Bioinformatician (Postdoc or PhD) Systems Toxicology for next generation chemical safety assessment

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

Bioinformatician – (Postdoc or PhD researcher) - in Systems Toxicology for next generation chemical safety assessment

Key Responsibilities

The research group of Prof. Bob van de Water and Dr. Giulia Callegaro is focused on systems toxicology approaches for safety assessment. We aim to unravel cell signaling programs that underlie adverse xenobiotic-induced adverse responses that drive pathological outcomes. A focus is on critical target organs of toxicity, e.g. liver, kidney, heart, lung and brain. We apply high throughput transcriptomics analysis in combination with innovative gene co-expression network models thus contributing to a system toxicology approach in qualifying and quantifying adverse responses.

In this project the candidate will work on innovative (data) approaches within the European funded PARC project (Partnership for the Assessment of Risks from Chemicals), actively participating in further implementation of high throughput transcriptomics for chemical hazard assessment. The objectives are to 1) develop co-expression models for a range of high-throughput test systems of high interest for industrial and regulatory application 2) improve the interpretation framework of transcriptomics data and co-expression models by implementing and designing natural language models (NLP) approaches 3) demonstrate the utilization of high-throughput transcriptomic approaches in collaboration with pivotal regulatory agencies, such as the European Chemical Agency (ECHA), the European Food Safety Agency (EFSA) and Organization of Economic Co-operation and Development (OECD).

The research group consists 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 within PARC.

The prospective candidate will join an enthusiastic research team of >25 researchers that conduct their work in the context of multiple European funded projects (RISK-HUNT3R, VHP4S, KWF, EFSA TD-TRAQ, EFSA 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:

• Develop transcriptomic co-expression models for a range of high-throughput test systems of high interest for industrial and regulatory application
• Improve the interpretation framework of transcriptomics data by developing ontologies for co-expression methods in the toxicology context using NLP approaches
• Connect the newly developed ontologies to the toxicology context, in particular the AOP framework
• Complete the circle of systems toxicology and experimentally test hypotheses for mechanism of toxicity;
• Contribute to scientific advancements of co-expression methods in the toxicology context, in particular in combination with bench-mark dose analysis;
• Contribute to the further developments of the co-expression application TXG-MAPr tool (R-Shiny);
• Interface with multiple partners in collaborative projects.

Selection criteria

• A PhD or MSc degree in bioinformatics, or toxicology but with a strong focus on data analysis and programming;
• Experience with transcriptomic analysis, and knowledge of common bioinformatics tools (experience with network approaches and WGCNA is considered a plus);
• Proficiency in R; experience with Shiny app development is considered a plus;
• Proficiency in machine learning approaches; experience with NLP and AI is considered a plus;
• Affinity with open-data and FAIR principles is considered a plus;
• Affinity with cell culture experiments.
• 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.

Our organization

Working at the Faculty of Science means being part of an exciting, dynamic scientific environment that 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 2,800 staff and over 5,900 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.

Terms and conditions

We offer a full-time, one year term position, with the possibility of renewal for an additional maximum of three years based on performance. Salary ranges from € 2.901,-- to € 3.707,-- gross per month (PhD pay scale P) or from € 3.378,-- to € 5.331,-- gross per month (Postdoc pay scale 10, 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.

Information

Inquiries can be made to Bob van de Water (b.water@lacdr.leidenuniv.nl) and Giulia Callegaro (g.callegaro@lacdr.leidenuniv.nl).