Phd Position in Molecular and Computational - Antwerpen, België - Springer Nature

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Sophie Dubois

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Sophie Dubois

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Beschrijving

PhD position in Molecular and Computational Neurogenomics:

  • Employer
  • VIB
  • Location
  • Antwerp
  • Closing date
  • 13 Apr 2024
  • Discipline
Life Science
Job Type
PhD Studentship
Employment - Hours
Full time
Duration
Permanent
Qualification
Professional certification
Sector
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  • Job Details
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Job Details:


  • Project description We are a highly motivated international team of researchers at the Molecular Neurogenomics group (Jordanova Lab) and the Computational Neurobiology group (Malysheva Lab) at the VIB CMN. We are excited to announce a call for a joint Ph.
D.

student in our labs to work on a challenging project at the interface of neurodegeneration, genomics, computational and systems biology.


  • Charcot-MarieTooth disease (CMT) represents the most common genetic disorder of the peripheral nervous system. Patients experience progressive distal muscle weakness and wasting, sensory loss, and skeletal deformities ultimately leaving them severely disabled. This lifelong disorder is currently incurable. The largest protein family implicated in the etiology of CMT are aminoacyltRNA synthetases (ARS). Ubiquitous and essential enzymes, ARS catalyse a critical step in protein biosynthesis by charging tRNA with their cognate amino acid. Jordanova Lab reported that dominant mutations in the tyrosyltRNA synthetase (YARS) cause a clinical variant of CMT and so far six additional cytoplasmic ARS have been implicated in the same pathology.
  • The overarching goal of this proposal is to understand why and how dysregulation of omnipresent and constantly expressed ARS proteins leads to dyingback neurodegeneration and affects specifically the peripheral neurons (PNs). This neuronal population contains the most polarized cells in our body and their sophisticated morphology and function render them highly susceptible to degeneration. The preliminary data generated inhouse as well as the available public data suggest mechanisms involving genetic, epigenetic and chromatin organisation factors governing the celltype specific response to ARS mutations. Therefore, an integrative genomewide cisregulatory network analysis approach, developed and employed in the Malysheva Lab, is required to reveal these mechanisms. With the proposed project we aim to bridge this gap in our knowledge of cisregulatory mechanisms underlying this disease. For this, we will generate highresolution spatial chromatin organisation, chromatin accessibility and gene expression data for all major cell types forming the peripheral nerve environment (as well as controls), and integrate these data into the cisregulatory networks in order to reveal the mechanisms underlying the strong celltype specific effect of the CMTcausing YARS mutations.
  • Profile
- have an MSc in Systems Biology, Molecular Biology, Natural Sciences, or related disciplines
- be very motivated and enthusiastic to learn and expand both computational and experimental skill sets
- be able to summarize data extracted from the literature and clearly shape research objectives
- be able to efficiently communicate with experimental and computational scientists
- have excellent communication and writing skills in English


Required skills
- confident in basic molecular biology techniques, such as cell cultures, basic genomics data generation
- basic/intermediate programming skills in R and/or Python

  • Ability to adapt to the research environments while being full members of two labs

Desirable skills
- knowledge of gene regulatory mechanisms
- statistical analysis
- basic processing of NGS data
- experience with iPSC culturing
- knowledge of and some experience with genetic perturbation assays, such as CRISPR


We offer As part of the VIB-UAntwerp Center for Molecular Neurology and VIB, the applicant will benefit from established collaborations and access to centralized facilities with expertise in genomics, functional genomics and cell biology, proteomics, cutting-edge microscopy, structural biology, technology development, and bioinformatics.


  • VIB
provides a highly interactive environment and ample training opportunities for its researchers. In addition, the VIB-UAntwerp Center for Molecular Neurology is located in the city of Antwerp, the capital of Flanders, offering a culturally and historically rich, and ethnically diverse environment.

  • The VIB-UAntwerp Center for Molecular Neurology has 7 PIs and hosts internationally recognized leaders in the field of Neurogenetics and Neuroinflammation. Current research groups address a broad set of questions related to neurodegenerative diseases of the central and peripheral nervous system, with an emphasis on understanding the genetic etiology and developing diagnostics and treatment methods for these diseases. Approaches range from human genetics, genomics, protein biochemistry and neuronal and glial cell biology to integrative systems and computational biology
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