Literature & References

The papers below underpin the science, methods, and tools used across AIR. They range from classroom-friendly overviews to advanced research — the Extension & Research stages draw on the modelling and hydraulics references in particular.

Citing AIR

AIR itself is public domain (CC0). If you use it, a citation is appreciated — see CITATION.cff in the repository.

Auxin transport, gravitropism & root development

• Grieneisen, V.A. et al. (2007). Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature 449:1008. https://doi.org/10.1038/nature06215
• Band, L.R. et al. (2014). Systems Analysis of Auxin Transport in the Arabidopsis Root Apex. The Plant Cell 26:862. https://doi.org/10.1105/tpc.113.119495
• Strohm, A.K. et al. (2011). Molecular mechanisms of root gravity sensing and signal transduction. WIREs Developmental Biology. https://doi.org/10.1002/wdev.14
• The Virtual Root: Mathematical Modeling of Auxin Transport in the Arabidopsis Root Tip Using the Open-Source Software SimuPlant (2021). Methods in Molecular Biology. PubMed 34822153 — the model behind our Virtual Root simulator.

Root system architecture & whole-plant modelling

• Zhou, X.-R. et al. (2020). CPlantBox, a whole-plant modelling framework for the simulation of water- and carbon-related processes. in silico Plants. https://doi.org/10.1093/insilicoplants/diaa001
• Root architecture & hydraulics modelling (MARSHAL). Annals of Botany 121(5):1033 (2018). https://academic.oup.com/aob/article/121/5/1033/4844040

Root hydraulics & water transport

• Baca Cabrera, J.C. et al. (2024). Root hydraulic properties: an exploration of their variability across scales. Plant Direct. https://doi.org/10.1002/pld3.582
• Passot, S. et al. (2018). Connecting the dots between computational tools to analyse soil–root water relations. Journal of Experimental Botany. https://doi.org/10.1093/jxb/ery361
• Couvreur, V. et al. (2018). Going with the Flow: Multiscale Insights into the Composite Nature of Water Transport in Roots. Plant Physiology. https://doi.org/10.1104/pp.18.01006
• Couvreur, V. et al. (2021). Evidence for a multicellular symplasmic water pumping mechanism across vascular plant roots. bioRxiv. https://doi.org/10.1101/2021.04.19.439789
• Heymans, A. et al. (2019). GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy. Plant Physiology. https://doi.org/10.1104/pp.19.00617
• Pascut, F.C. et al. (2021). Non-invasive hydrodynamic imaging in plant roots at cellular resolution. Nature Communications. https://doi.org/10.1038/s41467-021-24913-z
• Root hydraulics (Plant Direct). https://doi.org/10.1002/pld3.334

Methods, education & outreach

• Lobet, G. et al. (2020). QuoVidi: an open-source web application for the organisation of large-scale biological treasure hunts. bioRxiv. https://doi.org/10.1101/2020.06.30.177006
• Oladosu, Y. et al. (2020). Submergence Tolerance in Rice: Review of Mechanism, Breeding and Future Prospects. Sustainability 12:1632. https://doi.org/10.3390/su12041632

Other sources cited across the site

• Genetics 208(4):1337 — https://www.genetics.org/content/208/4/1337
• PRIMAL root image-analysis pipeline (protocols.io) — https://dx.doi.org/10.17504/protocols.io.h7bb9in
• R-Shiny statistics in the classroom (eScholarship) — https://escholarship.org/uc/item/00d4q8cp

Spotted a missing or incorrect reference? Use the edit pencil at the top of the page or open an issue on GitHub.