Measuring Information Propagation and Processing in Biological Systems

2009 ◽  
pp. 190-226
Author(s):  
Juha Kesseli ◽  
Andre S. Ribeiro ◽  
Matti Nykter
Keyword(s):  
Information Processing ◽  
Dynamical Systems ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Dynamical Behavior ◽  
Measurement Data ◽  
Distribution Data ◽  
Information Propagation ◽  
Information Management Systems ◽  
Element Activity

In this chapter the authors study the propagation and processing of information in dynamical systems. Various information management systems can be represented as dynamical systems of interconnected information processing units. Here they focus mostly on genetic regulatory networks that are information processing systems that process and propagate information stored in genome. Boolean networks are used as a dynamical model of regulation, and different ways of parameterizing the dynamical behavior are studied. What are called critical networks are in particular under study, since they have been hypothesized as being the most effective under evolutionary pressure. Critical networks are also present in man-made systems, such as the Internet, and provide a candidate application area for findings on the theory of dynamical networks in this chapter. The authors present approaches of annealed approximation and find that avalanche size distribution data supports criticality of regulatory networks. Based on Shannon information, they then find that a mutual information measure quantifying the coordination of pairwise element activity is maximized at criticality. An approach of algorithmic complexity, the normalized compression distance (NCD), is shown to be applicable to both dynamical and topological features of regulatory networks. NCD can also be seen to enable further utilization of measurement data to estimate information propagation and processing in biological networks.

Discrete Networks as a Suitable Approach for the Analysis of Genetic Regulation

2009 ◽  
pp. 530-540
Author(s):  
Elizabeth Santiago-Cortés
Keyword(s):  
Transcription Factors ◽  
Dynamical Systems ◽  
Regulatory Networks ◽  
Dynamical Behavior ◽  
Genetic Regulation ◽  
Genetic Regulatory Networks ◽  
Theoretical Studies ◽  
Biological Interpretation ◽  
Complex Dynamical Behavior ◽  
Discrete Networks

Biological systems are composed of multiple interacting elements; in particular, genetic regulatory networks are formed by genes and their interactions mediated by transcription factors. The establishment of such networks is critical to guarantee the reliability of transcriptional performance in any organism. The study of genetic regulatory networks as dynamical systems is a helpful methodology to understand the transcriptional behavior of the genome. From a number of theoretical studies, it is known that networks present a complex dynamical behavior that includes stability, redundancy, homeostasis, and multistationarity. In this chapter we present some particular biological processes modeled as discrete networks to show that the theoretical properties of networks have a clear biological interpretation.

scholarly journals Evolution in the Debian GNU/Linux software network: analogies and differences with gene regulatory networks

2020 ◽  
Vol 17 (163) ◽  
pp. 20190845
Author(s):  
Pablo Villegas ◽  
Miguel A. Muñoz ◽  
Juan A. Bonachela
Keyword(s):  
Information Processing ◽  
Gene Regulatory Networks ◽  
Biological Networks ◽  
Degree Distribution ◽  
Regulatory Networks ◽  
Average Distance ◽  
Scale Free ◽  
Software Network ◽  
Gene Regulatory ◽  
Over Time

Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural features such as scale-free degree distributions, high modularity and low average distance between connected genes. Such networks result from complex evolutionary and adaptive processes difficult to track down empirically. On the other hand, there exists detailed information on the developmental (or evolutionary) stages of open-software networks that result from self-organized growth across versions. Here, we study the evolution of the Debian GNU/Linux software network, focusing on the changes of key structural and statistical features over time. Our results show that evolution has led to a network structure in which the out-degree distribution is scale-free and the in-degree distribution is a stretched exponential. In addition, while modularity, directionality of information flow, and average distance between elements grew, vulnerability decreased over time. These features resemble closely those currently shown by gene regulatory networks, suggesting the existence of common adaptive pathways for the architectural design of information-processing networks. Differences in other hierarchical aspects point to system-specific solutions to similar evolutionary challenges.

scholarly journals Functional resilience of mutually repressing motifs embedded in larger regulatory networks

