Theoretical Biology & Bioinformatics

tree of life
Monica Garcia Gomez

Monica Garcia Gomez

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Exciting opportunity to to join the group in shared position with the ten Tusscher group!!

Computational PhD position on modeling Arabidopsis
resilience to drought and temperature stress
We are looking for an enthusiastic PhD candidate to develop dynamical, process-driven computational models for the effects of combined temperature and drought stress on plant growth and performance. The successful candidate will develop state of the art functional-structural plant models simulating plant growth dynamics and integrate these with the molecular signalling networks linking drought and temperature perception to responses in plant physiology, growth and development. To arrive at the relevant molecular signalling networks, the PhD candidate will collaborate with experimentalists and machine learning experts. The ultimate goal is to identify the interplay between temperature and drought stresses and pinpoint the molecular hubs at which trade-offs and synergies arise that can be modulated through targeted breeding approaches.

The project is part of Crop-XR, a large Netherlands-based initiative aimed at increasing sustainability of agricultural practices by making crops less dependent on fertilizers and pesticides and more resilient to climate change and environmental stress. For this an increased understanding of plant stress responses is essential.

For this position we are looking for candidates with an Msc degree in Computational Biology, Biophysics, Applied Mathematics or a related field that have a strong interest in plant science and are keen to bridge biological and computational approaches. Experience with differential equation based modeling and programming are a requisite, while affinity with data analysis and bioinformatics will be considered a bonus. For more information and to apply please get in touch with me , and/or Prof. dr. Kirsten ten Tusscher.

Projects for internships

Students interested in developing computational models to understand root development, please see below the list of available projects in the lab and feel free to contact me to share more details.

  • Regulatory networks controlling stem cell niche patterning in uncut and cut roots: here you will explore the genetic-hormonal regulatory network that underlies the establishment of a root stem cell niche de novo. For this you will use a multi-scale model of the root tip, where you will simulate root cuts and recover the ordered cell fate changes observed during the regeneration process.
  • Agent based models of the intracellular transport of key root patterning regulators: here you will study the strategies that allow proteins to rapidly reach a target (plasmodesmata) without prior information. This model is centered on mobile transcription factors that play a key role in root patterning, and you will assess the impact of different transport strategies on the organization of the root stem cell niche.