Vacancy Intern Bioinformatics & Modeling

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KeyGene – the crop innovation company
KeyGene is the go-to AgBiotech company for higher crop yield & quality. With our intellectual capital, solution driven approach and collaborative spirit, we work for the future of global agriculture with partners in the AgriFood sector. We support customers and partners with the development of new, improved crops by providing cutting edge breeding technologies, bioinformatics expertise and plant-based trait platforms. KeyGene employs more than 135 people and has sites in Wageningen, the Netherlands and in Rockville, USA. To support the research in Bioinformatics & Modeling we are looking for a student Bioinformatics/Molecular Biology (MSc/BSc) to strengthen our team:

Intern Regulatory Region Analysis

for Agronomic Trait Selection

Vacancy number 16.intern001

Introduction
Transcription factors (TFs) regulate gene expression by binding to promoters as well as distal enhancers regions. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Interactions between TFs and TFBSs help the cell respond to internal and external stimuli.

ConBind, a novel tool developed at the VU University is able to identify known functional TFBSs on regulatory regions. The relevance and applicability of the tool has been previously shown in higher-order animals. Also in plant breeding identification of, and variation in, TFs and TFBS sites is important for the identification of elements responsible for agronomic traits. KeyGene and life sciences software company ENPICOM have a collaboration in this area.

Under the guidance of the two supervisors the student will have the opportunity to learn and apply sequence analysis, comparative genomics, and its potential role in trait selection in a challenging and stimulating industrial setting.

Tasks
The student is asked to explore and report on the applicability of regulatory regions analysis in the plant breeding domain for the purpose of agronomic traits selection. In particular the student will have to:
1. Benchmark different state-of-the-art tools (e.g. MEME, ConBind, ConSite) for TFBSs discovery and scanning and assess their strength, weakness, and applicability in the plant genome analysis.
2. Identify a suitable measure for plant genomes to enable (optimal) phylogenetic footprinting.
3. Determine what variation in TFBS can potentially explain trait differences.

Your qualifications
1. BSc/Msc student Bioinformatics, Molecular Biology or similar
2. Knowledge of Python
3. Basic knowledge of Linux shell scripting
4. Good communication skills in English
5. Knowledge of gene regulatory processes, especially in plants, is helpful

Supervision
The project will be co-supervised by Dr. Ir. Raymond van Daelen (KeyGene) and Dr. Nicola Bonzanni (ENPICOM).

Duration
The internship will have a duration of 6 months.

Location
The student will conduct the research 50% at KeyGene (Wageningen) and 50% at ENPICOM (Amsterdam).

More information
If you are interested in this position you can send your letter of application and resume to:
KeyGene Attn. Ms Tiny Swemers, Personnel Advisor, P.O. Box 216, 6700 AE Wageningen, The Netherlands or by email: tiny.swemers@keygene.com. Please mention the vacancy number 16.intern001 in your application.