In silico LIMB DEVELOPMENT
Limb bud development has long served as a paradigm of organogenesis and pattern formation. Decades of genetic and biochemical studies provide us with a wealth of information about the molecular circuits that control cell expansion and position-dependent cell differentiation in the developing limb bud. In spite of much detailed biological knowledge and much theoretical work, a detailed mechanistic understanding of how the genes and regulatory circuits interact to control limb organogenesis is still lacking.
In collaboration with the Zeller group at the Department of Biomedicine of the University of Basel we are now developing a detailed computational model. By combining mathematical modeling with experimentation we seek to understand how key processes at the microscopic level interact to give rise to patterning at the macroscopic level. Here, we particularly focus on early patterning events, but we are also interested in the control of digit patterning and long bone development.
In collaboration with the Zeller group at the Department of Biomedicine of the University of Basel we are now developing a detailed computational model. By combining mathematical modeling with experimentation we seek to understand how key processes at the microscopic level interact to give rise to patterning at the macroscopic level. Here, we particularly focus on early patterning events, but we are also interested in the control of digit patterning and long bone development.
PUBLICATIONS
JOURNAL PUBLICATIONS
CONFERENCE PROCEEDINGS
REVIEWS
Book Chapters
- Javier Lopez-Rios*, Amandine Duchesne*, Dario Speziale, Guillaume Andrey, Kevin A. Peterson, Philipp Germann, Erkan Ünal, Jing Liu, Sandrine Floriot, Sarah Barbey, Yves Gallard, Magdalena Müller-Gerbl, Andrew D. Courtney, Christophe Klopp, Sabrina Rodriguez, Robert Ivanek, Christian Beisel, Carol Wicking, Dagmar Iber, Benoit Robert, Andrew P. McMahon, Denis Duboule and Rolf Zeller (* shared first authors) Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature (2014)
- Tanaka S and Iber D, Inter-dependent tissue growth and Turing patterning in a model for long bone development. Physical Biology (2013) 10: 056009
- Badugu A, Kraemer C, Germann P, Menshykau D and Iber D, Digit patterning during limb development as a result of the BMP-receptor interaction. Scientific Reports (2012) 2:991
- Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R and Zuniga A, SHH propagates distal limb bud development by enhancing CYP26b1-mediated retinoic acid clearance via AER-FGF signalling. Development (2011) 138, 1913-1923
CONFERENCE PROCEEDINGS
- Karimaddini Z, Ünal E, Menshykau D and Iber D, Simulating Organogenesis in COMSOL: Image-based Modeling, Proceedings of COMSOL Conference 2014, Cambridge
- Velten B, Uenal E and Iber D (2014) Image-based Parameter Inference for Spatio-temporal models of Organogenesis. NOLTA 2014 (Luzern, CH) International Symposium on Nonlinear Theory & its Applications
- Menshykau D, Adivarahan S, Germann P, Lemereux L and Iber D (2013) Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models. Proceedings of COMSOL Conference 2013, Rotterdam
- Menshykau D and Iber D (2012) Simulating Organogenesis in Comsol: Deforming and Interacting Domains, Proceedings of COMSOL Conference, 2012
- Germann P, Tanaka S, Menshykau D and Iber D (2011) Simulating Organogenesis in Comsol, Proceedings of COMSOL Conference, 2011
REVIEWS
- Iber D and Germann P How do digits emerge? - Mathematical Models of Limb Development, Birth Defects Research Part C: Embryo Today: Reviews (2014)
- Iber D, Zeller R, Making sense - data-based simulations of vertebrate limb development, Current Opinion in Genetics & Development (2012)
Book Chapters
- Iber D, Tanaka S, Fried P, Germann G and Menshykau D Simulating Tissue Morphogenesis and Signaling. Springer Book Series: Methods in Molecular Biology. Book Title: Tissue Morphogenesis: Methods and Protocols (Editor Celeste Nelson), in press