PhD student computational pangenomics

19 Mar 2024
Job Information

Organisation/Company

Wageningen University & Research

Research Field

Physics

Researcher Profile

First Stage Researcher (R1)

Country

Netherlands

Application Deadline

15 Apr 2024 - 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 interested in algorithm development for genomics? Do you want to innovate methods for computational pangenomics and mine massive amounts of genomics data? Then this PhD vacancy may be of interest to you .

In bioinformatics, traditional approaches to compare genomes, centered on a single reference, no longer suffice when faced with hundreds to thousands of genomes. The field of genomics is therefore switching to so-called pangenomics. PanTools is a platform developed in the Bioinformatics Group that uniquely integrates a sequence-based and a gene-based pangenome representation. Resting on a compacted De Bruijn graph sequence representation, PanTools has been extended with functions to accommodate comparative genomic analyses at different levels of genomic organization, from genes to gene clusters and syntenic regions. However, the single underlying sequence representation is increasingly becoming a bottleneck in the development of new, scalable algorithms. There is a need for a novel, space-efficient sequence representation of genomes at various levels.

As a PhD student you will work on addressing this challenge, by:

• performing independent research, supported by your supervisors and the Comparative Pangenomics team;
• developing software contributing to the improvement of PanTools;
• writing publications on your scientific work, culminating in a PhD thesis.

In particular, you will investigate, select and implement an efficient representation of DNA and protein sequence in PanTools; extend this representation to allow the incorporation of incomplete/ fragmented genome representations; and add layers to this representation to represent genome similarity over longer evolutionary distances.

You will work here
The research is embedded within the Bioinformatics Group (http://www.bif.wur.nl/ ) led by prof. Dick de Ridder, specifically in the Comparative Pangenomics team led by dr. Sandra Smit. The PhDs and postdocs in the team work on different organisms, but all contribute to the common aim of method development for pangenomics. 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 (including evolutionary genomics), algorithm development (including the development and application of machine learning approaches to study proteins), and tool construction. There are many national and international collaborations with researchers studying molecular evolution and the application of machine learning in bioinformatics.

Requirements
Specific Requirements

You are driven to solve biological challenges using your computer science expertise. You are also an enthusiastic team player, with well-developed communication and collaboration skills.
You also possess:

• a successfully completed MSc degree in computer science, bioinformatics, or a related discipline;
• experience in the development of algorithms, preferably for the analysis of (gen)omics data;
• a demonstrable proficiency in programming (in Java and Python)
• a collaborative attitude towards algorithm/software development;
• affinity for the green life sciences;
• perseverance in problem solving;
• good writing and oral communication skills in English.

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:

• 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 € 2.770 - per month rising to € 3.539,- 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 19th 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 for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

Selection process

For more information about this position, please contact dr. Sandra Smit or prof. Dick de Ridder, telephone +31 317 484074 or by e-mail: [email protected] or [email protected] .
For more information about the procedure, please contact Dax Teunissen, corporate recruiter (+31 317 487820, e-mail: [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 April 15, 2024. We hope to schedule the first job interviews in the week of April 22.

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. 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. Sandra Smit or prof. Dick de Ridder, telephone +31 317 484074 or by e-mail: [email protected] or [email protected] .
For more information about the procedure, please contact Dax Teunissen, corporate recruiter (+31 317 487820, e-mail: [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 April 15, 2024. We hope to schedule the first job interviews in the week of April 22.

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. 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/339174/

Work Location(s)

Number of offers available

1

Company/Institute

Wageningen University & Research

Country

Netherlands

City

Wageningen

Postal Code

6708 PB

Street

Droevendaalsesteeg

Geofield

Where to apply

Website

https://www.academictransfer.com/en/339174/phd-student-computational-pangenomic…

Contact

City

Wageningen

Website

http://www.wageningenur.nl

Street

Droevendaalsesteeg

Postal Code

6708 PB

STATUS: EXPIRED