Tag Archives: postdoc

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

BACKGROUND

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

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

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

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

http://sterg001.wixsite.com/stergiopoulos-lab

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

Postdoc: Evolution of downy mildew pathogens

Postdoctoral Researcher – Evolution of downy mildew pathogens

The Quesada Lab at North Carolina State University invites applications for a Postdoctoral Researcher position. The Postdoc will be responsible for performing evolutionary genomics research with downy mildew plant pathogens affecting specialty crops. The project will focus on studying host adaptation in downy mildew pathogens and shifts in pathogen populations that have resulted in failure of control methods such as host resistance and fungicides. Next generation sequencing and multi-locus sequencing will be used for isolate genotyping. Phenotyping assays to characterize pathogen virulence and sensitivity to fungicides will be performed in growth chambers and in the field. The candidate will be responsible for collecting and analyzing data, writing scientific publications, giving oral and poster presentations, and assisting with grant writing and reports. The Postdoc will also assist with activities related to lab management, training and supervision of other lab staff and stakeholders, and field trials.

This position requires a recent PhD degree (within the last 4 years) in plant pathology, plant-microbe interactions, microbiology, or evolution. Self-motivation, independence, good time management skills, and a high level of written and spoken English are required. Experience working with filamentous pathogens in a lab setting, using CLC Genomics workbench or similar packages, R or similar statistical analysis platforms, experience in statistical analysis, demonstrated ability to publish scientific papers, ability to search and read scientific literature pertinent to job, mentor other staff, and developing new research protocols are also required. Experience with population genetics and evolutionary analysis of filamentous plant pathogens, analysis of Illumina and PacBio sequencing data, and coding experience (bash, perl, python) is preferred but not required.

The lab is located on the main campus in Raleigh. NC State’s location in the Research Triangle Park provides unique opportunities for interactions with the Ag. Biotech industry, including AgBiome, Novozymes, Bayer Crop Science, BASF, Syngenta, and the North Carolina Biotechnology Center; other major universities, including Duke University and the University of North Carolina at Chapel Hill; local research networking groups such as the North Carolina Microbiome Consortium; NC Department of Agriculture and several federal agencies. Interested applicants should send a cover letter describing qualifications, a resume or CV with contact information for three references, college transcripts, and a one-page abstract of Ph. D. thesis to Dr. Lina Quesada (lmquesad@ncsu.edu).

The position will be open until filled.

PDF of advertisement

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: Fungal Ecology and Evolution

Postdoctoral Position in Fungal Ecology and Evolution

Contact: Dr. Serita Frey, Department of Natural Resources & the Environment,University of New Hampshire, Durham, NH USA Serita.Frey@unh.edu

(Questions can also be directed to Dr. Anne Pringle, University of Wisconsin-Madison, anne.pringle@wisc.edu)

Our laboratory aims to understand connections between microbial community structure and ecosystem function. We document the impacts of environmental change on the diversity, community composition, and function of the soil microbial community, and test whether shifts in the community subsequently influence ecosystem-scale carbon and nutrient cycling dynamics. A recent focus is on anthropogenic drivers of fungal evolution, in collaboration with Dr. Anne Pringle at the University of Wisconsin.

This two-year position will focus specifically on fungal evolution within global change contexts, with an emphasis on how fungi evolve in response to soil warming and simulated nitrogen deposition. The candidate will have the flexibility to explore questions that fall within this general topic area, while building on previous research conducted in the Frey and Pringle Labs. The candidate is expected to have strong interests and experience in evolution and ecology. Expertise in cultivation-based and genomic analyses as applied to soil fungi is highly desirable. The candidate will be expected to work independently, but also cooperatively with other members of the lab and with the Pringle Laboratory. A Ph.D. degree in evolution, ecology, natural resources, microbiology, or related field, along with relevant research experience is required. The target start date is Oct. 1, 2017, though an earlier start date is possible. Review of applications will begin April 15, 2017 and continue until the position is filled.

To apply please send the following items in a single PDF file to Serita Frey (serita.frey@unh.edu): letter of interest/experience, CV, and the names and contact information of three professional references.

