Related papers: Modules in the metabolic network of E.coli with re…
The idea that complex systems have a hierarchical modular organization originates in the early 1960s and has recently attracted fresh support from quantitative studies of large scale, real-life networks. Here we investigate the hierarchical…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
Modular structure is ubiquitous in real-world complex networks, and its detection is important because it gives insights in the structure-functionality Modular structure is ubiquitous in real-world complex networks, and its detection is…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Escherichia coli has long been a trusty companion, maintaining health in our guts and advancing biological knowledge in the laboratory. In light of recent findings, we discuss multicellular self-organization in E. coli and develop general…
To better understand the overlapping modular organization of large networks with respect to flow, here we introduce the map equation for overlapping modules. In this information-theoretic framework, we use the correspondence between…
We focus on the detection of communities in multi-scale networks, namely networks made of different levels of organization and in which modules exist at different scales. It is first shown that methods based on modularity are not…
We present an approach to study functional segregation and integration in the living brain based on community structure decomposition determined by maximum modularity. We demonstrate this method with a network derived from functional…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarse-grained description of complex systems, often revealing functional subunits of these systems. A variety…
The observed spatio-temporal ciliary beat patterns on multiciliated epithelia are suspected to be the result of self-organizing processes on various levels. Here, we present an abstract epithelium model at the pluricellular level, which…
Correlation networks derived from multivariate data appear in many applications across the sciences. These networks are usually dense and require sparsification to detect meaningful structure. However, current methods for sparsifying…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
Given a graph of interactions, a module (also called a community or cluster) is a subset of nodes whose fitness is a function of the statistical significance of the pairwise interactions of nodes in the module. The topic of this paper is a…
In this work we propose a novel algorithmic strategy that allows for an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. The algorithm, based on the well-known Bethe approximation,…
Detecting community structure is fundamental to clarify the link between structure and function in complex networks and is used for practical applications in many disciplines. A successful method relies on the optimization of a quantity…