PhD researcher in Systems Toxicology: connecting co-expression networks to injury and pathology

PhD researcher in Systems Toxicology: connecting co-expression networks to injury and pathology

Published Deadline Location
7 Nov 29 Nov Leiden

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

PhD researcher in Systems Toxicology: connecting co-expression networks to injury and pathology
Vacancy number:14246

Job description

Key responsibilities
Systems toxicology is emerging as key methodology to analyze and interpret omics data in the chemical safety: it mimics the modular and multi-factorial nature of diseases and perturbational statuses. In particular, Dr. Callegaro and colleagues in the PI group of Bob van de Water have previously successfully applied this concept and Weighted Gene Co-expression Network Analysis (WGCNA) to model liver and kidney toxicity with preclinical in vitro and in vivo test systems. In this project, we aim at fully unlocking the potential of systems toxicology by determining which gene regulatory networks are predictive of human adverse events and how specific they are for a certain target organ class. The prospective candidate will get access to uniquely large and extensive transcriptomics databases covering the whole pipeline of drug and chemical safety testing, ranging from in vitro test systems of increasing complexity (such as HepG2 cell line, Primary Human Hepatocytes, iPSC-induced hepatocyte like cells, human liver microtissues) the rat preclinical system and human clinical pathology samples. The research group consist of a one-of-a-kind mixture of computational and experimental scientists that foster the implementation of both state of the art and novel bioinformatic tools as well as experimental validation via high-throughput and cutting edge technologies executed in the same pipeline. This research will represent the next step to impact both drug development practices as well as regulatory practices.

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, EFSA TD-TRAQ and TXG-MAP), 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:
  • Developing computational toxicology models, including co-expression models for several liver and neuronal test systems and patient biopsies, incorporating clinical information; ML and AI algorithm to predict adverse outcomes and contribute to the further developments the co-expression application TXG-MAPr tool (, R-Shiny);
  • Integrate experimental data validating findings obtained computational work, or, depending on interest, carry out the experiments themself (stem cell culturing, CRISPR array screen to identify the role of each gene for cellular adversity or survival and morphology)
  • Design and apply case studies to demonstrate the value of co-expression methods and the TXG-MAPr tool for safety assessment;
  • Interface with multiple partners in collaborative projects;


Leiden University


Selection criteria
  • A MSc degree in experimental toxicology or biopharmaceutical sciences but with a strong affinity/interest for bioinformatics, or a MSc degree in bioinformatics but with a deep understanding for experimental work;
  • Experience with transcriptomic analysis, knowledge of common bioinformatics tools.
  • Proficiency in R, experience with Shiny app development;
  • Experience with network approaches/WGCNA or stem cell culturing andCRISPR array is considered a plus;
  • 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.

Conditions of employment

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 €2.770,- to €3.539,- gross per month (fulltime, pay scale P, depending on experience), 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 ( ), see the website.

D&I statement
Diversity and inclusion are core values of Leiden University. Leiden University is committed to becoming an inclusive community which enables all students and staff to feel valued and respected and to develop their full potential. Diversity in experiences and perspectives enriches our teaching and strengthens our research. High quality teaching and research is inclusive.


Universiteit Leiden

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


  • PhD
  • Natural sciences
  • €2770—€3539 per month
  • University graduate
  • 14246



Leiden, 2312TT, Leiden

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