Postdoc, Student: Evolutionary Genomics Plant Pathogens

POSITIONS IN EVOLUTIONARY GENOMICS OF FUNGAL PLANT PATHOGENS
We are seeking talented and motivated postdoc (research associate) and PhD student (research assistant) candidates in the Fungal Genomics and Evolution Lab within the Synthetic and Systems Biology Unit of the Biological Research Center, with experience in molecular biology, microbiology, light microscopy or bioinformatics.
The successful candidate(s) will be responsible for studying the evolution of the interaction between pathogenic fungi and host plants in the context of multicellular development using a wide range of high-throughput techniques, including single-cell transcriptomics, comparative genomics and bioinformatics.  Candidates are welcome for both bioinformatics and wet-lab projects (please specify).
The successful Candidate has:
• PhD/Msc or equivalent in biology with specialization in molecular biology, functional genomics, bioinformatics or microbiology
• Solid skills in molecular biology assays, microscopy and/or basic microbiological methods
• Experience or interest in bioinformatics, phylogenetics
• Fluency in English
• Good team player traits
We offer:
• Top notch projects and instrumentation
• International environment
• Competitive salaries (420 000 HUF, equivalent to EUR 3 400 in Paris when adjusted to cost of living in Szeged [numbeo.com])
• Extensive collaborator network
Preferred candidates will have diverse research interest, high motivation, excellent communication skills and willingness to work both independently and as part of a team.  For more details on our research see the lab website: http://group.szbk.u-szeged.hu/sysbiol/nagy-laszlo-lab-index.html
Related Publications:
Kohler A, Kuo A, Nagy LG, et al. (2015) Nature Genetics 47:410-5. DOI: 10.1038/ng.3223
Nagy LG, Ohm R, et al. (2014) Nature Communications 5:4471. DOI:10.1038/ncomms5471
Contact and application
If interested, send a motivation letter along with your CV to Laszlo Nagy (cortinarius2000@gmail.com).

Postdoc: Institute Pasteur working on Candida albicans

2 postdoc positions for work on Candida albicans from Christian d’Enfert’s group at Institute Pasteur

Post-doctoral position: Candida albicans regulatory networks

A post-doctoral position is available starting January 2, 2017 in the Fungal Biology and Pathogenicity Unit in the Department of Mycology at Institut Pasteur, Paris, to characterize regulatory networks governing morphogenesis and stress responses in the fungal pathogen Candida albicans.

The successful candidate will join our group to characterize a set of C. albicans transcription factors using genome-wide approaches and contribute to the definition of a global regulatory network of morphogenesis and stress responses in C. albicans. The project will involve collaboration with other groups in the Paris area in the frame of the Candihub project (https://candihub.eu/).

The position, funded by the French National Research Agency, is available starting January 2, 2017. We are looking for a highly motivated postdoctoral researcher with expertise in yeast molecular genetics and omics approaches. Expertise in bioinformatics would be appreciated. Institut Pasteur in Paris offers an excellent international, dynamic and stimulating scientific campus with more than 1500 researchers working in 11 Departments.

Application: Please send a cover letter by October 1st detailing motivation and research interests, a concise summary of previous research activities, a complete CV and contact information for three referees to Christophe d’Enfert, christophe.denfert@pasteur.fr.

https://research.pasteur.fr/en/job/post-doctoral-position-candida-albicans- regulatory-networks/

Post-doctoral position: Molecular mechanisms governing the formation and antifungal tolerance of Candida albicans biofilms

A post-doctoral position is available starting January 2, 2017 in the Fungal Biology and Pathogenicity Unit in the Department of Mycology at Institut Pasteur, Paris, to study the molecular mechanisms involved in the formation and antifungal tolerance of biofilms of the fungal pathogen Candida albicans.

Biofilms formed by C. albicans on indwelling devices play a major role in the persistence of nosocomial infections, largely because of their elevated tolerance to antifungals. The successful candidate will join our group to perform a genome-wide evaluation of the role of C. albicans genes in biofilm formation and antifungal tolerance and subsequently investigate the function of selected genes. The project will involve development of high-throughput methods for the analysis of biofilms in collaboration with the Center for Innovation and Technological Research at Institut Pasteur.

