Two PhD positions in computational genomics and metabolomics for natural products discovery

Two PhD positions in computational genomics and metabolomics for natural products discovery
Two PhD positions in computational genomics and metabolomics for natural products discovery

Published	Deadline	Location
7 Jan	15 Jan	Wageningen

Job description
Would you like to participate in an exciting interdisciplinary European network of young scientists to transform natural product discovery using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with expertise in computational genomics and computational metabolomics, respectively to pioneer new technologies for omics-based natural product discovery.
Microorganisms are an untapped resource natural bioactive compounds that constitute a source of candidates for the development of pharmaceuticals and crop protection agents. Computational integration of different types of omics data, such as genomics and metabolomics profiles, constitutes a promising avenue to uncover this potential. Within the European network, two PhD positions are available within the Bioinformatics Group at WUR.
In project 1, the candidate will develop innovative computational approaches to chart the biosynthetic diversity found in microbial (meta)genomes. You will improve current software and workflows for analysing the modular architecture and composition of biosynthetic gene clusters, to facilitate enhanced comparative analysis as well as predictions of their metabolic products. To validate the efficacy of the approach, you will apply it to microbiome data.
In project 2, the candidate will improve current computational metabolomics workflows to make them better compatible with natural products metabolomics profiles, integrate the metabolomics workflow with omics-based bioactivity predictions into a genome-metabolome mining workflow, and apply this pipeline to paired omics data obtained by network partners.
Extensive international collaboration is foreseen, as these positions are part of a European training network and also will include a secondment at an international company. Specifically, the Doctoral Network MAGic-MOLFUN aims to integrate Natural Products Genome Mining, computational metabolomics and state-of-the art metabolic engineering and pathway discovery to develop ground-breaking tools and approaches to improve natural products discovery and characterization in bacteria and fungi, two major sources of bioactive compounds for applications in medicine, agriculture, food and biotechnology.
The research is embedded within the chair Bioinformatics (headed by Prof. dr. Dick de Ridder), and member of the teams led by Prof. dr. Marnix Medema and Dr. Justin van der Hooft.
Specifications

• max. 38 hours per week
• Wageningen View on Google Maps

Wageningen University & Research

Requirements
We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:

• a solid academic record (MSc) in bioinformatics, biology, chemistry or a related discipline
• experience in computational omics analysis and proficiency in programming (in, e.g., Python)
• at least basic to intermediate statistical and mathematical skills• demonstrable experience in working with next-generation sequencing data (for position 1) or (mass spectrometry-based) metabolomics data analysis (position 2)
• affinity with microbiology, metabolism and/or biosynthetic pathways
• team player attitude, enjoying multidisciplinary science
• a very good level of oral and written English. You are required to show us a certification of English skills. For more information about the required level please take a look at: https://www.wur.nl/en/Education-Programmes/PhD-Programme/English-language-requirements.htm ;
• you meet all the entry requirements of the WUR PhD programme .
• to accept a position within the Marie-Curie training network, researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary (i.e., The Netherlands) for more than 12 months in the 3 years immediately before the recruitment date.

Conditions of employment
Wageningen University & Research offers excellent terms of employment . A few highlights from our Collective Labour Agreement include:

• study leave and partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• the option to accrue additional compensation / holiday hours by working more, up to 40 hours per week;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed December bonus of 8.3%;
• excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.
In addition to these first-rate employee benefits, you will of course receive a good salary. We offer a competitive gross salary starting at € 2.541,- per month for a full-time working week of 38 hours, increasing yearly until € 3.247,- in the fourth year, in accordance with the Collective Labour Agreements for Dutch Universities (CAO-NU) . Additionally, a contract for 0.8 FTE can be discussed.
There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.
You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the " Best University " in the Netherlands for the 17th consecutive time.
Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees. Applicants from abroad moving to the Netherlands may qualify for a special tax relief , known as the 30% ruling. Our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. Wageningen University & Research's International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about helping your partner to find a job, housing, schooling, and other issues.
Employer
Wageningen University & Research
The mission of Wageningen University & Research is "To explore the potential of nature to improve the quality of life". Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,200 employees (6,400 fte) and 13,200 students and over 150.000 participants to WUR's Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.
This project will be carried out at the Bioinformatics Group, in collaboration with the Biosystematics Group, both within Plant Sciences. The Bioinformatics Group is a rapidly expanding research group that focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of -omics data. The group has a strong track record in genome analysis, algorithm development, and tool construction. There are many national and international collaborations with researchers studying plant and microbe metabolism, biotechnology and genomics.
Read the 5 reasons why your future colleagues enjoy working at WUR and watch this video to get an idea of our green campus!
Additional information
For more content-related information about position 1, please contact Marnix Medema, Associate Professor Bioinformatics, by email ([email protected] ). For information about position 2, please contact Justin van der Hooft, Assistant Professor in Computational Metabolomics, by email ([email protected] ).
For more information about the procedure, please contact [email protected] .
Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website, which will allow us to process your personal information with your approval. We are especially curious how you would prefer to contribute to this project and which skills you would like to develop.
In your motivation letter, please indicate whether you are interested in position/project 1, position/project 2 or both.
This vacancy will be listed up to and including January 15th, 2023. After that, the selection will be made. We hope to schedule the first job interviews by late January or early February 2023.
Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. For more information please go to our inclusivity page . A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment .
Join us and come work at WUR

At Wageningen University & Research, you work at improving the quality of life. Together with your colleagues, you seek to answer the challenges within our domain 'healthy food and living environment.'

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Back to the vacancy
Application procedure
For more content-related information about position 1, please contact Marnix Medema, Associate Professor Bioinformatics, by email ([email protected] ). For information about position 2, please contact Justin van der Hooft, Assistant Professor in Computational Metabolomics, by email ([email protected] ).
For more information about the procedure, please contact [email protected] .
Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website, which will allow us to process your personal information with your approval. We are especially curious how you would prefer to contribute to this project and which skills you would like to develop.
In your motivation letter, please indicate whether you are interested in position/project 1, position/project 2 or both.
This vacancy will be listed up to and including January 15th, 2023. After that, the selection will be made. We hope to schedule the first job interviews by late January or early February 2023.
Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. For more information please go to our inclusivity page . A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment .