Tag: Computational Biology

Front. Genetics. In this paper, the authors model the metabolism in Arabidopsis using Petri nets (PN). PNs are dynamic models that use “tokens” to represent movement between the places and edges of the model, representing the products of a reaction. The model was simplified using reduction techniques,…

Proc. Natl Acad. Sci. USA. Xanthophylls zeaxanthin and lutein are involved in the nonphotochemical quenching (NPQ) pathway which is triggered in response to excess photons. The roles of zeaxanthin and lutein in NPQ are studied using mathematical models and Arabidopsis mutants. The authors hope that future…

This week's papers were seleted by Renee Dale. Renee is a PhD student in biology and an MS student in statistics at Loiusiana State University who is studying mathematical biology and biostatistics for plant biology applications. She is also working on an educational video game! Renee selected these…

PLOS Comp. Biol. Plant biologists need basic programming skills (see Friesner et al. for a discussion of why this is true and how to achieve it).  As part of the “Ten Simple Rules” series in PLOS Computational Biology, Carey and Papin describe Ten simple rules for biologists learning to program.…

Wang et al. discover unexpected connections between humidity and ion transport using a model that bridges guard cell-to-leaf scales https://doi.org/10.1105/tpc.17.00694 By Maria Papanatsiou Background: Plants rely on stomata on the leaf epidermis for their survival. Stomata are small pores formed…

The application of systems biology is quite phenomenal these days for prediction-based modeling and interactive data visualization. Along with the genome sequencing of the model plant Arabidopsis thaliana, there has been a parallel increase in systems biology tools. Unfortunately, these tools have been…

Classic genetic approaches have been instrumental in identifying genes that control developmental and defense networks, but as Hillmer et al. point out, analysis of single mutants is complicated by network buffering. They describe network buffering as occurring when the effect of losing a gene’s function…

Plant roots develop on a very heterogeneous environment surrounded by a myriad of environmental clues that can change at different spatiotemporal scales. The ability of roots to sense and respond to these clues is fundamental to ensure an efficient exploration of the rhizosphere. In this paper, Robbins…