The position, funded by Institut Pasteur, is available starting January 2, 2017. We are looking for a highly motivated postdoctoral researcher with expertise in yeast molecular genetics and high-throughput approaches. Expertise in the analysis of biofilms would be appreciated. Institut Pasteur in Paris offers an excellent international, dynamic and stimulating scientific campus with more than 1500 researchers working in 11 Departments.

Application: Please send a cover letter by October 1st detailing motivation and research interests, a concise summary of previous research activities, a complete CV and contact information for three referees to Christophe d’Enfert, christophe.denfert@pasteur.fr.

https://research.pasteur.fr/en/job/post-doctoral-position-molecular- mechanisms-governing-the-formation-and-antifungal-tolerance-of-candida- albicans-biofilms/

Postdoc: UMichigan Fungal Genomics

The lab of Tim James in the Department of Ecology and Evolutionary Biology at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny and molecular evolution of uncultured and poorly known fungi, including the Cryptomycetes, Zygomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing fungal genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (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 microbiology with an interest in fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (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.

Anticipated Start Date: Between Oct. 1, 2016 and Jan. 1, 2017.

The University of Michigan is a non-discriminatory/affirmative action employer. The Department of Ecology & Evolutionary Biology at the University of Michigan harbors multiple labs with a focus on evolutionary genetics (http://www.lsa.umich.edu/eeb).

Timothy Y. James
Associate Professor
Associate Curator of Fungi
Department of Ecology and Evolution
University of Michigan
Ann Arbor, MI 48109
734-615-7753
tyjames@umich.edu
http://www.umich.edu/~mycology/

Postdoc: Population Genetics/Genomics of Fungal Plant Pathogens

The Department of Plant Pathology at the University of Nebraska-Lincoln is pleased to accept applications for a Post-Doctoral Research Associate position in Population Genetics/Genomics of Fungal Plant Pathogens. This is a 12-month, non-tenure leading position established for a period of one year. This position is available immediately.

Continuation of the position beyond one year is dependent upon satisfactory performance of the incumbent in successfully accomplishing assigned duties, and upon availability of grant funds.

The core purpose of research in this position is to develop new molecular and computational tools that will improve understanding of continental-scale population structure of the notorious plant pathogen, Sclerotinia sclerotiorum. The successful candidate will have responsibilities in two areas: mining and development of novel SSR markers and development of a reactive website via RShiny with a reference database of genotypes to allow comparisons by other researchers. Development of new SSR markers will require mining available genomes to identify new candidate loci. Implementation of the reactive website will require modification of existing R scripts and HTML pages. Previous work experience with population genetic analyses, computational biology, and fluency in one or more computer programming languages are desired (R, Linux, Perl, Python, etc.). Opportunities for teaching and supervisory experience will be provided. The incumbent will be expected to publish research results in refereed journals, present their research findings at national and international scientific meetings, and assist in preparation of nationally competitive grant proposals. The incumbent should have the ability to work independently as well as with a diverse team of researchers.

Requires a Ph.D. degree in place by date of employment. The successful candidate must have strong oral and written communication skills and publication record.

To apply for this position, email a single pdf file containing a letter of application describing research interests, professional goals, and specific qualifications, a CV, copy of transcripts, and contact information of three references to:
Dr. Sydney Everhart, Assistant Professor of Plant Pathology, everhart@unl.edu
Phone: 402-472-2879

Review of applications will begin on August 8, 2016 and continue until the position is filled or the search is closed.

Full advertisement available as PDF here: Postdoc_SscPopGen_7-28-2016

Postdoc: Stress biology using Neurospora as a model system (SLU – Sweden)

Stress biology using Neurospora as a model organism
Research at the Department of Forest Mycology and Plant Pathology center on fundamental and applied aspects of fungal, microbial and plant biology. Important research topics include fungal interaction with other microorganisms and plants as well as ecological functioning and evolution. Central themes are plant pathology and nutrient cycling in agricultural and forest ecosystems. The department is placed at Bio Center at SLU, Uppsala with approx. 300 employees in plant science, microbiology, plant pathology, chemistry, molecular biology, food science and computing biology. At the campus, active collaborations are established with the ecology and soil science departments.

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