2022 ◽  
Author(s):  
Pradyumna Harlapur ◽  
Atchuta Srinivas Duddu ◽  
Kishore Hari ◽  
Mohit Kumar Jolly
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Dynamical Behavior ◽  
Design Principles ◽  
Network Motifs ◽  
Toggle Switch ◽  
Pairwise Correlation ◽  
Single Positive

Elucidating the design principles of regulatory networks driving cellular decision-making has important implications in understanding cell differentiation and guiding the design of synthetic circuits. Mutually repressing feedback loops between 'master regulators' of cell-fates can exhibit multistable dynamics, thus enabling multiple 'single-positive' phenotypes: (high A, low B) and (low A, high B) for a toggle switch, and (high A, low B, low C), (low A, high B, low C) and (low A, low B, high C) for a toggle triad. However, the dynamics of these two network motifs has been interrogated in isolation in silico, but in vitro and in vivo, they often operate while embedded in larger regulatory networks. Here, we embed these network motifs in complex larger networks of varying sizes and connectivity and identify conditions under which these motifs maintain their canonical dynamical behavior, thus identifying hallmarks of their functional resilience. We show that the in-degree of a motif - defined as the number of incoming edges onto a motif - determines its functional properties. For a smaller in-degree, the functional traits for both these motifs (bimodality, pairwise correlation coefficient(s), and the frequency of 'single-positive' phenotypes) are largely conserved, but increasing the in-degree can lead to a divergence from their stand-alone behaviors. These observations offer insights into design principles of biological networks containing these network motifs, as well as help devise optimal strategies for integration of these motifs into larger synthetic networks.

Generalized Boolean Networks

2010 ◽  
pp. 429-449 ◽  
Author(s):  
Christian Darabos ◽  
Mario Giacobini ◽  
Marco Tomassini
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Dynamical Behavior ◽  
Real Life ◽  
Network Models ◽  
Cell Types ◽  
Boolean Networks ◽  
Genetic Regulatory Networks ◽  
Point Of View ◽  
Scale Free

Random Boolean Networks (RBN) have been introduced by Kauffman more than thirty years ago as a highly simplified model of genetic regulatory networks. This extremely simple and abstract model has been studied in detail and has been shown capable of extremely interesting dynamical behavior. First of all, as some parameters are varied such as the network’s connectivity, or the probability of expressing a gene, the RBN can go through a phase transition, going from an ordered regime to a chaotic one. Kauffman’s suggestion is that cell types correspond to attractors in the RBN phase space, and only those attractors that are short and stable under perturbations will be of biological interest. Thus, according to Kauffman, RBN lying at the edge between the ordered phase and the chaotic phase can be seen as abstract models of genetic regulatory networks. The original view of Kauffman, namely that these models may be useful for understanding real-life cell regulatory networks, is still valid, provided that the model is updated to take into account present knowledge about the topology of real gene regulatory networks, and the timing of events, without loosing its attractive simplicity. According to present data, many biological networks, including genetic regulatory networks, seem, in fact, to be of the scale-free type. From the point of view of the timing of events, standard RBN update their state synchronously. This assumption is open to discussion when dealing with biologically plausible networks. In particular, for genetic regulatory networks, this is certainly not the case: genes seem to be expressed in different parts of the network at different times, according to a strict sequence, which depends on the particular network under study. The expression of a gene depends on several transcription factors, the synthesis of which appear to be neither fully synchronous nor instantaneous. Therefore, we have recently proposed a new, more biologically plausible model. It assumes a scale-free topology of the networks and we define a suitable semi-synchronous dynamics that better captures the presence of an activation sequence of genes linked to the topological properties of the network. By simulating statistical ensembles of networks, we discuss the attractors of the dynamics, showing that they are compatible with theoretical biological network models. Moreover, the model demonstrates interesting scaling abilities as the size of the networks is increased.

