Category Archives: fungi

Webinar: VEuPathDB – Introduction to FungiDB – Data and Functionality

The merger of VectorBase and EuPathDB into VEuPathDB has brought together additional tools and data for host, microbe, and interactions datasets. The data mining capabilities of the VEuPathDB will be demonstrated in the upcoming webinar. This Thursday July 16 10AM Eastern will feature a focused webinar on the new FungiDB site ( and demos of the searches and functionalities.

When: 16 July 2020 @10AM US Eastern Time
This webinar will cover:
  • What type of data is in FungiDB
  • How do we find out about data and schedule it for release
  • Demo of key searches
  • Demo of key search and analysis tools

PostdoC: JGI fungal and Algal multi-omics

Postdoctoral Scholar Positions at the Joint Genome Institute in Berkeley, CA
Apply at

Berkeley Lab’s Joint Genome Institute (JGI) Division has an opening for a Postdoctoral Scholar. You will work as part of the Fungal and Algal Program in the Joint Genome Institute division investigating genomes and multi-omics of fungi and algae, both represent promising targets for sustainable bioenergy. The key to algae’s potential as a renewable energy source involves the increase of algal biomass production. Fungi are critical for both the growth of plants and plant biomass decomposition and encode collections of enzymes and pathways to use for bioenergy applications. You will collect and analyze genomics, metabolomics, and other ‘omics’ data to model biological processes in these organisms. You will develop and use new approaches and tools for machine learning, metabolic reconstruction, and gene network analysis. 

What You Will Do:

  • Assemble, annotate and analyze genomes of fungi and algae using JGI annotation pipelines and comparative genomics tools.
  • Use advanced cheminformatic and bioinformatic approaches to analyze and integrate the metabolomics results with other omics datasets.
  • Develop and apply innovative computational and mass spectrometry-based metabolite profiling approaches to characterize algal or fungal metabolism including novel secondary metabolites and their pathways.
  • Publish scientific papers in peer-reviewed journals, release data onto public data repositories, and present findings at seminars and conferences.
  • Collaborate with other members of the program project research team both onsite/offsite team at Berkeley Lab.
  • Develop Unix-based scripts for data analysis; analyze data using both high-performance computing and web-based genome portals.

What Is Required:

  • Ph.D. within the last three years in Life Sciences, Computer Sciences, Bioinformatics, or related field.
  • Experience with genomics, transcriptomics, metabolomics or related analytical approaches
  • Strong cheminformatic or bioinformatics training.
  • Robust understanding of organismal biology, metabolic processes, and gene networks.
  • Programing experience (python/perl) and familiarity with database systems (MySQL).
  • Demonstrated ability to interact effectively with technical and scientific staff.
  • Proven ability to perform independent research and organize data for publications and presentations.
  • Effective oral and written communication skills to present findings at group meetings and conferences, and to publish results.

Additional Desired Qualifications:

  • Experience in algal or fungal characterization.
  • Strong background in LC/MS/MS.
  • Strong publication record.

Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4.  Click here to view the poster and supplement: “Equal Employment Opportunity is the Law.”

Click here to apply:

Contact: Igor Grigoriev, PhD
Head, Fungal and Algal Genomics Program, DOE Joint Genome Institute, Walnut Creek, CA 
Senior Scientist, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
Adjunct Professor, Department of Plant and Microbial Biology, University of California, Berkeley, CA

Job: Assistant Professor in Fungal Biology – Cornell University

Assistant Professor; Fungal Biology; tenure track, academic year appointment (9-month)

The search is looking for someone with research interests and expertise in the biology of plant-associated fungi and are particularly interested in learning of talented postdoctoral scholars or junior faculty who are or identify with underrepresented groups in science, representing diversity in its broadest sense.

The School of Integrative Plant Science at Cornell University ( invites applications for a tenure track position at the Assistant Professor level in the area of biology of plant associated fungi. With an immense diversity of virulence mechanisms and lifestyles, plant pathogenic fungi cause disease throughout the plant kingdom and are a major threat to global food security. Conversely, fungal mutualists improve plant stress tolerance and health. The new faculty member is expected to develop a strong, internationally recognized program that addresses the biology of fungi and/or oomycetes that associate with plants. Candidates whose research integrates empirical, genetics, genomics and/or metabolomics approaches to fungi and/or fungal populations with computational approaches are particularly sought. Examples of research topics include, but are not limited to: i) the exploration of basic cellular processes related to fungal pathogenic or mutualistic lifestyles, ii) virulence determinants (e.g. secondary metabolites and protein effectors), iii) translational research that builds solutions to agricultural problems based on mechanistic understanding of fungal genetics and cell biology, iv) dynamics and variation in fungal populations, and ecology and evolutionary biology of genome adaptation with regard to pathogenicity.

