Post Doc in Scalable Pangenomics

Wageningen University

PostDoc in Scalable Pangenomics

Location Wageningen

We are looking for

A postdoctoral researcher to work on scalability of state-of-the-art pangenome algorithms. Are you skilled in computer science with an affinity for (plant) genomics? Then this may be the right position for you.

Our comparative (pan)genomics team develops innovative data structures and algorithms to analyze large amounts of genomics data simultaneously to gain insights into genome organization, function and evolution. In many areas of the life sciences, there is a clear need for pangenomic data organization and analysis, but scalability is currently a limiting factor. In this project we will address the scalability of our pangenome software, PanTools, using eScience technologies. This will involve the identification and resolution of bottlenecks in the data structure, algorithms, and underlying technology. Specifically, we will explore the combination of Apache Spark technology and Neo4j/GraphX to improve scalability and speed of analytics. The research will be performed using a set of pre-defined use cases in plant breeding.

The postdoc on this eTEC-BIG project (https://www.esciencecenter.nl/projects/scaling-up-pan-genomics-for-plant-breeding/) will become part of a larger team with research engineers from the Netherlands eScience Center and SURFsara, co-developers and researchers from industry, requiring interdisciplinary communication. The postdoc will be based in the Bioinformatics Group of Wageningen University (www.bif.wur.nl), embedded in the comparative (pan)genomics team. This 2-year position offers the opportunity to apply your research skills in the domain of plant genomics and includes time for personal development. Are you an enthusiastic, pro-active computer scientist with an interdisciplinary mindset, interested in software scalability and challenged by big data? We look forward to your application.

We ask

  • A PhD degree in computer science, bioinformatics, or related field, with experience in algorithm development and software engineering.
  • Strong programming skills in Java and Python, fluency in Linux command-line use.
  • Experience with Spark, Neo4j, or high-performance computing is an advantage.
  • Affinity with (plant) genomics.
  • Strong communication skills, connecting technology to biology and developers to end users.
  • Curiosity, a critical research attitude, and an interdisciplinary mindset.

We offer

A challenging postdoc position with, depending on your experience, a competitive salary from a minimum of € 3217to a maximum of € 4402 for a full working week of 38 hours in accordance with the Collective Labor Agreement Dutch Universities (scale 10).

In addition, we offer:

  • 8% holiday allowance;
  • a structural year-end bonus of 8.3%;
  • excellent training opportunities and secondary employment conditions;
  • flexible working hours and holidays can possibly be determined in consultation so that an optimal balance between work and private life is possible;
  • excellent pension plan through ABP;
  • 232 vacation hours, the option to purchase extra and good supplementary leave schemes;
  • a flexible working time;
  • a choice model to put together part of your employment conditions yourself, such as a bicycle plan;
  • a lively workplace where you can easily make contacts and where many activities take place on the Wageningen Campus. A place where education, research and business are represented;
  • make use of the sports facilities on campus for a small fee.
Wageningen University & Research stimulates internal career opportunities and mobility with an internal recruitment policy. There are ample opportunities for own initiative in a learning environment.
We offer a versatile job in an international environment with varied activities in a pleasant and open working atmosphere.

More information

For more information about this function, please contact dr. Sandra Smit, assistant professor, by e-mail: Sandra.Smit@wur.nl.

For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.
General information about the Bioinformatics Group can be found on www.bif.wur.nl

This vacancy is open up to and including August 25, 2020.
You can only apply online through the application button on our website.


The first job interviews will take place early September.

We are

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Within Wageningen University & Research, nine specialised research institutes from the Wageningen Research Foundation and Wageningen University have joined forces to help answer the most important questions in the domain of healthy food and living environment.

With approximately 30 locations, 6,000 employees, and 12,000 students, Wageningen University & Research is one of the leading organisations in its domain worldwide. An integrated approach to problems and the cooperation between various disciplines are at the heart of the unique approach of Wageningen.

For further information about working at Wageningen University & Research, take a look at the special career site.

Equal opportunities employer

We are an employer that offers equal opportunities. We are happy to receive applications from all suitably qualified people regardless of race, gender, functional impairment, religion / belief, sexual orientation or age.
We believe that a diverse and inclusive working environment makes us a more relevant, competitive and resilient organization. Click here for more information about working at WUR with a functional impairment.

The Bioinformatics Group offers an excellent, collaborative working environment within a diverse group of researchers. We develop novel computational methods for the representation, analysis and integration of biological data, to understand how the interplay of genomes, transcripts, proteins and metabolites results in the phenotypic complexity observed in living systems. We maintain extensive computational resources and have access to the university’s high-performance compute systems. As a group, we value (inter)national collaboration and strive for excellence in education and research. We teach (advanced) courses in bioinformatics and data science at the BSc, MSc and PhD level. Our group is strongly embedded in the Plant Sciences Group, collaborates intensively with Wageningen Research and is involved in the efforts of Wageningen University & Research to promote the use and development of data science in its research areas.

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