Molecular Networks
Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal…
The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
Network alignment (NA) aims to find regions of similarities between molecular networks of different species. There exist two NA categories: local (LNA) or global (GNA). LNA finds small highly conserved network regions and produces a…
In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…
Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack clear naming conventions that would be required for…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
In spite of the recent interest and advances in linear controllability of complex networks, controlling nonlinear network dynamics remains to be an outstanding problem. We develop an experimentally feasible control framework for nonlinear…
Florigens, the leaf-derived signals that initiate flowering, have been described as mysterious, elusive and the Holy Grail of plant biology.
Alzheimer's disease is the most common form of dementia in the western world, however there is no cure available for this devastating neurodegenerative disorder. Despite clinical and experimental evidence implicating the intestinal…
The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This papers…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
In many models of the Calvin cycle of photosynthesis it is observed that there are solutions where concentrations of key substances belonging to the cycle tend to zero at late times, a phenomenon known as overload breakdown. In this paper…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
The MAP kinase cascade is an important signal transduction system in molecular biology for which a lot of mathematical modelling has been done. This paper surveys what has been proved mathematically about the qualitative properties of…
To cope with the complexity of large networks, a number of dimensionality reduction techniques for graphs have been developed. However, the extent to which information is lost or preserved when these techniques are employed has not yet been…
We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…