相关论文: Hierarchy and Feedback in the Evolution of the E. …
Hierarchical networks are prevalent in nature and society, corresponding to groups of actors - animals, humans or even robots - organised according to a pyramidal structure with decision makers at the top and followers at the bottom. While…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Topological features of gene regulatory networks can be successfully reproduced by a model population evolving under selection for short dynamical attractors. The evolved population of networks exhibit motif statistics, summarized by…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
In biological evolution complex neural structures grow from a handful of cellular ingredients. As genomes in nature are bounded in size, this complexity is achieved by a growth process where cells communicate locally to decide whether to…
In this paper we investigate networks whose evolution is governed by the interaction of a random assembly process and an optimization process. In the first process, new nodes are added one at a time and form connections to randomly selected…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
We explain how hierarchical organization of biological systems emerges naturally during evolution, through a transition in the units of individuality. We will show how these transitions are the result of competing selective forces operating…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down…
We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
In this paper, we proposed an evolving model via the hypergraph to illustrate the evolution of the citation network. In the evolving model, we consider the mechanism combined with preferential attachment and the aging influence. Simulation…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of…