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Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
In biochemical networks, complex dynamical features such as superlinear growth and oscillations are classically considered a consequence of autocatalysis. For the large class of parameter-rich kinetic models, which includes Generalized Mass…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multi-layer networks, i.e. networks where each layer stands for…
Collaboration networks are studied as an example of growing bipartite networks. These have been previously observed to have structure such as positive correlations between nearest-neighbour degrees. However, a detailed understanding of the…
The brain effortlessly extracts latent causes of stimuli, but how it does this at the network level remains unknown. Most prior attempts at this problem proposed neural networks that implement independent component analysis which works…
Biological networks have so many possible states that exhaustive sampling is impossible. Successful analysis thus depends on simplifying hypotheses, but experiments on many systems hint that complicated, higher order interactions among…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Local perturbations of individual metabolic reactions may result in different levels of lethality, depending on their roles in metabolism and the size of subsequent cascades induced by their failure. Moreover, essentiality of individual…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Existing studies on the degree correlation of evolving networks typically rely on differential equations and statistical analysis, resulting in only approximate solutions due to inherent randomness. To address this limitation, we propose an…
Distinct channels of interaction in a complex networked system define network layers, which co-exist and co-operate for the system's function. Towards realistic modeling and understanding such multiplex systems, we introduce and study a…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
This paper investigates how neurons can use metabolic cost to facilitate learning at a population level. Although decision-making by individual neurons has been extensively studied, questions regarding how neurons should behave to cooperate…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…