Coccidioides, Neurospora tetrasperma, and Coprinopsis cinerea.

New beginnings

The lab will open in July 2009 at UC Riverside and be housed in the new genomics building on campus. We are excited to be taking advantage of the existing computational and genomics resources available on campus as well as collaborating with our evolutionary, mycological, and bioinformatics colleagues.Specific information about positions for postdocs, graduate students, and technicians will be available in late spring, but interested persons should feel free to contact Jason.

News

Videos

Jesus Pena introduces his research on sexual reproduction in the zygomycete fungi in the lab through a new video as part of the UCR Microbiology Graduate Ambassador. Have a watch and learn more about the research Jesús is working on.