Tag Archives: fungi

Job: USDA-ARS Research Plant Pathologist, Salinas, CA

USDA-ARSThe USDA-ARS lab in Salinas, California has a permanent scientist positions open to work on Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae. The position will support regional agricultural production, which in the Salinas Valley alone has a value in excess of $4.8 billion per year. Historically researchers at our location have enjoyed strong support from our regional agricultural producers. Our location is 2 hours south of San Francisco and 40 minutes away from the Monterey Peninsula and Big Sur area. Hiring level is at a GS-12 or GS-13 (Salary range of $88,582 to $136,969 per year)

As a Research Plant Pathologist the incumbent will be responsible for, but not limited to:

  • Develop and test biological and/or chemical control measures for the soilborne fungal pathogens affecting strawberry production with emphasis on Fusarium oxysporum and Macrophomina phaseolina;
  • Apply metagenomic approaches based on next generation sequencing to characterize soil microbial communities associated with infected and healthy strawberries;
  • Conduct population analyses of Fusarium oxysporum and Macrophomina phaseolina affecting strawberry through molecular and microbiology based studies;
  • Screen and evaluate plant genetic resistance against Fusarium oxysporum and Macrophomina phaseolina; and
  • Develop or improve diagnostic tests for both Fusarium oxysporum and Macrophomina phaseolina.

Additional details about the position (ARS-D18W-0156) may be found at the website www.usajobs.gov
USAJOBS – The Federal Government’s official employment site
www.usajobs.gov
USAJOBS is the Federal Government’s official one-stop source for Federal jobs and employment information.
(https://www.usajobs.gov/GetJob/ViewDetails/512971900);

Postdoc: Fungal Endophyte Genomics, U’Ren lab, U Arizona

Postdoc Position Fungal Endophyte Genomics • U’Ren lab

A postdoctoral position is available in the lab of Jana U’Ren at the University of Arizona to study the ecology and evolution of plant-endophyte symbioses. The project centers on enriching genomic, transcriptomic, and metabolomic knowledge of phylogenetically diverse endophytic fungi in collaboration with the DOE Joint Genome Institute. The start date is flexible, but anticipated to be in Fall/Winter 2018 or when the suitable candidate is identified. The position has an initial appointment for one year with a strong likelihood of extension to a second year pending performance review.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with a background in plant-microbe interactions, ecology, and evolution. Minimum requirements: a PhD in ecology, evolutionary biology, microbiology, mycology, plant pathology, or a related discipline. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Preferred candidates will have excellent communication skills, high motivation, and a strong willingness to work independently and as part of an integrative team. Potential duties include (but are not limited to) comparative genomic and transcriptomic analyses, functional trait assays, and plant inoculation experiments, with potential for the development of independent research projects related to plant-fungal interactions.

As part of the UA Ecosystem Genomics Initiative and the BIO5 Institute, the successful candidate will have extensive opportunities to collaborate across departments at UA, as well as with collaborators at other universities. This collaborative environment is conducive to development of a pathway to independence in academic research. The position also includes opportunities to mentor graduate and undergraduate researchers from diverse backgrounds.

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. Outstanding UA benefits include health, dental, vision, and life insurance; paid vacation, sick leave, and holidays; UA/ASU/NAU tuition reduction for the employee and qualified family members; access to UA recreation and cultural activities; and more!

Applicants should submit a cover letter, CV, contact information for three references, and copies of three recent publications. All application materials should be submitted in a single email to Dr. Jana U’Ren (juren@email.arizona.edu).

PDF: Postdoc-URen-Lab-Arizona-2

Postdoc: Computational Transcriptomics. Massey University (NZ)

Postdoctoral Fellow in Computational Transcriptomics with Professor Barry Scott, Massey University, New Zealand

We are looking for a computational biologist with the necessary academic training and competency to analyse a large transcriptome data set generated from endophyte infected grass tissue. The project is collaborative with Professor Christopher Schardl at the University of Kentucky and Professor Murray Cox at Massey University. We are interested in identifying genes that are differentially expressed during the onset of stromata (sexual stage) development on the grass host. We have isolated RNA from different tissues of three different fungal-grass associations. We have gene models for the fungal components of all three associations but gene models for just one host. The post doc will be expected to develop their own hypotheses in analyzing this very large data set and work with a wider group working on the genomics, transcriptomics and functional analysis of fungal-grass associations. The analytical position requires solid quantitative and computational skills, with the ability to develop and apply new bioinformatics applications to the analyses.  At a minimum, some confidence in bioinformatics and a programming language is required. Training in fungal biology or 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 available for just one year from a research sub-contract with the Bioprotection Research Centre to Massey University. Salaries are competitive starting at $69,841 for step 1 of the post-doctoral scale.

