Category Archives: fungi

Postdoc: UMichigan Fungal Genomics

The lab of Tim James in the Department of Ecology and Evolutionary Biology at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny and molecular evolution of uncultured and poorly known fungi, including the Cryptomycetes, Zygomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing fungal genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (zygolife.org) and the Joint Genome Institute (JGI). The projects are supported by NSF and two JGI Community Sequencing Projects.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with an interest in fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (www.umich.edu/~mycology) pursues diverse projects in mycology, and the environment is conducive to development of a pathway to independence in academic research. The lab is in the Department of Ecology and Evolutionary Biology (http://www.eeb.lsa.umich.edu/eeb/index.html), which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James (tyjames@umich.edu) with a CV, cover letter, and the names and contact information of three references.

Anticipated Start Date: Between Oct. 1, 2016 and Jan. 1, 2017.

The University of Michigan is a non-discriminatory/affirmative action employer. The Department of Ecology & Evolutionary Biology at the University of Michigan harbors multiple labs with a focus on evolutionary genetics (http://www.lsa.umich.edu/eeb).

Timothy Y. James
Associate Professor
Associate Curator of Fungi
Department of Ecology and Evolution
University of Michigan
Ann Arbor, MI 48109
734-615-7753
tyjames@umich.edu
http://www.umich.edu/~mycology/

Postdoc: Population Genetics/Genomics of Fungal Plant Pathogens

The Department of Plant Pathology at the University of Nebraska-Lincoln is pleased to accept applications for a Post-Doctoral Research Associate position in Population Genetics/Genomics of Fungal Plant Pathogens. This is a 12-month, non-tenure leading position established for a period of one year. This position is available immediately.

Continuation of the position beyond one year is dependent upon satisfactory performance of the incumbent in successfully accomplishing assigned duties, and upon availability of grant funds.

The core purpose of research in this position is to develop new molecular and computational tools that will improve understanding of continental-scale population structure of the notorious plant pathogen, Sclerotinia sclerotiorum. The successful candidate will have responsibilities in two areas: mining and development of novel SSR markers and development of a reactive website via RShiny with a reference database of genotypes to allow comparisons by other researchers. Development of new SSR markers will require mining available genomes to identify new candidate loci. Implementation of the reactive website will require modification of existing R scripts and HTML pages. Previous work experience with population genetic analyses, computational biology, and fluency in one or more computer programming languages are desired (R, Linux, Perl, Python, etc.). Opportunities for teaching and supervisory experience will be provided. The incumbent will be expected to publish research results in refereed journals, present their research findings at national and international scientific meetings, and assist in preparation of nationally competitive grant proposals. The incumbent should have the ability to work independently as well as with a diverse team of researchers.

Requires a Ph.D. degree in place by date of employment. The successful candidate must have strong oral and written communication skills and publication record.

To apply for this position, email a single pdf file containing a letter of application describing research interests, professional goals, and specific qualifications, a CV, copy of transcripts, and contact information of three references to:
Dr. Sydney Everhart, Assistant Professor of Plant Pathology, everhart@unl.edu
Phone: 402-472-2879

Review of applications will begin on August 8, 2016 and continue until the position is filled or the search is closed.

Full advertisement available as PDF here: Postdoc_SscPopGen_7-28-2016

WRIFO: Women Researchers in Fungi & Oomycetes

In an effort to promote the diversity of women in fungal and oomycete biology research we started a list of Women Researchers in Fungi & Oomycetes (#WRIFO) in our fields. We hope this will make it easier for conference, seminar and award committees to consider a broad pool of candidates when inviting speakers or nominating individuals.

We seeded the WRIFO list with 150 women whose research we know or who were suggested by colleagues, but it is by no means complete. Please add names and add missing details to those already on the list. The WRIFO list is available as a google spreadsheet here (shortlink: http://s.fungidb.org/1SU45hk ). As an experiment in community dynamics WRIFO is an open sheet for editing. We will change this to “make comment-only” after a time to try to avoid getting overrun with spam. If you cannot add to the WRIFO list directly, comments on this post are accepted. However direct adding is preferred to avoid losing track of any suggestions.

