相关论文: Complexity reduction by symmetry: uncovering the m…
A symmetry is a `change without change'. As simple as it sounds, this concept is the fundamental cornerstone that unifies all branches of theoretical physics. Virtually all physical laws -- ranging from classical mechanics and…
We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits,…
A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
Escherichia coli and Bacillus subtilis are two of the best-studied prokaryotic model organisms. Previous analyses of their transcriptional regulatory networks have shown that they exhibit high plasticity during evolution and suggested that…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
Complex networks can be understood as graphs whose connectivity deviates from those of regular or near-regular graphs, which are understood as being `simple'. While a great deal of the attention so far dedicated to complex networks has been…
Symmetries found through automorphisms or graph fibrations provide important insights in network analysis. Symmetries identify clusters of robust synchronization in the network which improves the understanding of the functionality of…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Complex networks are the subject of fundamental interest from the scientific community at large. Several metrics have been introduced to characterize the structure of these networks, such as the degree distribution, degree correlation, path…
We consider the problem of designing synthetic cells to achieve a complex goal (e.g., mimicking the immune system by seeking invaders) in a complex environment (e.g., the circulatory system), where they might have to change their control…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles…
Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple…
Understanding the mechanisms behind neural network optimization is crucial for improving network design and performance. While various optimization techniques have been developed, a comprehensive understanding of the underlying principles…