What do we do?
The Computational Biology Group (CoBi) develops computational models of developmental processes. We place a particular focus on mechanistic 4D image-based in silico models of organogenesis (mouse lung, kidney, pancreas, limb, brain, Drosophila wing and eye) and on the delineation of fundamental mechanisms such as those that restrict the size of organs and those that maintain the proportions of structures in different-sized embryos. The group collaborates with tissue engineers to build spatially-organised tissue from stem cells, and with clinicians to apply its techniques to disease models.
One of the key open problems in developmental biology concerns the mechanism of size and growth control. The organ growth rate declines continuously during embryonic development, but the underlying mechanism is elusive. Jannik Vollmer, recipient of an SIB fellowship, now showed that the growth rate in the eye disc declines in a manner that is inversely proportional to the increase in the eye disc area (Vollmer et al., Development, 2016; see commentary). This observation is consistent with growth control by dilution of a cytokine. In a separate line of work, Patrick Fried and co-workers developed a quantitative model of eye disc development that is consistent with the experimental data and that explains the patterning dynamics in the eye disc, e.g. the linear progression of the morphogenetic furrow that separates proliferating and differentiated tissue (Fried et al., Plos Comp Biol, 2016). Both works were highlighted by the respective journals.
Together with the SBML development team, Harold Gomez published MOCCASIN, a software tool to automate the conversion of MATLAB ODE models into SBML (Gomez et al., Bioinformatics, 2016).
Main publications 2016
- Fried P, Sanchez M, Hidalgo D, Lehtinen B, Casares F, Iber D, A model of Spatio-temporal Dynamics of Drosophila Eye Disc Development. Plos Comp Biology (2016), http://dx.doi.org/10.1371/journal.pcbi.1005052
- Vollmer J, Fried P, Lopes CS, Sanchez M, Casares F, Iber D, A quantitative analysis of Drosophila Eye Disc Growth. Development (2016) 143:1482-1490; selected to feature in the "In this Issue" section of Vol. 143, Issue 09 of Development http://dev.biologists.org/content/143/9/e0903
- Gomez H, Hucka M, Keating SM, Iber D, Sealfon S, MOCCASIN: converting MATLAB ODE models to SBML, Bioinformatics (2016) pii: btw056