PhD Student

Job description

Long Read Sequencing for detecting cryptic genetic defects in patients with intellectual disability and congenital anomalies.

Background
The Genome Research group at the Center for Medical Genetics has longstanding expertise in introducing new technologies to elucidate genetic and genomic defects in individuals with intellectual disability and congenital anomalies.
Our research group is implementing third-generation sequencing (long-read sequencing) to detect currently hidden genetic variation in the genome.

Job description
We are looking for a talented and highly motivated PhD student to join our team and work on the elucidation of genetic variants in patients with intellectual disability and congenital malformations. We offer an open, highly dynamic, and challenging working environment in which teamwork, initiative, and originality are stimulated and appreciated.
In addition to extensive data analysis, wet lab work is included in the project.
1. Research Tasks:

• Experimental Design and Execution:
  
  • Implement long-read sequencing protocols using PromethION and Revio platforms.
  • Prepare and process genomic DNA samples for sequencing.
• Data Analysis:
  
  • Analyze long-read sequencing data to identify structural variations (SVs), including deletions, duplications, inversions, and translocations.
  • Develop methods for tandem repeat detection and characterization.
  • Investigate epigenetic signatures associated with specific genomic regions.

2. Bioinformatics Skills:

• Proficiency in Python and R for data analysis, visualization, and statistical modeling.
• Experience with bioinformatics tools commonly used in genome research (e.g., SAMtools, BCFtools, BEDtools, GATK, Dorado, Minimap2, etc.).
• Ability to work with large-scale genomic datasets and perform variant calling.
• Familiarity with Linux/Unix command-line environments.

WHAT WE CAN OFFER YOU

• We offer a full-time position as a doctoral fellow, consisting of an initial period of 12 months, which - after a positive evaluation, will be extended to a total maximum of 48 months.
• Your contract will start as soon as possible.
• The fellowship amount is 100% of the net salary of an AAP member in equal family circumstances. The individual fellowship amount is determined by the Department of Personnel and Organization based on family status and seniority. A grant that meets the conditions and criteria of the regulations for doctoral fellowships is considered free of personal income tax. Click here for more information about our salary scales
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits (in Dutch).

Job profile

• Master’s degree in Biomedical Sciences, Bioengineering, Biotechnology, Bioinformatics, or a related field.
• Strong interest in genome research and sequencing technologies.
• Experience with long-read sequencing platforms (PromethION, Revio) is advantageous.
• You take initiative, have a critical mindset, and strive to work independently.
• Proficiency in bioinformatics tools for SV detection and analysis.
• Excellent communication skills and ability to work in a collaborative environment.
• Fluency in English (both written and spoken).
• Candidates eligible to submit a PhD research project to other funding agencies will be considered an advantage.

How to apply

• Applications should be submitted by October 31, 2024.
• Send a motivation letter and curriculum vitae with detailed study results (per year) to Prof. Dr. Björn Menten (Email: Bjorn.Menten@UGent.be)

Please also include extracurricular activities and the contact information of two references.

This exciting opportunity allows you to contribute to cutting-edge genomics and long-read sequencing research.