Category Archives: postdoc

Postdoc: Fungal Evolution at University Arizona (Arnold Lab)

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 arnold@ag.arizona.edu (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

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.

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.

Background
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.

Description
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 (estukenbrock@bot.unikiel.de).

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.

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 bruno.lecam@angers.inra.fr or christophe.lemaire@univ-angers.fr. The cover letter should also include possible starting dates.

Postdoc: POSITION IN EUKARYOTE GENOME EVOLUTION

POST-DOCTORAL POSITION IN EUKARYOTE GENOME EVOLUTION

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 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.

NSF Poststdoc opportunity for Research using biological collections

Earlier this year the NSF released a postdoc opportunity for research to use Biological Collections. In particular these can be strain collections and stock collections. The US Culture Collection Network is a Research Coordination Network which brings together many collaborating culture collections. You can find many of the U.S. living collections there include fungal centers like the Phaff Yeast Collection and Fungal Genetics Stock Center. The Gilbertson Mycological Herbarium at U Arizona under Elizabeth Arnold‘s leadership has developed a rich collection of endophyte fungi which would be another excellent environment to work with these resources. Kyria Boundy-Mills who is the curator of the Phaff collection has also expressed interest in either hosting or helping working with a postdoc on this. There is tremendous biodiversity of the fungi available in these and other culture collections so seems like a great chance to tap into these.
This would be a great opportunity to link work in the 1000 Fungal genomes project and sampling from culture collections (not just sequencing, but growing and characterizing growth, carbon source utilization and integrating that with predictions made from genome comparisons). If this is something interesting to you – do get in touch with some of the curators at these collections, but also my lab and I expect many other labs would be interested hosting someone to work on these questions that take advantage of these living collections of fungi.
Proposals are to be submitted by potential post docs. Submitter must be a US citizen or US permanent resident. The next deadline is November 3, 2015Funding total for the program is $8 million, 40 awards anticipated, up to two years. Here’s some key text from the solicitation:

Competitive Area 2. Postdoctoral Research Fellowships Using Biological Collections.

Biological research collections represent the documented scientific history of life on Earth, and the U.S. museum community alone curates over a billion specimens ranging from bacteria to plants, insects and vertebrates, as well as fossils. Across the globe, collections represent critical infrastructure and support essential research activities in biology and its related fields. Scientists, government agencies, industry and citizens utilize collections to document and understand evolution and biodiversity, study global change, formulate advice on conservation planning, educate the general public, improve interactions between sciences, and devise new practical applications from science to every day life. New technologies supported by NSF in digitization, such as the Advancing Digitization of Biodiversity Collections (ADBC) program, are making collections and their associated data, whether they are physical specimens, text, images, sounds, or data tables, searchable in online databases. Despite this clear progress in improving access to physical specimens and their associated metadata, collections remain under-utilized for answering contemporary questions about fundamental aspects of biological processes. Thus, collections are poised to become a critical resource for developing transformative approaches to address key questions in biology and potentially develop applications that extend biology to physical, mathematical, engineering and social sciences. This postdoctoral track seeks transformative approaches that use biological collections in highly innovative ways to address grand challenges in biology. Priority may be given to applicants who integrate biological collections and associated resources with other types of data in an effort to forge new insight into areas traditionally funded by BIO. Examples of key questions in biology of interest include, but are not limited to, links between genotype and phenotype, evolutionary developmental biology, comparative approaches in functional and developmental neurobiology, and the biophysics of nanostructures. Using collections as a resource for grand challenge questions in biology is expected to present new opportunities to advance understanding of biological processes and systems, inspiring new discoveries in areas with relevance to other disciplines with overlapping interests in biological systems. Applicants must document access to the selected collection(s) in the research and training plan.

Postdoctoral Position in Bioinformatics – University of Ottawa

The Corradi Lab is currently seeking a postdoctoral fellow in Bioinformatics to work on projects related to Comparative and Population Genomics. The research will be led by Dr. Nicolas Corradi and carried out in a CIFAR (Canadian Institute for Advanced Research) – affiliated laboratory located in the Department of Biology of the University of Ottawa, Canada.

Website: http://corradilab.weebly.com/

The position is initially funded for one year, with the possibility of renewal for up to three years, depending on performance. The candidate is expected to work on two ongoing lab projects:

  1. Populations genomics of global samples of the bee-pathogen Nosema ceranae

    The recent decline in global populations of honey-bees has been attributed to a many factors, including infections from the microsporidian pathogen Nosema ceranae. Despite the potential threat that this parasite may have on global bee populations, the basic biology of this species is not well understood.
    The present project aims to increase our knowledge of the N. ceranae’s biology by exploring the extent, nature and function of genome diversity that exist both within and between dozens of parasite samples isolated globally (i.e. Spain, France, Turkey, Thailand, USA..etc…).
  2. Population genomics of global isolates of the model plant symbiont, Rhizophagus irregularis

    The Arbuscular Mycorrhizal Fungi (AMF) are ubiquitous plant symbionts that improve the ability of roots to uptake nutrients from soil and provide protection against plant pathogens. These organisms are intriguing as they harbor many nuclei within one cytoplasm throughout their entire life cycle. The genetic organization of these nuclei has been debated for years, but recent genome analyses in our lab are providing essential insights to this debate.

    The proposed projects aims to increase our knowledge of biology and evolution of these curious fungi and critical symbionts by investigating the genome diversity within and across different strains of the model AMF R. irregularis sampled globally.

For specific enquiries please contactDr. Nicolas Corradi (ncorradi@uottawa.ca).

Applicants are expected to have a strong background in either comparative genomics or populations genomics. Experience in either population genetics, environmental genomics, metagenomics, or ab-initio gene annotation and programming will be seen as an asset for the final selection of the candidate. Some basic training in bioinformatics (Perl, Python, or R) is desired.

A complete application package includes a CV, a one-page description of past research accomplishments and future goals, and the names and e-mail addresses of at least 2 references. The position opens immediately, and evaluation of applications will continue until a suitable candidate is found.

The University of Ottawa is a large, research-intensive university, hosting over 40,000 students and located in the downtown core area of Canada’s capital city. Ottawa is a vibrant, multicultural city with a very high quality of life.

Applications can be sent to Dr. Nicolas Corradi (ncorradi@uottawa.ca).

Representative publications:

  • Pelin A., Selman M., Laurent Farinelli, Aris-Brosou S. and N. Corradi. 2015. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology
  • Ropars J. and N. Corradi. 2015. Heterokaryotic vs Homokaryotic Mycelium in the Arbuscular Mycorrhizal Fungi: Different Techniques, Different Results? New Phytologist
  • Corradi, N. 2015. Microsporidians: Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfer. Annual Review of Microbiology
  • Riley R., Charron P., Idnurm A., Farinelli F., Yolande D. , Martin F. and N. Corradi. 2014. Extreme diversification of the mating type–high?mobility group (MATA?HMG) gene family in a plant?associated arbuscular mycorrhizal fungus. New Phytologist
  • Tisserant E., Malbreil M. et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. PNAS