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In this Chapter, we ask questions (1) What is the right way to measure the quality of information processing in a biological system? and (2) What can real-life organisms do in order to improve their performance in information-processing…
The subject of this paper is the evolution of the concept of information processing in regular structures based on multi-level processing in nested cellular automata. The essence of the proposed model is a discrete space-time containing…
Discrete Choice Modelling serves as a robust framework for modelling human choice behaviour across various disciplines. Building a choice model is a semi structured research process that involves a combination of a priori assumptions,…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
Organisations, whether in government, industry or commerce, are required to make decisions in a complex and uncertain environment. The way models are used is intimately connected to the way organisations make decisions and the context in…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Formal modelling provides a toolkit for understanding cultural dynamics, from individual decisions to recurring patterns of change. This chapter explains what models are and why they matter. Using a precise, shared language, they aid…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…