The ideal candidate will thrive in the highly collaborative environment of Cornell University, which includes diverse faculty and vibrant graduate programs affiliated with the School of Integrative Plant Science (SIPS) in the College of Agriculture and Life Sciences (CALS), the university-wide Cornell Institute of Host-Microbe Interactions and Disease, the Boyce Thompson Institute for Plant Research, and the USDA Agricultural Research Service. The expected affiliation for the position will be the SIPS Section of Plant Pathology and Plant-Microbe Biology (PPPMB) on the Ithaca campus. The position will have a 60% research and 40% teaching responsibility, and the successful candidate will teach in the broad area of the biology of fungi in courses that match the PPPMB core curriculum and the candidate’s expertise (such as Ecology and Evolution of Plant-Pathogen Interactions or Filamentous Fungal Genomics and Development).

SIPS and CALS at Cornell embrace diversity and seek candidates who will create a climate that attracts students of all races, nationalities, and genders. Diversity and Inclusion are a part of Cornell University’s heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans and Individuals with Disabilities. Cornell understands the needs of dual career couples, which it attempts to meet through a Dual Career program and membership in the Upstate New York Higher Education Recruitment Consortium, which assists dual career searches.

Visit to see positions available in higher education in the upstate New York area. Cornell and Ithaca are family-friendly communities: Cornell offers a rich array of services, programs and benefits to help employees advance in their career and enhance the quality of personal life, including employee wellness, workshops, childcare and adoption assistance, parental leave and flexible work options. For more details,

Qualifications: Ph.D. in a relevant field. The candidate should welcome the opportunity to work in a multidisciplinary and multicultural setting and create a collegial professional environment. Well- qualified applicants are expected to have a demonstrated record of publication excellence. Preferred qualifications include postdoctoral experience, ability to work as part of a team, and ability to communicate effectively with students, colleagues, and broader audiences.

Salary and Benefits: Salary is competitive and commensurate with background and experience. An attractive fringe benefits package is provided.

Application procedure: Submit as a single PDF file to Academic Jobs Online ( a cover letter, a statement of research accomplishments, interests and future plans (4 pages maximum), a statement of teaching experiences, philosophy and interests (2 page maximum), a statement of contribution to diversity, equity and inclusion ( diversity-equity-and-inclusion/), a detailed curriculum vitae, and the names and contact information of three or four references. (Letters will be requested after the applications are reviewed.) Inquiries may be sent to Prof. Maria Harrison, Search Chair ( or Prof. Gillian Turgeon, PPPMB Section Chair ( Initial screening of applications will begin on November 20, 2019 and continue until the position is filled.

Opportunity: The School of Integrative Plant Science Section of Plant Pathology and Plant-Microbe Biology includes internationally renowned faculty with abundant interactions and active teaching, research and extension programs in the College of Agriculture and Life Sciences (CALS). CALS is a pioneer of purpose-driven science and Cornell University’s second largest population of students, faculty and staff. CALS members work across disciplines to tackle the challenges of our time through world-renowned research, education and outreach. The questions we probe and the answers we seek focus on three overlapping concerns: natural and human systems; food, energy and environmental resources; and social, physical and economic well-being

Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students and staff impart an uncommon sense of larger purpose and contribute creative ideas to further the university’s mission of teaching, discovery and engagement. With our main campus located in Ithaca, NY, Cornell’s global presence includes the medical college’s campuses on the Upper East Side of Manhattan and Doha, Qatar, as well as the new Cornell Tech campus on Roosevelt Island in the heart of New York City.

Employment Assistance: If you require an accommodation for a disability in order to complete an employment application or to participate in the recruiting process, you are encouraged to contact Cornell University’s Office of Workforce Policy and Labor Relations at voice (607) 255-6866, fax (607) 255-0298, or email at

Applicants who do not have internet access are encouraged to visit your local library, or local Department of Labor. You may also visit Cornell’s Office of Workforce Recruitment and Retention Monday – Friday between the hours of 8:30 a.m. – 4:30 p.m. to use a dedicated workstation to complete an online application.

Notice to Applicants: Please read the required Notice to Applicants statement at . This notice contains important information about applying for a

Postdoc positions UMich

Bridging Positions in Ecology & Evolutionary Biology

The University of Michigan Department of Ecology & Evolutionary Biology ( invites applicants for two bridging postdoctoral programs: the Literature, Science, and the Arts Collegiate Fellows Program (LCFP) and the U­M Presidential Post­doctoral Fellowship Program (PPFP). Faculty members in EEB have successful records of providing a nurturing and productive postdoctoral experience through these programs. We are especially interested in future colleagues who engage in research in the fields of 1.) plant biodiversity or 2.) population and evolutionary genetics (with an emphasis on theoretical approaches).