As a test for how many will read directions:

  1. Please add new entries at the end of the sheet rather than trying to insert alphabetically.  You can always re-sort the sheet by last name after entries are made
  2. List institution, include 2 letter country code in parentheses.
  3. Select region from the available options.
  4. Pick up to two general research areas from the drop down lists.
  5. Add specific Keywords for research.  Make these as general as possible–a meeting organizer is much more likely to search “cytoskeleton”, than “tyrosinylated microtubules.”
  6. Include a laboratory website link. Use publicly available websites that do not require memberships to view
  7. Select the classification of career stage. Mapping this to job titles in the US
    • Junior: Assistant Professor, Assistant Research Scientist, or equivalent
    • Intermediate: Associate Professor, Associate Research Scientist,  or equivalent
    • Senior: Full Professor, Research Scientist or equivalent
    • Emeritus

–Michelle Momany (@mcmomany) & Jason Stajich (@hyphaltip)

Update 1: A landing page was made for info on WRIFO and where archive and Excel versions of the spreadsheet will be made available.

Postdoc & PhD positions in Evolutionary Biology – Genome organization of AM fungi

Postdoc & PhD positions in Evolutionary Biology – Genome organization of AM fungi

At the Department of Evolutionary Biology, Uppsala University, Sweden.

Description

Arbuscular mycorrhizal (AM) fungi form symbiotic interactions with almost all terrestrial plants and have done so since plants first colonized land. The postdoc and PhD position are both part of a newly funded ERC research program aimed at understanding the ecology and evolution of these widespread and important organisms. Using state-of-the art technology, e.g., PacBio long read sequencing and single nucleus genomics methods, the research program seeks to resolve the genome organization of AM fungi so that the evolutionary consequences of their genome organization can be studied. Specifically, the project aims at testing the hypothesis that genetically distinct nuclear genotypes coexist within AM fungi. The project involves culturing of AM fungi, sorting and genotyping of nuclei from individual fungal isolates, genome and meta-genome sequencing and assembly, as well as genome size estimation. Based on the outcome of this first part, the project will be developed to connect genotype and phenotype to mycorrhizal activity.

The postdoc and PhD student will work close together and be part of an expanding research team led by Anna Rosling (http://www.ieg.uu.se/evolutionary-biology/rosling/research/) in collaboration with Hanna Johannesson (http://www.iob.uu.se/research/systematic-biology/johannesson/) at the Evolutionary Biology Centre (EBC), Uppsala University. EBC constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (https://www.uppmax.uu.se/uppnex), NGS, SNP genotyping and proteomic analyses (http://www.scilifelab.se) ensure immediate access to state-of-the-art technology. This project will utilize several of the technological platforms at SciLifeLab in Uppsala, in particular the Microbial Single Cell Genomics Platform (https://www.scilifelab.se/facilities/single-cell/).

Qualifications

Experience in bioinformatics and genome analysis is necessary and experience in mycology is a merit. The ideal candidate is scientifically motivated and can work both independently and as part of a team. High standard of spoken and written English is required.

To apply for the PhD position you must have a Master Degree in Bioinformatics, Evolutionary Biology, Microbiology, Mycology or equivalent. Attach a copy of your diploma and your master thesis with the application.

To apply for the Post Doc position you must have acquired a PhD in Bioinformatics, Evolutionary Biology, Microbiology, Mycology or equivalent. Attach a copy of your PhD degree with the application.

Information about the position will be given by Anna Rosling tel +46 18-471 64 44, Anna.Rosling@ebc.uu.se.

Application: The application should include a letter with a short motivation of your interest in the position (one A4 page) and name and contact information to at least three reference persons and your CV. Use the link below to access the application form.

PhD candidates are welcome to submit their application using the link below no later than February 29, 2016. http://www.uu.se/en/about-uu/join-us/details/?positionId=88336

Post Doc candidates are welcome to submit their application by email to Anna.Rosling@ebc.uu.se no later than February 15, 2016

Postdoc: Plant-fungal symbiosis and evolution

The Vilgalys Mycology Lab at Duke University seeks a postdoctoral researcher in the area of plant-fungal symbiosis and evolution.  The selected candidate will contribute to ongoing studies on ecology and evolution of forest soil fungi and their interactions with trees including PopulusPinus and other species.  We are especially interested in metagenomic approaches for studying fungal interactions with plants including mycorrhizal fungi and root endophytes.

Major Duties/Responsibilities: Design, conduct and interpret laboratory and field based research; lead and contribute to the development of scientific manuscripts and proposals. The postdoc chosen for this position will also have opportunities to interact with collaborating institutions in the US and abroad.  Research is facilitated by state-of-the-art equipment/facilities for microbiology, molecular biology, and genomics, in a professional environment with excellent technical support.

Qualifications Required: Ph.D. degree in plant or fungal biology, microbial genomics, or related fields. Applicant should have demonstrated expertise in modern molecular ecology methods including nextgen sequencing, phylogenomics, phylogentics, and bioinformatics tools for microbiome and metagenomic studies. Demonstrated expertise must include a track record of peer-reviewed publications.