The position will be based with Professor Barry Scott at Massey University in the city of Palmerston North.
Please email if you have any further questions: d.b.scott@massey.ac.nz

PDF of job ad: Post doc in computational biology

To submit an application, please provide:

  1.  A brief statement of research interests and experience, focusing on short to medium term
    career goals and your fit for this position
  2. Curriculum vitae, including qualifications and scientific publications
  3. The names and contact details of three referees willing to provide a confidential letter of recommendation upon request

Closing Date: to be readvertised

JOB DESCRIPTION
Purpose Statement: To carry out individual and team-based research on changes in gene expression associated with the onset of endophyte sexual development on grass hosts.

Responsible To: The Head of the Institute of Fundamental Sciences through Professor Barry Scott

Key Accountability Areas:
The Fellow is required to:

  • Undertake computational research on fungal transcriptomics
  • Undertake other relevant duties as specified and approved by the Principal Investigator
  • Maintain accurate and orderly records of experiments, procedures and code, and store these records and data in the laboratory group archive.
  • Report weekly to the Principal Investigator summarizing research progress and planned future research, with a focus on work towards research publications
  • Publish at least one peer-reviewed publication in an international scientific journal
  • Be familiar with Institute guidelines and rules for safety and approved practices in experimental work
  •  Maintain an organised and safe working environment
  • Be familiar with Institute guidelines and safety rules.
  • Participate fully in the academic activities of the Institute and the University
  • Provide two monthly written reports to the project leader that summarise research progress and planned future experiments with a focus on publications
  • Devote themselves full-time to University duties
  • Diligently and faithfully serve the University and use their best endeavours to promote and protect the interests of the University
  • Maintain confidentiality both during and after the appointment as Postdoctoral Fellow

 

Qualifications:  A PhD in bioinformatics, computational biology, or otherwise applicable field (interpreted broadly)

Experience:
Miniumum Qualifications

  • Able to conduct independent cutting-edge research
  • Proven research experience, including evidence of a publication record
  • Quantitative skills, including some background in statistics and programming

Preferred Qualifications

  • Candidates will be conversant in at least one programming language (broadly defined)
  • Additional bioinformatics, computational and/or statistical experience would be an advantage
  • Candidates with a background in biology together with applied mathematics, physics or computer science are encouraged to apply
  • Some knowledge of biological systems

Attributes and Skills:

  • good quantitative skills
  • experimental and intellectual creativity
  •  initiative and enthusiasm
  • proven ability to write, and potential to take the lead on scientific publications
  • commitment to quality improvement, up-skilling and personal development
  • ability to organize and maintain quality records
  • integrity and confidentiality
  •  good time-management skills
  • ability to work as a member of a team

Postdoc: Fungal Evolution and Population, USDA-ARS

Postdoctoral Position in Fungal Evolution and Population Biology

USDA-ARS, Peoria, Illinois

We are searching for a highly-motivated postdoctoral associate with strong molecular and computational biology research experience with fungi or other microorganisms to conduct research aimed at understanding the diversity, global population structure, and evolutionary dynamics of Fusarium head blight (FHB) pathogens.  Scientists in the Mycotoxin Prevention and Applied Microbiology (MPM) Research Unit at the USDA-ARS in Peoria have an outstanding record of discovery and publication regarding Fusarium biology, chemistry, and evolution.  Thus, opportunities exist for the postdoc to engage in these and other areas of interest. This full-time position is funded for 1 year ($61,218 + benefits) with the possibility for annual renewal up to 4 years.  The successful candidate must hold a PhD in Biology or related field by appointment start date, be proficient in both written and oral English, and have experience in population genomic analyses.  To apply, please email a single PDF to Todd Ward (todd.ward@ars.usda.gov) that includes: (1) a cover letter with a short description of why you are interested in and qualified for the position, (2) a current CV that includes a list of peer-reviewed publications, and (3) names and contact information for three references.  Evaluation of applications will begin immediately.  U.S. Citizenship is required.

USDA/ARS is an equal opportunity employer and provider

Postdoc: Computational Fungal Genomics (Univ of New Zealand)

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
collection efforts.

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 (m.p.cox@massey.ac.nz). 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.ac.nz/9147/postdoctoral-fellow-in-computational-fungal-genomics

  1.  A brief statement of research interests, qualifications and
    experience.
  2.  A curriculum vitae, including a list of scientific publications.
  3. 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
Massey University
Palmerston North
NEW ZEALAND

http://massey.genomicus.com
m.p.cox@massey.ac.nz

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

Postdoc: Populus microbiome/mycobiome at ORNL

New postdoc position in Chris Schadt’s lab at Oak Ridge National Lab

Purpose
The Biosciences at Oak Ridge National Laboratory (http://www.ornl.gov) is seeking a postdoctoral researcher in the area of microbial ecology. The selected candidate will join an international team of investigators focused on understanding ecology of microbial communities as well as their responses to various anthropogenically induced changes (climate, contaminants, land use, etc.) in multiple systems.

