Lucas Mikaël (ed.) Plant Systems Biology: Methods and Protocols

2nd edition. — Humana Press, 2022 — 351 p. — (Methods in Molecular Biology 2395). — ISBN 978-1-0716-1814-1.This second edition volume expands on the previous edition with an update on the latest techniques used to study plant systems biology on three specific scales: the molecular level, the tissue level, and the whole plant. Chapters cover topics such as gene regulatory network inference and dynamic modeling using ordinary differential equations or Boolean formalisms; protocols for at-will induction of plant aerial or root organs, or quantification of tissue mechanical properties; mathematical modeling of plant tissue using SimuPlant or VirtualLeaf; and simulating crop root systems using OpenSimRoot or R-SWMS. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols or software tutorials, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Plants Systems Biology: Methods and Protocols, Second Edition is a valuable resource for plant biologists looking for different approaches to finding solutions to their questions and generating new ideas, as well as for students who desire to discover the field of plant systems biology.Plant Systems Biology:​ Lessons from Teaching
How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic Data
Gene Regulatory Network Investigation Using Ordinary Differential Equations
Gene Regulatory Network Dynamical Logical Models for Plant Development
Postembryonic Organogenesis in Plants:​ Experimental Induction of New Shoot and Root Organs
NanoIndentation, an ImageJ Plugin for the Quantification of Cell Mechanics
Introduction to Computational Modeling of Multicellular Tissues
The Virtual Root:​ Mathematical Modeling of Auxin Transport in the Arabidopsis Root Tip Using the Open-Source Software SimuPlant
Modeling Plant Tissue Development Using VirtualLeaf
Identifying Developmental Patterns in Structured Plant Phenotyping Data
Putting Plant Roots at Light:​ Temporal Imaging of Plant Roots and Soil Water with a Light Transmission Technique for Linking Water and Root Observations to Soil–Plant Models
RACINE2.​2:​ A Software Application for Processing and Mapping Spatial Distribution of Root Length Density and Potential Root Extraction Ratio from Root Counts on Trench Profiles
Investigating Soil–Root Interactions with the Numerical Model R-SWMS
How to Define the Appropriate Spatial Resolution of Root Segments When Solving Water Flow in Root System Hydraulic Architectures
Simulating Crop Root Systems Using OpenSimRoot
Future Challenges in Plant Systems Biology
Plant Systems Biology:​ Further Reading and Resources