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

2019 ◽  
Vol 19 (6) ◽  
pp. 413-425 ◽  
Author(s):  
Athanasios Alexiou ◽  
Stylianos Chatzichronis ◽  
Asma Perveen ◽  
Abdul Hafeez ◽  
Ghulam Md. Ashraf
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Review Paper ◽  
Boolean Networks ◽  
Diagnostic Tools ◽  
Complex Nature ◽  
Cellular Interactions ◽  
Protein Protein Interactions ◽  
Deterministic Models

Background:Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems.Objective:Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically.Methods:Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations.Results:GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools.Conclusion:In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

scholarly journals Discovering governing equations from data by sparse identification of nonlinear dynamical systems

2016 ◽  
Vol 113 (15) ◽  
pp. 3932-3937 ◽  
Author(s):  
Steven L. Brunton ◽  
Joshua L. Proctor ◽  
J. Nathan Kutz
Keyword(s):  
Dynamical Systems ◽  
Nonlinear Dynamical Systems ◽  
Measurement Data ◽  
Climate Science ◽  
Model Complexity ◽  
Governing Equations ◽  
Canonical Systems ◽  
Nonlinear Dynamical ◽  
Balance Accuracy ◽  
Wide Range

Extracting governing equations from data is a central challenge in many diverse areas of science and engineering. Data are abundant whereas models often remain elusive, as in climate science, neuroscience, ecology, finance, and epidemiology, to name only a few examples. In this work, we combine sparsity-promoting techniques and machine learning with nonlinear dynamical systems to discover governing equations from noisy measurement data. The only assumption about the structure of the model is that there are only a few important terms that govern the dynamics, so that the equations are sparse in the space of possible functions; this assumption holds for many physical systems in an appropriate basis. In particular, we use sparse regression to determine the fewest terms in the dynamic governing equations required to accurately represent the data. This results in parsimonious models that balance accuracy with model complexity to avoid overfitting. We demonstrate the algorithm on a wide range of problems, from simple canonical systems, including linear and nonlinear oscillators and the chaotic Lorenz system, to the fluid vortex shedding behind an obstacle. The fluid example illustrates the ability of this method to discover the underlying dynamics of a system that took experts in the community nearly 30 years to resolve. We also show that this method generalizes to parameterized systems and systems that are time-varying or have external forcing.

scholarly journals On attracting sets in artificial networks: cross activation

2018 ◽  
Vol 16 ◽  
pp. 01005
Author(s):  
Felix Sadyrbaev
Keyword(s):  
Dynamical Systems ◽  
Differential Equations ◽  
Mathematical Models ◽  
Ordinary Differential Equations ◽  
Critical Points ◽  
Regulatory Networks ◽  
Main Diagonal ◽  
Sigmoidal Function ◽  
Genomic Regulatory Networks ◽  
Over Time

Mathematical models of artificial networks can be formulated in terms of dynamical systems describing the behaviour of a network over time. The interrelation between nodes (elements) of a network is encoded in the regulatory matrix. We consider a system of ordinary differential equations that describes in particular also genomic regulatory networks (GRN) and contains a sigmoidal function. The results are presented on attractors of such systems for a particular case of cross activation. The regulatory matrix is then of particular form consisting of unit entries everywhere except the main diagonal. We show that such a system can have not more than three critical points. At least n–1 eigenvalues corresponding to any of the critical points are negative. An example for a particular choice of sigmoidal function is considered.

Information processing and dynamical systems approaches are complementary

2002 ◽  
Vol 25 (5) ◽  
pp. 639-640
Author(s):  
David Spurrett
Keyword(s):  
Information Processing ◽  
Dynamical Systems ◽  
Systems Theory ◽  
Dynamical Systems Theory ◽  
Communication Studies ◽  
New Paradigm ◽  
Systems Approaches ◽  
False Dichotomy ◽  
Language Research ◽  
Ape Language

Shanker & King (S&K) trumpet the adoption of a “new paradigm” in communication studies, exemplified by ape language research. Though cautiously sympathetic, I maintain that their argument relies on a false dichotomy between “information” and “dynamical systems” theory, and that the resulting confusion prevents them from recognizing the main chance their line of thinking suggests.

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