Modeling venation patterns in monocots

SMITH_J23DTP

The Smith lab is looking for a motivated computer scientist (or computationally gifted biologist/physicist) that would like to apply their skills to fundamental questions in plant development.

Working with the in-house image processing package MorphoGraphX (www.MorphoGraphX.org), quantitative data extracted from 3D confocal images will be use to develop computer simulation model of vasculature patterning in monocots.

The work will be done in collaboration with the lab of Prof. Jane Langdale at the University of Oxford.

During the project, the student will be exposed to cutting edge techniques in plant modelling, and become an expert in our 3D confocal image processing software MorphoGraphX (www.MorphoGraphX.org).

The Smith lab has a focus on spatial and biomechanical models, with a particular interest in models where patterning interacts with growth and cell division.
The project will position the student well for a postdoc in developmental modelling, an area currently in high demand.

If you like programming, have excellent spatial intuition, are drawn to computer animation and dynamic systems, and have an interest in plant developmental biology, then this could be the PhD project for you.

References

Bayer EM et al. (2009) Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3).

Mitchison GJ. (1980) A model of vein formation in higher plants. Proc. of the Royal Society B, 207(1166).

Perico C et al. (2022) Developmental regulation of leaf venation patterns: monocot versus eudicots and the role of auxin. New Phytologist, 234.

Runions A et al. (2005) Modeling and visualization of leaf venation patterns. ACM Transactions on Graphics 24(3).

Strauss et al. (2022) Using positional information to provide context for biological image analysis with MorphoGraphX 2.0, eLife 11, e72601.