All posts by Jason Stajich

Assistant Professor at UC Riverside

Postdoc: Molecular plant-pathogen interactions

A postdoctoral position is available for three years in the field of molecular biology of plant pathogen interactions with the Max Planck research group “Environmental Genomics” headed by Prof. Eva H. Stukenbrock. The Max Planck group is affiliated with the Max Planck Institute for Evolutionary Biology in Plön and the Christian-Albrechts University of Kiel in the North of Germany. The position is compensated at TV-L 13 (depending on qualifications), covers 38,7h/week and includes teaching.

Start of the position is January 2016.

We study the evolution and specialization of pathogens to new hosts and new environments, and integrate functional and experimental analyses with evolutionary genomics and transcriptome analyses to dissect the adaptive processes in plant pathogens. The project outlined for this post doc position aims at understanding the underlying molecular basis of host specialization of a fungal plant pathogen. As model system we use a group of closely related grass pathogens, Zymoseptoria spp., including the prominent wheat pathogen Z. tritici. Using evolutionary genomics and comparative transcriptome analyses, we have identified a number of candidate genes, which may have been instrumental for the specialization to distinct grass hosts. This includes genes, which have either diverged extremely between pathogen species, or genes, which show host-specific gene regulation. So far the functional role, of these genes as host determinants is unknown, but will be addressed in the research conducted by the post doc candidate. The post doc candidate will design and apply functional and experimental approaches to dissect the role of candidate genes in Zymoseptoria spp. The study will include the characterization of fungal mutants as well as the role of candidate proteins in host infection. A central goal will be to identify target proteins in the host to link protein function to evolutionary changes in sequences or expression patterns among pathogen species.

The candidate must have a PhD degree in molecular or cell biology or biochemistry and must have a proven record of independent research. Experience with functional genetic studies and fungal transformation are required. Experience in protein-protein interaction assays (e.g. yeast two-hybrid assays), confocal microscopy and phenotypic assays with plant pathogens are desirable. Good presentation, writing, computing and organizational skills and the ability to work independently are a must.

The selected candidate will have the opportunity to collaborate in an interdisciplinary team of biologists (molecular biologists, evolutionary biologists and population geneticists) as well as to pursue unique research in the field of molecular plant-pathogen interactions. For further information regarding the position please contact Eva Stukenbrock (

The University strives for a high proportion of women in research and teaching. Applications from qualified female scientists are therefore particularly encouraged. Applications from candidates with migration background are welcome. Disabled persons will be given preference in filling vacancies within the existing legal provisions if equally qualified.

Relevant Literature
Stukenbrock EH, Bataillon T, Duthei JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH (2011). The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Research 21.12 (2011): 2157-2166

 Poppe, Stephan, et al. “Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola).” PLoS Pathog 11.7 (2015): e1005055.

Dong, Suomeng, et al. “Effector specialization in a lineage of the Irish potato famine pathogen.” Science 343.6170 (2014): 552-555.

Application Interested candidates should send a motivation letter including a description of current research directions, an up-to-date CV (excluding photo), together with the names and the contact information of at least two references to Eva H. Stukenbrock as pdf. Application deadline is November 13th, 2015.

Job: Research Microbiologist (microbial ecology) at USDA-ARS in Peoria, IL

The USDA, ARS, Mycotoxin Prevention and Applied Microbiology Research Unit (MPM) in Peoria, IL is seeking a permanent, full-time Research Microbiologist to develop an innovative and productive research program on microbial ecology and diversity as part of a project to reveal how cereal crops, the cereal microbiome, and climate interact with mycotoxigenic fungi during infection to influence mycotoxin production and contamination. The goal of this research is to develop information and novel approaches to reduce mycotoxin contamination of food. The successful candidate will join a large and diverse group of scientists conducting research in molecular biology, microbiology, evolutionary biology, chemistry, and plant biology to produce information and technologies needed to enhance food safety and crop production in the U.S. and around the world.

U.S. Citizenship is required. For further information and complete application instructions, go to the USAJobs Web site: and refer to announcement number ARS-D15E-0651.

Applications must be received by the closing date of October 20, 2015.

Read the Full Advertisement

Postdoc: Population genomics and speciation in fungal pathogens

Post-doc position in genomics of introgressions in fungal pathogens

[from EvolDir]

We invite applications for a postdoctoral position in the Research Institute of Horticulture and Seeds. The position is for 1 year starting as soon as January 2016.

The Postdoc will conduct his research in the field of population genomics of secondary contacts and introgression in two fungal pathogens: Venturia inaequalis, an ascomycete responsible of the apple scab, and the Scedosporium apiospermum species complex which is responsible for pulmonary infections in children with cystic fibrosis.

