PhD position on machine learning-based prediction of protein-protein interactions

9 May 2023
Job Information

Organisation/Company

Wageningen University & Research

Research Field

Physics

Researcher Profile

First Stage Researcher (R1)

Country

Netherlands

Application Deadline

5 Jun 2023 - 22:00 (UTC)

Type of Contract

Temporary

Job Status

Not Applicable

Hours Per Week

38.0

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

Are you looking for a PhD position and like to participate in an exciting interdisciplinary research project to discover how proteins select their partners to interact with? Are you a bioinformatician with interest in machine learning, and its application to predict protein interactions? Then this PhD vacancy may be of interest to you.

Biological processes are controlled by transcription factor proteins (TFs), which interact in many different combinations to regulate gene expression. However, it is still largely unclear how the specificity of protein-protein interactions is encoded in protein sequence and structure and how this determines which combinations of proteins with unique functions can be formed. Ultimately, this knowledge is important to steer and control biological processes, and investigate for example the cause of human diseases or govern modern plant breeding approaches.

In the framework of the NWO-M2 project ‘Machine learning-based prediction of transcription factor protein-protein interactions’, two PhD candidates will collaborate to develop a robust computational method to predict protein-protein interactions of TFs with complex evolutionary histories. The method will be developed based on the MADS-domain transcription factor family, which regulates important plant processes such as flowering and fruit development. One of the PhD candidates will work in the Bioinformatics Group, the other PhD candidate in the Plant Developmental Systems group of the Laboratory for Molecular Biology to perform wet-lab experiments aiming to gain insight into the specific requirements for protein-protein interactions.

This vacancy only applies to the PhD position in the Bioinformatics group at Wageningen University. This PhD student will develop a computational method, based on machine learning, to predict MADS-domain TF protein-protein interaction specificity. This method will be used to identify features that influence protein interaction, and identify amino acid residues essential for MADS-domain TF protein-protein interaction specificity. As such, the PhD student will work in close collaboration with the PhD student at Plant Developmental Systems, where input for the model will be generated and model predictions will be tested.

The research is embedded within the Bioinformatics Group of Prof. Dick de Ridder, (web page ). Your daily supervisor will be Dr. Aalt-Jan van Dijk.

The Bioinformatics Group 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 (including the application of machine learning to study protein function and interaction), and tool construction. There are many national and international collaborations with researchers studying plant development, biotechnology and genomics.

Requirements
Specific Requirements

You have

• A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline
• Demonstrable experience in applying machine learning to biological data
• Good statistical and mathematical skills
• Proficiency in programming (e.g. in Python)
• Affinity with molecular biology and be interested in collaborating with researchers in this discipline
• Perseverance in problem solving

You are an independent person, but also a team player who enjoys working in a multidisciplinary team.

For this position your command of the English language is expected to be at C1 level . Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here .

Additional Information
Benefits

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

• sabbatical leave, 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.
The gross salary for the first year is € 2.541,- per month rising to € 3.247,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

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 18th 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.

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. For instance under the "30% rule", certain categories of international staff can receive tax exemption on approximately 30% of their gross salary.

Selection process

For more information about this position, please contact dr. Aalt-Jan van Dijk, associate professor bioinformatics, by e-mail at [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.
This vacancy will be listed up to and including June 5, 2023. We hope to schedule the first job interviews on June 20, 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 .

Additional comments

For more information about this position, please contact dr. Aalt-Jan van Dijk, associate professor bioinformatics, by e-mail at [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.
This vacancy will be listed up to and including June 5, 2023. We hope to schedule the first job interviews on June 20, 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 .

Website for additional job details

https://www.academictransfer.com/327542/

Work Location(s)

Number of offers available

1

Company/Institute

Wageningen University & Research

Country

Netherlands

City

Wageningen

Postal Code

6708 PB

Street

Droevendaalsesteeg

Where to apply

Website

https://www.academictransfer.com/327542/phd-position-on-machine-learning-based-…

Contact

City

Wageningen

Website

http://www.wageningenur.nl

Street

Droevendaalsesteeg

Postal Code

6708 PB

STATUS: EXPIRED