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Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression,…
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…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species.…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell…
The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semi-annealed approximation to study the stability properties of Random Boolean Networks…