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Understanding plant-microbe co-adaptation through integrative data analysis

Applications are invited for a PhD fellowship/scholarship at Graduate School of Natural Sciences, Aarhus University, Denmark, within the Department of Molecular Biology and Genetics PhD programme. The position is available from 1 August 2021 or later.

Title:
Understanding plant-microbe co-adaptation through integrative data analysis

Research area and project description:
The project is supervised by associate professor Stig U. Andersen. His group studies natural variation in plants and microbes and has developed extensive genetic and genomic resources for the model legume Lotus japonicus. These include a sequenced panel of natural accessions and a large insertion mutant resource (https://lotus.au.dk).

The aim of the PhD project is to project is to exploit Lotus japonicus natural variation to identify plant genetic components that are required for adaptation to the local microbiota and for shaping the plant microbiome. You will use network analysis, modeling and machine learning to integrate large quantities of plant RNA-seq and genotype data with microbiome profiles to identify candidate genes, which will be validated using plant mutants.

For examples of work on natural variation and Lotus japonicus resources, please see:

  • Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan (2020). PMID: 31937774. DOI: 10.1038/s41467-019-14213-y
  • Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex (2020). PMID: 32176601. DOI: 10.1099/mgen.0.000351
  • The LORE1 insertion mutant resource (2016). PMID: 27322352. DOI: 10.1111/tpj.13243

The activities are part of the InRoot project supported by the Novo Nordisk Foundation (https://mbg.au.dk/en/research/research-centres/inroot/). InRoot is dedicated to deciphering the molecular mechanisms and dynamics of plant-microbe interactions at the root–soil interface.

Qualifications and specific competences:
We are looking for a candidate that is able to solve problems independently, has good collaborative skills, and enjoys working at the interface between biology and data science. Experience with programming and statistical analysis using Python, R or similar languages is required, as are good communication skills and fluency in written and spoken English. Experience with RNA-seq and microbiome data analysis is an advantage. Aarhus University offers both 4+4 and 5+3 PhD study models (https://phd.au.dk/phd-fellowships-and-scholarships/). 4+4 candidates that do not yet have a Master’s degree, but can demonstrate a strong academic track record during their bachelor and first year Master’s studies are preferred.

Place of employment and place of work:
You will be part of dynamic study environments at the section for Plant Molecular Biology, Department of Molecular Biology and Genetics, where work is focused on the study of plant-microbe interactions, and at the Bioinformatics Research Centre that focuses on algorithm development and analysis of large-scale biological data. The research environment is cross-disciplinary with PIs specialized in bioinformatics, biochemistry, microbiology, molecular biology, and genetics, ensuring excellent possibilities for sparring and discussion. You will be advised by associate professor Stig U. Andersen, Aarhus University (main supervisor, plant genomics and bioinformatics), associate professor Cranos Williams, North Carolina State University (NCSU) (co-supervisor, modelling and machine learning), and professor Mikkel H. Schierup, Aarhus University (co-supervisor, bioinformatics and population genetics). Your places of work will be the Department of Molecular Biology and Genetics, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark and the Bioinformatics Research Centre, C.F. Møllers Allé 8, DK-8000 Aarhus C, Denmark. The study will include research visits to NCSU.

Aarhus is the second largest city in Denmark with top museums and dining available in a relaxed atmosphere (https://www.visitaarhus.com). The campus is located within walking distance of the city center, providing easy student access to all the city has to offer.

Contacts:
Applicants seeking further information are invited to contact:
Associate professor Stig U. Andersen, e-mail: sua@mbg.au.dk


Application procedures


Before you apply

Information and attachments:

Please be aware that you must have all relevant appendices, attachments, addresses for referees, etc. ready when you apply, as the entire application must be uploaded to the system in one go.

Documentation of language skills:

The English language requirement at the graduate school is comparable to an “English B level” in the Danish upper secondary school (“gymnasium”).

