Recent Posts

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

Potato is susceptible to many pathogens. To facilitate breeding programs, Ramšak et al. combined transcriptomic data from potato/virus interactions with a defense network model developed mainly from Arabidopsis. Their model revealed a previously undescribed interaction between ethylene and salicylate…

Review: The spring of systems biology-driven breeding ($) (TIPS)

In this excellent review, Lavarenne et al. provide an accessible introduction to the tools and objectives of gene regulatory network (GRN) analysis. They include a glossary, show diagrams displaying different stages of GRN analysis, and provide links to key papers in which different methods have been…

What We're Reading: January 19th

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…

Review: Plant systems biology at the single-cell level

The establishment and enormous developments in -omics and systems biology over the last years have increased our understanding and ability to analyze complex biological processes at entire plant, organ or tissue levels. However, these arrays of datasets have the limitation of cellular complexity in terms…

Modeling guard cell-to-leaf scales with OnGuard2

While much is known about the processes involved in stomatal movement and the processes involved in the transpiration of leaves, there has been no framework to bridge this micro-macro divide. Wang and colleagues bridge this divide through OnGuard2, a quantitative systems platform that uses the molecular…

Tomato Genome Goes Nano

Schmidt et al. demonstrate that nanopore technology can be applied to plant genomes https://doi.org/10.1105/tpc.17.00521 By Schmidt, M. H.-W., Vogel, A., Denton, A. K., Bolger, A. M., Bolger, M. E., and Usadel, B. Background: An organism’s genome contains all the necessary information for its…

4D root gene expression

It becomes more and more clear that regulation of complex traits and processes, such as root growth and lateral root growth, involves not only gene expression quality (which genes are expressed), quantity (how much transcript is present) and space (in which cell-type transcripts are accumulating) but…

ePlant: Visualizing and exploring multiple levels of data for hypothesis generation ($)

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…

Using Metabolism to Improve Maize Breeding

Cañas et al. study the relationships between maize leaf metabolism and grain yield to identify putative markers for breeding http://www.plantcell.org/content/29/5/919 By Rafael A. Cañas, Peter J. Lea and Bertrand Hirel In crops, several metabolic pathways are involved in the control of biomass…