The Postdoc will have to identify genomics regions involved in introgression between divergent populations of Venturia inaequalis and Scedosporium species. Indeed, secondary contacts between divergent genomics pools may favour the creation of new genetic combination of loci involved in pathogenicity. New hybrids should then exhibit hitherto unseen epidemiological properties. The Postdoc will work in a team involved in several projects of genetics or genomics, functional genomics, and evolutionary epidemiology (IRHS – ECOFUN team).

Using resequenced genomes (89 for V. inaequalis and 23 for the Scedosporium species complex), the Postdoc will be in charge of the assembling, genome aligning and SNP calling, prior to population genomics analyses. The Postdoc will have to infer evolutionary histories at the interspecies and species levels for both datasets, identify and characterise genomic regions involved in introgressions. He [or she] will possibly collaborate with all the researchers involved in this project : population geneticists, microbiologists, functional genomicists, phytopathologists.

We are looking for a candidate with a keen interest for population genomics and evolutionary history in structured populations. The candidate must hold a PhD in population genomics with strong skills in bioinformatics (manipulation of NGS data, assembling, demographic inferences). Good written communication skill and ability to work as part of a team are required.

How to apply:
Applicants should submit

  1.  a cover letter describing their research interests and background,
  2.  a detailed CV (including list of publications), and
  3. the contact details of three references to or The cover letter should also include possible starting dates.

Job: Assistant Professor of Microbiology, Clark University

Assistant Professor of Microbiology
Biology Department, Clark University
*Review of applications will begin November 1, 2015*

The Department of Biology at Clark University, Worcester MA ( invites applications for a tenure-track appointment at the rank of Assistant Professor to begin Fall 2016. The successful candidate will have research space in the LEED-certified Lasry Center for Biosciences and is expected to develop an externally-funded research program involving Ph.D., MS, and undergraduate students in Biology or in Biochemistry and Molecular Biology (BCMB). Postdoctoral experience and evidence of external funding success are desired. Promise of teaching excellence at undergraduate and graduate levels is expected. Any area of microbiology will be considered, although preference will be given to those incorporating genome-enabled approaches in their research. The successful candidate will teach microbiology and courses in their area of expertise.

Clark University is especially interested in qualified candidates who can contribute, through their research, teaching, and/or service, to the diversity and excellence of the academic community. We are an affirmative action/equal employment opportunity university and we strongly encourage women and members of minority groups to apply. Applicants should submit a curriculum vitae, statements of research and teaching interests, and three key publications in one electronic file.  Three letters of reference should be submitted electronically by the referees to the Microbiology Search Committee( Letters can also be mailed to the Chair of the Microbiology Search Committee, Department of Biology, Clark University, 950 Main St, Worcester, MA 01610-1477.  E-mail inquiries may be directed to Justin Thackeray (  Review of applications will begin November 1, 2015.



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

State-of-the art sequencing technology has opened opportunities to comprehensively investigate structural variants (SVs: such as deletions, insertions, duplications, inversions and translocations) in genomes of natural populations. Such SVs are often associated with gene expression changes and may be of large phenotypic effects. The main goal of this postdoc project is to use sequencing data (e.g. PacBio long read sequence data) for the model system Neurospora, emerging from our most recent sequencing projects, to increase our understanding of the impact of SVs for the evolution of eukaryote genomes. In particular, we can use the well-established phylogenetic framework of Neurospora to study the accumulation of SVs over evolutionary time, and connect them to characters such as genome size expansion/retraction, mating-system transition and speciation. By combining comparative genomic, phylogenetic and population genetic analyses, the evolutionary significance of SVs in natural populations can be traced. The project will be developed after the interest of the applicant, but should encompass a perspective of genome evolution addressed by bioinformatic/genomic approaches.

Applicants should have a PhD in biology/evolutionary biology and have documented experience in bioinformatics. Documented skills in comparative genomics, molecular phylogenetics and/or population genetics is highly valued.

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

Please send your application materials by September 25 to 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.

Remembering fungal genetics legends

The passing of two members of the fungal genetics community has saddened many of us but also brought smiles in remembering all the wonderful things they brought to the community. So sending this out to ask you to take some time to remember Rowland Davis  and Hans Van Etten who have passed away in the past month.

