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This thesis is focused in the study of the evolution of the metabolic repertoire of Streptomyces, which are renowned as proficient producers of bioactive Natural Products (NPs). The main goal of my work was to contribute into the…
We present a network model in which words over a specific alphabet, called {\it structures}, are associated to each node and undirected edges are added depending on some distance between different structures. It is shown that this model can…
Transformations to create more sustainable social-ecological systems are urgently needed. Structural change is a feature of transformations of social-ecological systems that is of critical importance but is little understood. Here, we…
Recent genomic analyses on the cellular metabolic network show that reaction flux across enzymes are diverse and exhibit power-law behavior in its distribution. While one may guess that the reactions with larger fluxes are more likely to be…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
A new class of micromechanically motivated chain network models for soft biological tissues is presented. On the microlevel, it is based on the statistics of long chain molecules. A wormlike chain model is applied to capture the behavior of…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary…
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with…
For applications on the extreme edge, minimal networks of only a few dozen artificial neurons for event detection and classification in discrete time signals would be highly desirable. Feed-forward networks, RNNs, and CNNs evolved through…
We present a general and flexible procedure which allows for the reduction (or expansion) of any dynamical network while preserving the spectrum of the network's adjacency matrix. Computationally, this process is simple and easily…
When studying social, economic and biological systems, one has often access to only limited information about the structure of the underlying networks. An example of paramount importance is provided by financial systems: information on the…
Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
Despite the remarkable success of deep learning systems over the last decade, a key difference still remains between neural network and human decision-making: As humans, we cannot only form a decision on the spot, but also ponder,…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
Repeating patterns of spike sequences from a neuronal network have been proposed to be useful in the reconstruction of the network topology. Reverberations in a physiologically realistic model with various physical connection topologies…