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PhD student: Machine learning in plant regulatory genomics

Employer
VIB
Location
Ghent
Closing date
2 Sep 2024

View more

Discipline
Life Science
Job Type
Research Assistant
Employment - Hours
Full time
Duration
Permanent
Qualification
Professional certification
Sector
Academia

Job Details

Job description The Vandepoele research lab (Comparative Network Biology - https://www.vandepoelelab.be/ ) invites applications for a fully-funded PhD project for 1 year and extended with another 3 years (after positive evaluation) to study regulatory genomics in plants using different computational and -omics approaches.

Starting from large-scale experimental datasets (e.g., bulk and single-cell RNA-Seq, ChIP/DAP-Seq protein-DNA interaction data, bulk, and single-cell ATAC-Seq) and the application of diverse supervised machine learning approaches (e.g., feature-based, deep learning, and explainable artificial intelligence), the goal of the project is to unravel the complex regulatory code controlling gene expression in the multicellular model plant Arabidopsis thaliana

Together with your colleagues in the Vandepoele lab, sharing complementary expertise in plant biology, genomics, and informatics, you will focus on characterizing the regulatory sequences driving context-specific gene expression in different organs, cell types, and stress conditions. Experimental validation of your computational results will be performed through collaboration with wet lab colleagues in the VIB-UGent Center for Plant Systems Biology.

Relevant publications

  • Obtaining genetics insights from deep learning via explainable artificial intelligence. Novakovsky G, Dexter N, Libbrecht MW, Wasserman WW, Mostafavi S. Nat Rev Genet. 2023 Feb;24(2):125-137. doi: 10.1038/s41576-022-00532-2
  • Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice. Smet D, Opdebeeck H, Vandepoele K. Front Plant Sci. 2023 Jul 17;14:1212073. doi: 10.3389/fpls.2023.1212073
  • MINI-EX: Integrative inference of single-cell gene regulatory networks in plants. Ferrari C, Manosalva Pérez N, Vandepoele K. Mol Plant. 2022 Nov 7;15(11):1807-1824. doi: 10.1016/j.molp.2022.10.016
  • Charting plant gene functions in the multi-omics and single-cell era. Depuydt T, De Rybel B, Vandepoele K. Trends Plant Sci. 2023 Mar;28(3):283-296. doi: 10.1016/j.tplants.2022.09.008
Profile

Essential

  • You obtained excellent grades in your bachelor and MSc degree (i.e., you belong to the top 25% of your cohort).
  • Good programming (Python) and Linux/Unix/command-line skills are a must.
  • You have a good understanding of molecular biology and recent RNA and DNA-based -omics profiling methods.
  • You are enthusiastic about computational / systems biology and want to learn more about applying machine learning for (single-cell) regulatory data analysis.
  • You have good communication and writing skills and have an excellent knowledge of written and spoken English.
  • You are highly motivated, self-critical, you work with rigor, and you work accurately.
  • You combine being a team player with a strong sense of autonomy and responsibility.
  • You are willing to apply for additional funding when eligible.

Desirable but not required 

  • Experience with machine learning (e.g., Scikit-learn/PyTorch/Tensorflow/Keras) is a plus.
  • Experience with explainable AI (e.g., SHAP) is a plus.
  • Experience with high-performance computing, software containers is a plus.
  • Knowledge about plant biology/genomics is a plus.
  • Experience with software development tools (e.g., GIT/Nextflow) is a plus.
We offer
  • An intellectually stimulating, international and multi-disciplinary research environment
  • Access to state-of-the-art tools and (CPU/GPU) infrastructure
  • High-quality training to develop hard and soft skills (VIB and UGent Doctoral Schools)
  • Opportunities to participate in (inter)national workshops and scientific conferences
  • A competitive salary including benefits

The VIB-UGent Center for Plant Systems Biology is a world-leading science institution on the Techlane Campus in Ghent, Belgium. Ghent University is among the top 100 global universities according to several international rankings.

Tentative starting date: August 2024 (to be discussed).

How to apply? Interested candidates are invited to submit a detailed CV (clearly mentioning your computational skills), a cover letter outlining their research interests and relevant experience, academic transcripts, and contact information for at least one reference.

Please submit your application via the VIB application tool.

For more information or inquiries about the position, mail to klaas.vandepoele@psb.vib-ugent.be

We look forward to welcoming you to our team at the VIB-UGent Center for Plant Systems Biology!



 

Company

VIB’s core mission is to generate disruptive insights in the molecular underpinning of life and to translate these actively into impactful innovations for patients and society. VIB is an independent research institute where some 1,800 top scientists from Belgium and abroad conduct pioneering basic research. As such, they are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants, and microorganisms. Based on a close partnership with five Flemish universities – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel, and Hasselt University – and supported by a solid funding program, VIB unites the expertise of all its collaborators and research groups in a single institute. VIB’s technology transfer activities translate research results into concrete benefits for society such as new diagnostics and therapies and agricultural innovations. These applications are often developed by young start-ups from VIB or through collaborations with other companies. This also leads to additional employment and bridges the gap between scientific research and entrepreneurship. VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information. 

More info can be found on www.vib.be.

Company info
Website
Telephone
09446611
Location
Rijvisschestraat 120
Zwijnaarde
Belgium
9052
BE

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