English language qualifications comparable to an “English B level” are documented by one of the following tests:

  • TOEFL test (internet-based), minimum score: 83. The graduate school does not accept the paper-based test, nor the TOEFL ITP test. Remember to ask the test center to send your test results to Aarhus University in order to enable verification of your test results. Aarhus University’s TOEFL code is 8935.
    Currently, the TOEFL iBT Special Home Edition test (available in selected areas) will also be accepted.
  • IELTS (academic) test, minimum average score: 6.5 points
  • Cambridge English Language Assessment:
    Cambridge Certificate of Proficiency (CPE)
    Cambridge English: Certificate of Advanced English with grade A,B or C (CAE)
    Cambridge English: First Certificate with grade A (FCE)

When to take the test and how to upload the documentation:
The test result must not be more than two years old at the time of application.

The English language test should be taken before applying for admission and uploaded under “language skills documentation” in the online application form.

It is possible to apply for admission before you have taken the test. In this case, documentation stating that you have signed up for a test (please state expected submission date) must be uploaded under “Language skills - proof” in the online application form. If the test result is not part of the original application, the test result must be sent to gsns@psys.au.dk no later than one month after the application deadline.

The following applicants are exempted from documenting their English qualifications/taking a test:

  • Applicants with citizenship from the following countries: Australia, Canada, Ireland, New Zealand, the United Kingdom, the United States, or one of the Nordic countries (Denmark, Finland, Iceland, Norway or Sweden).
  • Applicants with a Bachelor’s or Master’s programme completed in Australia, Canada, Ireland, New Zealand, the United Kingdom, or the United States. In this case, please upload your Bachelor’s or Master’s diploma under the section ”Language skills documentation”.
  • Applicants with a Bachelor’s or Master’s programme completed at a Danish university for which the requirement was English B level at the time of admission. In this case, please upload your Bachelor’s or Master’s diploma under the section ”Language skills documentation”.

The programme committee may request further information or invite the applicant to attend an interview.

How to apply:

1)      Find the application form:
Go to https://phd.nat.au.dk/for-applicants/apply-here/ - Note, the online application system opens on 1 March 2021.
Choose May 2021 Call with deadline 1 May 2021 at noon (11.59 AM CEST).
You will be directed to the call, and must choose the programme “Molecular Biology and Genetics”.

2)      Fill in the following information:

  • Personal information
  • Academic background
  • Admission
  • Financing (if any)
  • Study: In the dropdown menu you must choose the project: “Understanding plant-microbe co-adaptation through integrative data analysis”
  • Source (how you found out about the call)

Next to some of the information fields you will find a number. Click on the number to get further directions on how to fill in the information field/what information is needed.

3)      Application attachments:
Please be aware that you cannot submit the application if one or several of these documents have not been uploaded.

If you wish to upload more than one document under each section, you must scan/merge all documents into one large PDF file and upload this. Please note that we reserve the right to remove scientific papers, large reports, theses and the like. Instead you can indicate a URL where the information is available.

All information in the application must be in English or Danish, preferably English. A certified English translation is required for documents written in languages other than English or one of the Scandinavian languages (i.e. Norwegian, Swedish or Danish) languages.

As a minimum all applications must include (pdf-files only, max. 20 MB, no zip):

  • One reference (template for references)
  • Curriculum vitae,
  • Motivation (max. 1 page)
  • Transcripts, grade point averages (weighted and unweighted), and diploma(s) for both Bachelor’s and Master’s degree. If the original documents are not in English or one of the Scandinavian languages (i.e. Norwegian, Swedish or Danish) then copies of the original documents as well as a certified English translation must be attached.
  • Project description (½-4 pages). This document should describe your ideas and research plans for this specific project. If you wish to, you can indicate an URL where further information can be found. Please note that we reserve the right to remove scientific papers, large reports, theses and the like.
  • Documentation of language skills if required.

After submission of the application, you will receive a confirmation e-mail with an application ID, you should use for reference if needed.

The graduate school reserves the right to verify the authenticity of your educational diploma and transcripts:

  • Request additional information to verify an application.
  • Reject the application if it is proven, or if the University has reasonable belief, that the information provided is false or if the applicant refuses to provide the requested information, whether or not an offer has already been made. 
  • For further information on applying, assessment procedures, etc. please see the GSNS Application Guide.

Please note:

  • The programme committee may request further information or invite the applicant to attend an interview.

All interested candidates are encouraged to apply, regardless of their personal background.

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