Qualifications Preferred: Priority will be given to applicants with a successful history of interdisciplinary, integrative, and innovative research in this area. Interested applicants should send a cv, research statement, and names of 3 references (preferably in a single pdf) to Dr. Rytas Vilgalys, fungi@duke.edu.   The position is available immediately and will remain open until a suitable candidate has been hired. For more information on the Vilgalys Lab see: http://sites.duke.edu/vilgalyslab/

Postdoc: 2 positions in RNA Biology of Fungal Pathogens @UCDavis

Two post-doctoral positions are available in the field of RNA biology in fungal pathogens in the laboratory of Ioannis Sterigiopoulos in the Department of Plant Pathology at UC Davis.  One position is for “a highly motivated post- doctoral candidate to conduct basic fundamental and translational research in the field of RNA silencing in fungi” and the second is for  “a highly skilled and motivated post-doc in the field of RNAseq and transcriptomics”.
Please see the advertisements attached.

Neurospora 2016 conference registration

A reminder the Neurospora conference will be held March 10-13, 2016 at scenic Asiomar Conference grounds in Pacific Grove, CA. We look forward to seeing you there, at least 1/3 of the talks will come from submitted abstracts and there will be lots of room and time for discussions of research poster

Registration and Abstract Submission  are now open for submission. Abstract deadline is Jan 15, Early Bird registration deadline is December 31.

 

Postdoc: Early diverging fungi in the James lab at U. Michigan

The James Lab at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny, life cycles, and nutrition of early diverging fungi, including the Zygomycetes, Cryptomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (zygolife.org) and the Joint Genome Institute (JGI). The projects are supported by NSF and two JGI Community Sequencing Projects.

The ideal candidate will be skilled in bioinformatics, molecular biology, and cultivation/microscopy of fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (www.umich.edu/~mycology) pursues diverse projects in mycology, and the environment is conducive to development of a pathway to independence in academic research. The lab is in the Department of Ecology and Evolutionary Biology (http://www.eeb.lsa.umich.edu/eeb/index.html), which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James (tyjames@umich.edu) with a CV, cover letter, and the names and contact information of three references.

Postdoc: Uppsala University on Meiotic Drive in Fungi

POST-DOCTORAL POSITION IN THE EVOLUTION OF MEIOTIC DRIVE

A two-year postdoctoral position is available in the research group of professor Hanna Johannesson, at the Evolutionary Biology Centre (EBC), Uppsala University.

Conflicts arising from selfish genetic elements are important drivers for evolutionary change and innovation, and thus of crucial importance for genetic form and function.  The main goal of this project is to study the evolutionary dynamics of meiotic drive in fungi.  The study system is the Spore killers of Podospora anserina, a filamentous ascomycete. The ultimate aim of our research group is to combine large-scale genomic analyses with theoretical and experimental investigations to study the evolutionary dynamics of this meiotic drive system, both on a short and a long evolutionary timescale. This postdoc project will be developed after the interest of the applicant, but should preferably encompass a combination of experimental and genomic aspects. It will be a part of a collaborative effort within our research group.

Applicants should have a PhD in biology/evolutionary biology. Documented skills in molecular phylogenetics and/or population genetics, experimental and genomic work, especially using fungal model systems, is highly valued.

Start date is flexible, ideally February 1, 2016. The position may be
extended for up to two more years.

Please send your application materials by November 25 to
Hanna.Johannesson@ebc.uu.se. The application shall include: 1) a cover letter stating research interests, 2) a CV, including publication
record, 3) a short (1-2 page) description of research accomplishments, and 4) name and contact information for three references.

Please feel free to contact me at the above listed e-mail with
questions.

Meeting: Exploring the genomic complexity and diversity of eukaryotes

Registration for the 2015 EMBO meetingExploring the genomic complexity and diversity of eukaryotes is open. The meeting is held from 17 – 22  of October 2015 in Sant Feliu de Guixols, Spain. This is a beautiful venue and a It should be an excellent opportunity to discuss and hear about work on genome evolution, pathogenesis, and complexity in fungi and protists.

Unicellular eukaryotes comprise the overwhelming majority of eukaryotic diversity, pervading all branches of the eukaryotic tree of life. Recent sequencing efforts have significantly increased the number and diversity of unicellular eukaryotes for which genomic/cellular/proteomic data is available. Metagenomics, transcriptomics, single- cell genomics, and other ‘omics’ approaches are being applied to unravel the ecology, physiology, diversity and evolution of microbial eukaryotes and are shedding light on fundamental questions such as the origin of the eukaryotic cell, endosymbiosis, the origin of multicellularity and the evolution of major cellular processes in eukaryotes.