Universiteit Leiden

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PhD student / post-doc researcher in Quantitative transcriptional gene network analysis in systems toxicology.

Vacancy number
PhD positions
Internal , External
Publication date
23 August 2022
Closing date
30 September 2022 Vacancy closed

The Faculty of Science and the Leiden Academic Centre for Drug Research are looking for a:

PhD student / post-doc researcher in Quantitative transcriptional gene network analysis in systems toxicology.

Vacancy number: 22-530

Key responsibilities

The research group of Prof. Bob van de Water aims to unravel cell signaling programs that underlie adverse xenobiotic-induced adverse response as well as anticancer drug resistance. In particular, high throughput transcriptomics analysis is applied with innovative co-regulated gene network analysis thus contributing to a system toxicology approach in qualifying and quantifying adverse responses. While co-regulated gene networks have been established for several in vitro and in vivo target organs there is a lack in the translation of these approaches to the human in vivo setting. In this project the candidate will actively participate to establish co-regulated gene networks for human target organs and relevant cancers based on available public data as well as new transcriptomics data from liver and kidney biopsy biobanks available at Dutch clinical centers. Gene network associations with disease state and progression as well as systematic preservation of gene networks between in vitro and human in vivo will be part of the work. Moreover, the overall applicability of the tools established in the context of (pre)clinical safety assessment will be determined in the context of target organ toxicity and non-genotoxic carcinogenesis and cancer progression.

The prospective candidate will join an enthusiastic research team of >25 researchers that conduct their work in the context of multiple European funded projects (EU-ToxRisk, RISK-HUNT3R, eTRANSAFE, TransQST, VHP4S, PARC, KWF), where successful interactions between academia, industry and regulatory agencies assures excellent scientific and societal impact, as well as a strong support network.

The successful applicant will:

  • Develop co-expression models for patient liver and kidney biopsies as well as cancer datasets, incorporating clinical information and digital pathology images;
  • Contribute to the further developments the co-expression application TXG-MAPr tool (https://txg-mapr.eu/, R-Shiny);
  • Contribute to scientific advancements of co-expression methods in the toxicology context, in particular in combination with bench-mark dose analysis and qAOP development;
  • Design and apply case studies to demonstrate the value of co-expression methods and the TXG-MAPr tool for risk assessment;
  • Interface with multiple partners in collaborative projects;

Selection criteria

  • A MSc or PhD degree in bioinformatics, or toxicology but with a strong focus on data analysis and programming;
  • Experience with transcriptomic analysis, knowledge of common bioinformatics tools;
  • Experience with network approaches and WGCNA is considered a plus;
  • Proficiency in R, experience with Shiny app development;
  • Strong analytical skills, critical and lateral thinking;
  • Strong communication skills and team player;
  • Strong ability to work independently and creative thinker;
  • Entrepreneurship interest or disposition is considered a plus.

Our organization
Working at the Faculty of Science means being part of an exciting, dynamic scientific environment which sets high standards for its students and staff. The research carried out at the Faculty of Science is diverse, ranging from computer science, mathematics, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences.

The faculty has grown strongly in recent years and now has more than 2,300 staff and over 5,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. For more information, see https://www.universiteitleiden.nl/en/science.

Terms and conditions
We offer a full-time, one year term position, with the possibility of renewal for an additional maximum of three year based on performance. Salary range from € 2,541.- to € 3,247.- gross per month for PhD (fulltime, pay scale P, depending on experience in accordance with the Collective Labour Agreement for Dutch Universities), or € 2.960,- to € 4,670.- for postdoc (fulltime, scale 10, in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break. For more information ( https://www.universiteitleiden.nl/en/working-at/job-application-procedure-and-employment-conditions), see the website.

Enquiries can be made to Bob van de Water ( b.water@lacdr.leidenuniv.nl ) and/or Giulia Callegaro ( g.callegaro@lacdr.leidenuniv.nl ). If you have any questions about the procedure, please contact the secretariat of the Division of Drug Discovery & Safety, Marjolijn Lugthart (m.j.l.lugthart@lacdr.leidenuniv.nl).

To apply for this vacancy, please send an email to Marjolijn Lugthart ( m.j.l.lugthart@lacdr.leidenuniv.nl ).

Please ensure that you upload the following additional document quoting the vacancy number:

  • Cover letter
  • Curriculum vitae with a list of publications
  • Research Interests Statement (max a A4 page)
  • 2 reference letters

Only applications received before September 30, 2022 can be considered

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