PhotoGEA Publications

Overview

This page contains a list of all publications about or using the PhotoGEA R package, including links to publicly-available analysis scripts whenever possible. If we are missing any publications, please let us know!

Publications About PhotoGEA

The PhotoGEA R package was first described in:

1. Lochocki, E. B., Salesse-Smith, C. E. & McGrath, J. M. “PhotoGEA: An R Package for Closer Fitting of Photosynthetic Gas Exchange Data With Non-Gaussian Confidence Interval Estimation.” Plant, Cell & Environment (2025).

   • DOI:10.1111/pce.15501

   • PhotoGEA version: v1.1.0

   • Analysis scripts: https://github.com/ripeproject/PhotoGEA-paper/

If you use PhotoGEA for your own work, please cite this publication and specify the version of the package you used.

Publications Using PhotoGEA

2. Salesse-Smith, C. E. et al. “Greater mesophyll conductance and leaf photosynthesis in the field through modified cell wall porosity and thickness via AtCGR3 expression in tobacco.” Plant Biotechnology Journal 22, 2504–2517 (2024).

   • DOI:10.1111/pbi.14364

   • PhotoGEA used for: Calculating mesophyll conductance from tunable diode laser absorption measurements (calculate_gm_busch), C3 A-Ci fitting (fit_c3_aci), C3 A-Ci + CF Variable J fitting (fit_c3_variable_j)

   • PhotoGEA version: v0.10.0

   • Analysis scripts: https://github.com/ripeproject/CGR3-tobacco-2024

3. Pelech, E. A., Stutz, S. S., Wang, Y., Lochocki, E. B. & Long, S. P. “Have We Selected for Higher Mesophyll Conductance in Domesticating Soybean?” Plant, Cell & Environment 48, 1594–1607 (2025).

   • DOI:10.1111/pce.15206

   • PhotoGEA used for: Calculating limitations to C3 photosynthesis (calculate_c3_limitations_grassi and calculate_c3_limitations_warren)

   • PhotoGEA version: v1.0.0

   • Analysis scripts: https://doi.org/10.13012/B2IDB-7809185_V2

4. Salesse-Smith, C. E. et al. “Adapting C₄ photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane.” Proceedings of the National Academy of Sciences 122, e2419943122 (2025).

   • DOI:10.1073/pnas.2419943122

   • PhotoGEA used for: Fitting C4 A-Ci curves using the mechanistic model (fit_c4_aci), reading and plotting induction curves (read_gasex_file)

   • PhotoGEA version: v0.11.0

   • Analysis scripts: https://github.com/cabbi-bio/sorghum-sugarcane-RBCS-RAF1-2024