Job:PostDoc or PhD researcher: Bioinformatician in Systems Toxicology for Chemical Safety Assessment. Leiden, the Netherlands.

Question

[Giulia]

Full vacancy here: https://www.universiteitleiden.nl/vacatures/2023/q4/14202-postdoc-or-phd-researcher-bioinformatician-in-systems-toxicology-for-chemical-safety-assessment

Key Responsibilities The research group of Prof. Bob van de Water aims to unravel cell signaling programs that underlie adverse xenobiotic-induced adverse responses. In particular, high throughput toxicogenomics analysis is applied with innovative gene co-expression network models thus contributing to a system toxicology approach in qualifying and quantifying adverse responses.

In this project, we aim for shaping the future mechanism-based risk assessment based on gene co-expression models and the Adverse Outcome Pathway (AOP) concept in particular for food and feed safety, in collaboration with the European Food Safety Authority (EFSA). The successful candidate will get access to uniquely large and extensive transcriptomics databases, ranging from in vitro test systems of increasing complexity to human clinical pathology samples, related to several target organ toxicities (liver, kidney, lung and brain). The objectives are to 1) increase the understanding whether transcriptional responses in vitro test systems are representative for human (patho)physiology, 2) establish and apply gene co-expression models to demonstrate AOP activation, 3) define and apply a consensus framework on biological interpretation of toxicogenomics.

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. In addition, the candidate will work in collaboration with other excellent (inter)national academic and regulatory partners and tight cooperation with a regulatory agency pivotal for European safety science (EFSA).

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), 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 transcriptomic co-expression models for several in vitro methods capturing target organ toxicities and clinical samples of the same target organ, taking into account technical variability and biological stochastics of transcriptomics data
  • Define fit for purpose of in vitro test systems towards a certain target organ based on the captured biological programs; define the specificity of test systems relating to different target organs
  • Development of interpretation ontology for co-expression methods in the toxicology context, in particular in combination with the AOP framework;
  • Contribute to the further developments of the co-expression application TXG-MAPr tool (https://txg-mapr.eu/, R-Shiny); Design and apply case studies to demonstrate the value of co-expression methods and the TXG-MAPr tool for food risk assessment;
  • Interface with multiple partners in collaborative projects.

Selection criteria

• A PhD degree (for Postdoc) or Msc degree (for PhD) in bioinformatics, or toxicology but with a strong focus on data analysis and programming;
• Familiarity with data-driven research in an academic environment, including various kinds of qualitative and quantitative research, and combinations thereof;
• Experience with transcriptomic analysis, and knowledge of common bioinformatics tools (experience with network approaches and WGCNA is considered a plus);
• Proficiency in R, and experience with Shiny app development is considered a plus;
• Personal competencies are important in this function: planning and organizing, persuasion, vision development, network skills and quality orientation, communicative, curious, careful, analytical, and team player.

Information Inquiries can be made to Bob van de Water ([e-mail]) and Giulia Callegaro ([e-mail]). If you have any questions about the procedure, please contact the secretariat of the Division of Drug Discovery & Safety, Marjolijn Lugthart ([e-mail]).