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Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Emulation has been successfully applied across a wide variety of scientific disciplines for efficiently analysing computationally intensive models. We develop known boundary emulation strategies which utilise the fact that, for many…
To understand dynamic developmental processes, living tissues must be imaged frequently and for extended periods of time. Root development is extensively studied at cellular resolution to understand basic mechanisms underlying pattern…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores…
Developmental transcriptional networks in plants and animals operate in both space and time. To understand these transcriptional networks it is essential to obtain whole-genome expression data at high spatiotemporal resolution. Substantial…
Quantitative assessment of the growth of biological organisms has produced many mathematical equations. Many efforts have been given on statistical identification of the correct growth model from experimental data. Every growth equation is…
Arabidopsis roots show oscillatory growth patterns on homogeneous agar surfaces, whereas other plants, such as maize, do not. Although several explanations have been proposed, a simple and general model that makes testable predictions…
Computer models are now widely used across a range of scientific disciplines to describe various complex physical systems, however to perform full uncertainty quantification we often need to employ emulators. An emulator is a fast…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
Arabidopsis root hair patterning is controlled by a complex transcription factor network containing positive and negative feedback loops, epidermal cell-cell signalling, and positional signalling from underlying tissue. Recently, several…
One of the central problems in animal and plant developmental biology is deciphering how chemical and mechanical signals interact within a tissue to produce organs of defined size, shape and function. Cell walls in plants impose a unique…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
The global population increase leads to a high food demand, and to reach this target products such as pesticides are needed to protect the crops. Research is focusing on the development of new products that can be less harmful to the…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
In this paper we undertake a multiscale analysis of nutrient uptake by plant root hairs, considering different scale relations between the radius of hairs and the distance between them. We combine the method of formal asymptotic expansions…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
The adoption of agroecological practices will be crucial to address the challenges of climate change and biodiversity loss. Such practices favor the cultivation of plants in complex mixtures with layouts differing from the monoculture…
Accurate predictions and representations of plant growth patterns in simulated and controlled environments are important for addressing various challenges in plant phenomics research. This review explores various works on state-of-the-art…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…