The University of Michigan Department of Ecology & Evolutionary Biology views these postdoctoral fellowships as providing an exceptional opportunity to recruit potential new faculty to the University by offering the possibility of either a postdoc alone or a combined postdoc and tenure track faculty appointment.

N.B. Applications for the LCFP and PPFP open September 1. In addition to the materials required by both programs, applicants should submit their materials directly to EEB by October 1.


• Ph.D. in a relevant field

• Demonstrated potential for high scholarly impact

• Evidence of successful classroom teaching experience (as a student or professional)

• A strong commitment to diversity, equity, and inclusion

• Candidates with tenure track appointments are not favored in the selection process unless there

is a clear explanation of how an award to the candidate would further the goals of the LCFP or PPFP

How to Apply:

  1. Send materials to the LCFP (­awards/lsa­collegiate­ postdoctoral­fellowship.html) and/or PPFP via their respective online applications, and
  2. Send materials electronically to EEB by emailing Molly Hunter at

Time to register for Fungal Genetics

It is time to get excited for that biennial gathering of fungal geneticists, mycologists, and generally scientists who study fungal biology at many scales from communities to molecules. Registration is open for 30th Fungal Genetics Conference held at Asilomar Conference Center in Pacific Grove, California.  The abstract submission deadline is December 5 and that is also the early registration deadline (save money!). 

I look forward to this meeting as it is a chance to hear about the latest work on fungi from genetics, genomics, molecular biology, evolution, medical mycology, and molecular ecology. Personally it was the meeting I first attended as a graduate student where I built so many collaborations, was introduced to mentors, and established friendships that have carried me in my career. It also is an important meeting to get the pulse of what are the trends in technology and molecular techniques that are can improve the way research questions are framed and tested. 
The program schedule and list of invited talks and session topics is posted here and there will be more talks chosen from submitted abstracts as well as multiple poster sessions to hear about and share your work.

 So go register!

Postdoc: Bioinformatics for Fungal Genomics and Transcriptomics, UC Davis, California


The Stergiopoulos lab at the Department of Plant Pathology at the University of California Davis is seeking for a highly skilled and motivated post-doc in the field of fungal genomics and transcriptomics. The lab studies the molecular mechanisms of fungal pathogenesis on plants with an emphasis on characterizing computationally and by functional analyses critical molecular and cellular functions required for virulence. As part of our studies we use a systems-level approach that integrates comparative genomics, genome-wide transcriptome profiling, targeted proteomics, and functional analysis of selective gene candidates to study the mechanisms that control gene expression and transcriptome diversity of fungal virulence associated genes.

The successful candidate will work on sequencing using cutting-edge next- generation sequencing technologies and assembling at the chromosome level the genomes of important fungal pathogens of agronomic importance as well as mining these genomes for candidate pathogenicity genes. The candidate is also expected to analyze and mine dual RNAseq data of compatible plant- pathogen interactions that are already available in the lab. The position will become available in January 2019 and is initially for one year, renewable for a second year upon satisfactory performance. Salary is based on experience and qualifications according to UC Davis pay-scales. UC Davis provides a highly vibrant intellectual atmosphere, a pleasant college environment and career development activities specifically designed for post-doctoral scholars.

Highly motivated candidates with an interest in applying cutting-edge next- generation sequencing-based technologies to host-microbe interactions research are encouraged to apply. Ideal candidates should have received recently a Ph.D. in bioinformatics, computational biology or related fields. A strong record of scientific accomplishment by peer-reviewed publications as well as experience in analyzing high-throughput genomics and transcriptomics data is a plus for this position. Candidates should also be proficient in at least one of the common programming languages used in bioinformatics (C, C++, Java etc.) and have excellent verbal and written communication skills

Interested candidates should send to Prof. Ioannis Stergiopoulos ( a single pdf file that includes a cover letter, their full CV, a statement of research interests, and contact information of three references.

PDF of the job announcement UC Davis_Postdoc in Fungal Genomics and Transcriptomics

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 ( 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 ( 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 (, which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James ( 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 (

Timothy Y. James
Associate Professor
Associate Curator of Fungi
Department of Ecology and Evolution
University of Michigan
Ann Arbor, MI 48109

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,
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: ). 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.


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 ( in collaboration with Hanna 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 (, NGS, SNP genotyping and proteomic analyses ( 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 (


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,

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.

Post Doc candidates are welcome to submit their application by email to no later than February 15, 2016