23 papers · ranked by Valyu relevance
Carlos Espinosa-Soto, Andreas Wagner, M. Madan Babu
Organismal development and many cell biological processes are organized in a modular fashion, where regulatory molecules form groups with many interactions within a group and few interactions between groups. Thus, the activity of elements within a module depends little on elements outside of it. Modularity facilitates…
Colin R. Tosh, Luke McNally
Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a…
Borja Esteve-Altava
Form is a rich concept that agglutinates information about the proportions and topological arrangement of body parts. Modularity is readily observable in both the variation of proportions (variational modules) and the organization of topology (organizational modules). The study of variational modularity and of…
Flávia Maria Darcie Marquitti, Paulo R. Guimarães, Mathias M. Pires, Luiz F. Bittencourt
'Luiz F. Bittencourt'] Ecological systems can be seen as networks of interactions between individual, species, or habitat patches. A key feature of many ecological networks is their organization into modules, which are subsets of elements that are more connected to each other than to the other elements in the network.…
Zhihua Zhang, Jianzhi Zhang, I. King Jordan
Real networks, including biological networks, are known to have the small-world property, characterized by a small “diameter”, which is defined as the average minimal path length between all pairs of nodes in a network. Because random networks also have short diameters, one may predict that the diameter of a real…
Blai Vidiella, Salva Duran‐Nebreda, Sergi Valverde
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 represent inter-dependencies among many system components, facilitating the study of…
Sergio Antonio Alcalá-Corona, Santiago Sandoval-Motta, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
'Jesús Espinal-Enríquez' 'Enrique Hernández-Lemus'] Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide variety of…
Cong-Doan Truong, Yung-Keun Kwon
Background Biological networks consisting of molecular components and interactions are represented by a graph model. There have been some studies based on that model to analyze a relationship between structural characteristics and dynamical behaviors in signaling network. However, little attention has been paid to…
Arend Hintze, Christoph Adami
Background Much work in systems biology, but also in the analysis of social network and communication and transport infrastructure, involves an in-depth analysis of local and global properties of those networks, and how these properties relate to the function of the network within the integrated system. Most often…
Marcelo Serrano Zanetti, Frank Schweitzer
Modularity is a desirable characteristic for software systems. In this article we propose to use a quantitative method from complex network sciences to estimate the coherence between the modularity of the dependency network of large open source Java projects and their decomposition in terms of Java packages. The…
Sergi Valverde
The presence of modular organisation is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological…
Claus Kadelka, Matthew Wheeler, Alan Veliz-Cuba, David Murrugarra + 1 more
This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene…
Filip Milisav, Andrea I. Luppi, Laura E. Suárez, Guillaume Lajoie + 1 more
Modularity is a fundamental principle of brain organization, reflected in the presence of segregated sub-networks that enable specialized information processing. These small, densely connected modules are often nested within larger, higher-order modules, giving rise to a hierarchical modular architecture. This…
Md Fahmid Islam, Md Moinul Hoque, Rajat Suvra Banik, Sanjoy Roy + 5 more
'Sharmin Sultana Sumi' 'F M Nazmul Hassan' 'Md Tauhid Siddiki Tomal' 'Ahmad Ullah' 'K M Taufiqur Rahman'] Background Large scale understanding of complex and dynamic alterations in cellular and subcellular levels during cancer in contrast to normal condition has facilitated the emergence of sophisticated systemic…
Sergi Valverde
The presence of modular organization is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological…
Dirk M. Lorenz, Alice Jeng, Michael W. Deem
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may…
Carmel Farage, Daniel Edler, Anna Eklöf, Martin Rosvall + 1 more
Ecological networks often have a modular structure with groups of nodes that interact strongly within the group and weakly with other nodes in the network. A modular structure can reveal underlying dynamic ecological or evolutionary processes, influence dynamics that operate on the network, and affect network…
Kazuhiro Takemoto, Kaori Kihara
Molecular signaling networks are believed to determine cancer robustness. Although cancer patient survivability was reported to correlate with the heterogeneous connectivity of the signaling networks inspired by theoretical studies on the increase of network robustness due to the heterogeneous connectivity, other…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
Benjamin Ries, Richard J Gowers, James RB Eastwood, Irfan Alibay + 4 more
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy…
Jana Weber, Pietro Lio’, Alexei Lapkin
Networks of chemical reactions represent relationships between molecules within chemical supply chains and promise to enhance planning of multi-step synthesis routes from bio-renewable feedstocks. This study aims to identify strategic molecules in chemical reaction networks that may potentially play a significant role…
Authors not listed
Active assembly of matter is a defining trait of living systems, enabling the creation of far-from-equilibrium materials essential for the functionality of life. This is achieved through energy-dissipative, multi-step processes facilitated by various biomolecular agents for chemical and mechanical assembly of matter.…
Matthew Bailey, Mark Wilson
One of the critical tools of persistent homology is the persistence diagram. We demonstrate the applicability of a persistence diagram showing the existence of topological features (here rings in a 2D network) generated over time instead of space as a tool to analyse trajectories of biological networks. We show how the…