Understanding the complex cis-regulatory grammar underlying cell and tissue identity is of great importance for stem cell research and regenerative medicine. However, due to the inherent complexity of gene regulatory networks, our understanding of how they shape complex phenotypes remains incomplete. The proposed PhD project is part of the recently funded Vidi project 'Inference of gene regulatory logic in metazoan development'. This project aims to determine conserved gene regulatory modules in early animal development using genome-wide gene regulatory network inference in a large collection of species.
 
As a PhD candidate you will combine state-of-the-art computational algorithms and large data sets with an evolutionary developmental biology approach to gain insight into the rules by which regulatory elements define cell identity and behaviour. You will work on inference of genome-scale regulatory networks from integration of large and diverse experimental data sets (RNA-seq, ATAC-seq, ChIP-seq). Your work will include method development as well as application to analyse gene regulatory networks in development across metazoan species. You will also have the opportunity to develop novel ideas and work on an independent project aligning with our research interests.

• a Master’s degree in computational biology, bioinformatics/biology, molecular sciences or a related field, and a strong interest in computational biology or computer science, statistics, machine learning or a related field including a solid foundation in biology;
• demonstrable programming experience;
• willingness to adopt open science practices (sharing code and data, publishing preprints);
• excellent communication skills in written and spoken English;
• strong analytical skills, a problem-solving and result-oriented attitude;
• the ability to work and interact with others in an energetic and supportive research environment;

Experience with the following would be an advantage:

• research in one or more of the following areas: (single-cell) genomics, high-throughput sequencing, gene regulation, biological networks, statistics, machine learning, deep learning, large-scale data analysis;
• Python and/or R;
• software version control such as Git;
• Unix/Linux.

• employment: 0.8 - 1.0 FTE
• a maximum gross monthly salary of € 2,897 based on a 38-hour working week (salary scale p)
• the gross starting salary amounts to €2,266 per month, and will increase to €2,897 in the fourth year (P scale)
• in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus
• you will be appointed for an initial period of 18 months, after which your performance will be evaluated. If the evaluation is positive, the contract will be extended by 2.5 years
• you will be classified as a PhD Candidate in the Dutch university job-ranking system (UFO)
• you will be able to make use of our Dual Career Service where our Dual Career Officer will assist with family related support, such as child care, and help your partner prepare for the local labour market and with finding an occupation

Are you interested in our excellent employment conditions?

Faculty of Science
You will join our research team in the Department of Molecular Developmental Biology at the Radboud Institute for Molecular Life Sciences (RIMLS), Faculty of Science, Radboud University (Nijmegen, Netherlands). We offer a first-class international research environment in regulation of gene expression and epigenetics using state-of-the-art genomic, single cell analysis, proteomic technologies and bioinformatics. We run next-generation sequencers, single-cell equipment, and mass spectrometers, accommodate a bioinformatics team, and have a local computational infrastructure.
 
Further information on Molecular Developmental Biology