Biological Networks: An Introductory Review

Abstract

All aspects of life activities in living cells are mediated/executed and regulated by a vast number of networks, comprising a wide spectrum of components, starting with simple biomolecules and ending with the whole organism, and functioning within a precisely organized tight framework. Proper mediation of cellular activities necessitates their inclusion within the context of structured and organized network systems capable of regulating/coordinating and synchronizing the countless numbers of biological processes occurring within living cells. The number of biological networks and pathways within the living cell is considerably huge, being dependent on the structural complexity and functional capabilities of the cell. Pathogenesis and progression of human diseases result from functional disturbances of biological networks within the cell as disturbed network function leads to deleterious effects on physiological processes dependent on, and mediated by, affected network(s). Ensuing pathological processes, defined by the nature of disturbed networks and the specific organs or tissues affected, pave the way for the development of pathognomonic and characteristic disease entities. As most network functions are dependent on relatively small number of key regulatory biomolecules, i.e. enzymes/proteins and signal transducing factors, it follows that functional disturbances of biological networks and pathogenesis of disease states can be attributed, in most instances, to quantitative and/or qualitative abnormalities of these key regulatory molecules. Study and analysis of the structural designs and the functional mechanisms of biological networks would have crucial and important impacts on many theoretical and applied aspects of biology, in general, and of medical sciences in particular. Meticulous study of biological networks represents an important and integral aspect in study of biology. Interpretation and analysis of key information deduced from observing and analyzing structural designs and functional characteristics and dynamics of biological networks discloses and defines the basic framework within which life activities in living cells are initiated, adapted to physiological requirements, maintained, and terminated upon completion of their aims. More important, however, is the contribution of this information to proper understanding of the different mechanisms responsible for regulating and synchronizing the functions and performances of the vast spectrum of different network categories within the cell. In addition to its vital scientific significance, discovering and defining the key pivotal structural and regulatory molecules within life-mediating networks, and along different pathways responsible for controlling functional dynamics of the network, represent an indispensable diagnostic approach insistent for designing proper therapeutic approaches to diseases caused by network defects.

Exploring the Molecular Terrain: A Survey of Analytical Methods for Biological Network Analysis

“…Simulating drug or signal spread, studying disease progression, or understanding information flow in cellular processes [1].…”

“…With the field constantly evolving and expanding, it is crucial to stay informed about new trends, methods, and uses. The figure provides a sneak peek into the upcoming directions of network analysis, highlighting essential areas of growth and potential paths for exploration [1]. By following this map, researchers and professionals can more effectively navigate the intricacies of network analysis and leverage its full capabilities to tackle diverse real-world problems.…”

“…Biological networks embody a complex interplay of molecular entities, intricately woven to form life's very fabric and underpin living organisms' functioning [1,2]. These networks, aptly termed the "molecular terrain", are a testament to the delicate balance between symmetry and asymmetry, encompassing diverse biomolecules such as proteins, metabolites, and genes.…”

Learning Patterns from Biological Networks: A Compounded Burr Probability Model

“…Clauset et al [36] analyzed various real-world datasets and demonstrated that while some datasets supported the power-law claim, others did not, using maximum-likelihood estimation and statistical tests for goodness-of-fit, utilizing Kolmogorov-Smirnov statistic and likelihood ratios. Salem [37] discussed the impact of disturbances in biological networks on disease susceptibility in living cells. Broido and Clauset [2] argued that strictly scalefree networks are rare and introduced notions of weak or strong scale-free networks.…”

Self-Organization of Enzyme-Catalyzed Reactions Studied by the Maximum Entropy Production Principle

“…The structures, functions, and kinetic properties of modern enzymes have changed considerably during evolution. Since biological evolution is widely regarded as an optimization process, the evolution of enzymes could be explained as the result of evolutionary optimization [1][2][3][4][5]. In recent decades, various optimization principles have been proposed to explain the kinetic properties of modern enzymes [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17], but a general agreement on this topic has not yet been reached among researchers.…”