Major Duties/Responsibilities
Design, conduct and interpret laboratory and field based research; lead and contribute to the development of scientific manuscripts and proposals for the Plant-Microbe Interfaces (PMI) project. The available project position will focus on understanding community structure and function of microbes associated with Populus tree species as driven by host genotypic and environmental factors [more at: http://pmi.ornl.gov/]. Research is facilitated by a full range of state-of-the-art equipment/facilities for microbiology, molecular biology, and genomics, in a professional environment with excellent technical support.

Qualifications Required

Qualifications Required: Ph.D. degree in microbiology, ecology, molecular biology, or related field. Applicant should have demonstrated expertise in both modern molecular ecology methods such as quantitative PCR, DNA sequence analyses, as well as working with the informatics tools for microbiome and metagenomics studies. Demonstrated expertise must include a track record of primary contributions to peer-reviewed publications.

Qualifications Preferred: Priority will be given to applicants with a successful history of interdisciplinary, integrative, and innovative research in this area. Familiarity with software tools for next generation DNA sequence analysis of rRNA and metagenomic microbial datasets as well as the ability to program and script in R, Python or Perl to customize such analyses would also be preferred.

Applicants cannot have received the most recent degree more than five years prior to the date of application and must complete all degree requirements before starting their appointment.

Postdoc: Unculturable Protists & Fungi, Single Cell Genomics

Two postdoctoral research positions are available in the laboratory of Dr. Thomas Richards at the University of Exeter, UK.

The project focuses on using environmental sequence data, including meta- genomics and transcriptomics, combined with single cell genomic data to investigate the biology and evolutionary significance of unculturable protist and fungal microbes from marine environments including deep-sea sediments.

One post is focused entirely on bioinformatic based analysis while the second post can include both bioinformatic and laboratory work. However, both applicants should be interested in working with second-generation sequence datasets and feel confident with post genomic analysis including for example: phylogenetic tree reconstruction and metabolic pathway reconstruction.

For more details please see:

https://jobs.exeter.ac.uk/hrpr_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=7490968mXd&WVID=3817591jNg&LANG=USA

https://jobs.exeter.ac.uk/hrpr_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=7733318mXd&WVID=3817591jNg&LANG=USA

This is a Gordon and Betty Moore Foundation funded project and is part of an international collaboration including associated laboratories at the University of British Colombia, University of Maryland Center for Environmental Science, Monterey Bay Aquarium Research Institute and the Department of Energy Joint Genome Institute and should include the opportunity for travel

To ask questions or apply please e-mail your CV and contact information for three referees to t.a.richards@exeter.ac.uk . Materials must be received by the 13th November but late applications will be considered until the position is filled.

2012 Fungal Genomes: a review of mycological genomic accomplishments

2012 was certainly a banner year in genome sequence production and publications. The cost of generating the data keeps dropping and the automation for assembly and annotation continues to improve making it possible for a range of groups to publish genomes.

I made a NCBI PubMed Collection of these here Fungal Genomes 2012

Some notable fungal genome publications include

There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes

(Now I might have missed a few in my attempt to get this done before holidays overtake me – if so, please post comments or tweets and I’ll be sure to amend the list on pubmed and here.)

A new trend for fungal genome papers can be seen now in the Genome Announcements of Eukaryotic Cell which aim to get the genome data out quickly with a citateable reference. These are short descriptions which I expect will become more popular ways to insure data made public can also be cited. I only counted about 5 published in 2012 but I expect to see a lot more of these in the 2013 either at EC or other journals. I’m sure there will still be some tension between providers making data public as soon as possible and the sponsoring authors’ desire to have first crack at analyzing and publish interpretations and comparison of the genome(s). The bacterial community has been doing this for Genome Reports in the SIGS journal and the Journal of Bacteriology so will see what happens as these small eukaryotic genomes become even easier to produce.

I look forward to exciting year with more of the 1000 Fungal genomes and other JGI  projects start to roll out more genomes.  I also predict there will be many more resequencing datasets published as functional and population genomics. It will also probably be a countdown for what are the last Sanger sequenced genomes and how the many flavors of next generation sequencing will be optimized for generation.  I am hopeful work on automation of annotation and comparisons will be even easier for more people to use and that we start to provide a shared repository of gene predictions.  I’ve just launched the latter and look forward to engaging more people to contribute to this.