Postdoctoral Fellow in Computational Fungal Genomics
I am looking for a motivated and productive postdoctoral fellow
to explore the evolutionary implications of interactions between
genome structure, epigenetic modification and gene expression, with a particular focus on the 3D arrangement of unraveled chromosomes in the nucleus. Using a fungal model system with direct agricultural applications (Epichloe festucae), the postdoc will validate genome assemblies using long-read data, build 3D models of genome packing in the nucleus, and explore statistical associations with gene expression using extensive transcriptome data. This position is primarily analytical with an emphasis on producing high-quality publications from existing and ongoing data
The position requires solid quantitative and computational skills in bioinformatics, with an emphasis on next generation sequencing and genome analysis. At minimum, a practical ability in basic scripting is required. Training in fungal biology and genomics can be provided as needed, and candidates from non-standard research backgrounds with a clear fit to the position are encouraged to apply.
Funding is guaranteed for two years. Salaries are extremely competitive, starting at NZ$68,000 (~US$46,000) per year.
The postdoc will be based in the Cox research group at Massey University, New Zealand. My research team is firmly embedded in the international scientific community, with extensive collaborative links to Australia, Europe and the United States. This position offers a rare opportunity to experience New Zealand¢s unique natural and cultural environment, while undertaking world-leading research. Palmerston North, a university town with a large international community, offers a full range of social and cultural amenities. The city is located close to both mountains and the sea, and presents regular opportunities for hiking, skiing, surfing and adventure sports.
If you have any questions, please contact Prof Murray Cox (firstname.lastname@example.org). Information about the Cox research group (http://massey.genomicus.com) and the Bio-Protection Research Centre (http://bioprotection.org.nz) are available online.
To apply for this position, upload the following documents (in PDF format) at the official Massey University job website: http://massey-careers.massey.
- A brief statement of research interests, qualifications and
- A curriculum vitae, including a list of scientific publications.
- The names and contact details of three referees willing to provide a confidential letter of recommendation upon request.
Prof Murray Cox
Statistics and Bioinformatics Group
Institute of Fundamental Sciences
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 (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/).
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.
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
The Arnold lab at the University of Arizona seeks a postdoctoral researcher as part of a recently funded, collaborative project
supported by the National Science Foundation’s Genealogy of Life (GoLife) program. The project centers on enriching phylogenetic knowledge of the Pezizomycotina through new collections of endophytic and endolichenic fungi, with special attention to the evolution of symbioses with photosynthetic prokaryotes and eukaryotes. The position will begin on or near April 15, 2016, with an expected duration of two years (potentially expandable to three).
The position will be based in Tucson, Arizona, in the School of Plant Sciences and in affiliation with the Department of Ecology and Evolutionary Biology, with opportunities for fieldwork in Panama, Chile, South Africa, and Borneo. The project represents a collaborative network with researchers at Duke University, North Carolina State University, the University of Connecticut, and the University of Mississippi, with ample opportunity for interactions among labs. The position also includes a meaningful outreach component to foster training in STEM for local high school students and opportunities to mentor undergraduate researchers from diverse backgrounds.
Minimum requirements: a PhD in ecology, evolutionary biology, microbiology, plant pathology, or a related discipline, and a strong background in molecular and/or fungal ecology (including next-generation sequencing), biodiversity informatics, computation, and/or mycology. Preferred candidates will have diverse research interests, excellent communication skills, high motivation, and a strong willingness to work independently and as part of an integrative team.
Home to the world-class University of Arizona, Tucson is a vibrant southwestern city with a rich and distinctive heritage, fabulous access to outdoor activities, and diverse opportunities for cultural engagement. The University of Arizona is currently in a dynamic phase of hiring new faculty, making the timing ideal for a candidate interested in engaging with a major initiative in ecosystem genomics.
At the University of Arizona, we value our inclusive climate because we know that diversity in experiences and perspectives is vital to advancing innovation, critical thinking, solving complex problems, and creating an inclusive academic community. We translate these values into action by seeking individuals who have experience and expertise working with diverse students, colleagues and constituencies. Because we seek a workforce with diverse perspectives and experiences, we encourage minorities, women, veterans, and individuals with disabilities to apply. As an Employer of National Service, we also welcome alumni of AmeriCorps, Peace Corps, and other national service programs.
Applicants should submit a cover letter, CV, copies of three recent publications, and a one-page lesson plan for a hands-on, one-day activity to teach a core concept in fungal biology, ecology, or evolutionary biology at the high school level. All application materials should be submitted in a single email to email@example.com (please put GoLife postdoc in the subject line) AND to the University of Arizona Human Resources website ( https://uacareers.com, posting # P20132). Please also arrange for three letters of recommendation to be submitted as above.
Application review will begin on Jan. 20, 2016, and will continue until the position is filled.
A. Elizabeth (Betsy) Arnold
School of Plant Sciences
The University of Arizona
Tucson, AZ 85721
The Hibbett lab at Clark University is seeking a postdoc starting in June 2016 to work on evolutionary genomics of fungi with a focus on mushrooms and either evolution of wood decay or mushroom development. Exciting work and excellent datasets to tackle are awaiting an interested postdoc so take a look.
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/
Interested applicants should email Tim James (firstname.lastname@example.org) with a CV, cover letter, and the names and contact information of three references.
Dear Colleague –
The Eukaryotic Pathogen Genomics Resource (EuPathDB.org) is searching for suitable candidates for a full-time outreach staff position. EuPathDB has long provided support for protozoan parasite researchers, but the recent integration of FungiDB brings many new communities on board. The EuPathDB outreach team is therefore looking to grow, with particular interest in fungal biology expertise.
The ideal candidate would be a recent molecular genetics / genomics post-doc with expertise in one or more experimental systems, and excellent communications skills. EuPathDB databases including FungiDB provide users with the ability to integrate and explore diverse data types: not just genome sequences, but also polymorphisms, transcriptomics & proteomics data, chromatin marks, metabolic pathways, comparative genomics datasets etc … and the outreach team is responsible for ensuring that bench scientists around the world can make effective use of these data, through workshops, meeting presentations, webinars, on-line tutorials, publications, etc. Responsibilities also include keeping up with the relevant research literature, and working closely with supported communities to define targeted areas for curatorial effort, and high priority datasets for inclusion in the database.
This job is an exciting opportunity for the right person, with good pay and long-term career prospects. The successful candidate could be based in Philadelphia PA, Athens GA or Liverpool UK, and will work closely with a dynamic and collaborative team of ~30, including curators & annotators, data loaders, systems & database administrators, software developers, web site designers, data analysis specialists, and other outreach staff members. Applications may be submitted to http://tinyurl.com/
POST-DOCTORAL POSITION IN THE EVOLUTION OF MEIOTIC DRIVE
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
The lab of Lina Quesada has an open position for a postdoc to work on comparative genomics & evolution of oomycete & fungal pathogens of specialty crops at NC State University. Please see the full advertisement at their lab website.
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 (email@example.com).
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.
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.