Rowland Davis, an eminent figure in the fungal genetics community, died on 18 July at his home in California. Rowland was 81 years old. He made many contributions to the community as a researcher, as an editor and reviewer, as a mentor, and as a valuable source of wise counsel, always delivered with intellect and humor. As a graduate student at Harvard University he developed an interest in microbial genetics and began to work with Neurospora. As a postdoc at Caltech with Herschel Mitchell he started his lifelong involvement in biochemical genetics. His early years as a Professor were at the University of Michigan (1960-1975). He subsequently moved to the Department of Molecular Biology and Biochemistry at the University of California, Irvine and became Emeritus in 2005. Rowland’s graduate research focused on heterokaryosis. As a young assistant professor he began to investigate the pyrimidine biosynthetic pathway, discovering that the pyr-3 gene encoded two catalytic activities – one of the first examples of “one gene, two enzymes.” He then went on to show that carbamyl phosphate, required for two different metabolic pathways, was synthesized by the enzyme products two different genes, each in a different organelle. This was a foundational discovery in understanding the role of compartmentation in the regulation of metabolism. He pursued this with seminal studies of arginine metabolism, showing that 99% of cellular arginine is sequestered in vacuoles, thereby avoiding wasteful catabolism by enzymes in the cytosol. In the latter half of Rowland’s career, he investigated the enzymes responsible for synthesizing polyamines. His lab group identified the genes that encoded these enzymes, discovered novel mechanisms by which polyamine levels are controlled, and described the systems by which polyamines were transported across the cell membrane. Rowland was a key player in the decision to open the Neurospora Information Conference to the larger Fungal Genetics Community. He served this community in many ways. He was a supportive presence on NSF and NIH review panels and a long-term Editor for Genetics. He wrote the definitive “methods guide” for Neurospora (Davis and De Serres, Methods in Enzymology, 1970). The breadth of his knowledge is illustrated by his book, Neurospora, Contributions of a Model Organism (Oxford, 2000). In his retirement Rowland pursued his life-long interest in writing by publishing two novels (co-authored with his wife Margot [Norris] Davis) and a collection of short stories. Rowland was always available to help people. Young and not-so-young investigators went to him to discuss research ideas, grant proposals, and manuscripts. He was a superb teacher at all levels, delivering flawless lectures to huge undergraduate classes and providing hands-on instruction to graduate students. He will be greatly missed. — Barry Bowman, Neurospora Policy Committee

Hans Van Etten finished his career at University of Arizona and trained so many scientists and students. I have heard some great stories from student who took his classes, or where he sat on their committee, those who trained in his lab, or collaborated with him on research all remark on what a positive and enthusiastic person for the science and for the people he worked with.  A longer remembrance from those who can tell even better stories will be circulated soon I am sure but I wanted to just post something now to note his passing.




An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to

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.

Job: Montana State University Assist/Assoc/Full Environmental Microbiology

The Department of Microbiology & Immunology at Montana State University- Bozeman ( invites candidates with a PhD in Microbiology or related area to apply for a full-time, nine-month tenure-track position in Environmental Microbiology (Assistant/Associate/Full Professor) beginning January 2016. The successful candidate will have postdoctoral and/or Assistant Professor experience and will be responsible for developing/growing an extramurally funded, nationally recognized research program within the broad field of environmental microbiology. Scientists that use interdisciplinary approaches that include biochemical, cellular, physiological, ecological, genomic, and/or molecular tools to investigate areas including microbe-environment interactions, microbe biology/ecology, and/or microbial engineering are encouraged to apply. We are seeking an individual with a research program to complement and expand expertise in the Department. The Department, which is nationally recognized for its strengths in both environmental and human-related microbiology, includes state-of-the-art core facilities both in the department and campus research centers. The Department strives to maintain a diverse faculty group, and women and underrepresented minorities are encouraged to apply. The position includes a competitive institutional salary (9-months) and generous start- up package. While a funded research program is preferred, it is not required. Full details about the position and application procedure are available at

Potential candidates are encouraged to contact the Search Committee Chairperson, Dr. Matthew Fields, ( for more details. Screening will begin September 9th, 2015 and will continue until a suitable applicant is hired. ADA/EO/AA/Veterans Preference.

PDF of the advertisement: Faculty Position in Microbiology at MSU

Research Microbiologist at USDA-ARS (UC Davis)


Research Microbiologist, USDA-ARS

A new Research Microbiologist position is available with the USDA-ARS located on the campus of the University of California, Davis.  The successful candidate will conduct independent research to discover and develop novel fumigation independent approaches to control soil-borne pathogens.  This work will focus on developing an understanding of the ecological, structural and functional aspects of the soil-borne microbial communities shown to suppress target pathogens.  Applicants with a strong computational biology/metagenomics background are encouraged to apply.  We would greatly appreciate it if you would forward this announcement to prospective candidate(s) for their consideration.  The position announcement can be found at

This is a competitive, permanent appointment and U.S. citizenship is required.  For further details about this position and how to apply, go to the vacancy on-line at:  vacancy announcement number ARS-D15W-0129 (all US citizens) or ARS-M15W-0128 (Current federal employees).  For questions contact: Dr. Daniel Kluepfel, Research Leader at