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Moved page from wikipedia:en:Biological network (history)
此词条暂由彩云小译翻译，未经人工整理和审校，带来阅读不便，请见谅。
{{Network Science}}
{{refimprove|date=October 2011}}
A '''biological network''' is any [[network science|network]] that applies to [[biological system]]s. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole [[food web]]. Biological networks provide a [[graph theory|mathematical representation]] of connections found in [[ecological network|ecological]], [[phylogenetic network|evolutionary]], and [[physiological]] studies, such as [[neural networks]].<ref name="Proulx05">{{cite journal | last1=Proulx | first1=S. R. | last2=Promislow | first2=D. E. L. | last3=Phillips | first3=P. C. | title=Network thinking in ecology and evolution | journal=Trends in Ecology and Evolution | volume=20 | issue=6 | pages=345–353 | year=2005 | doi=10.1016/j.tree.2005.04.004 | url=http://eeb19.biosci.arizona.edu/Faculty/Dornhaus/courses/materials/papers/Proulx%20Promislow%20Phillips%20networks%20ecol%20evol.pdf | pmid=16701391 | url-status=dead | archiveurl=https://web.archive.org/web/20110815122330/http://eeb19.biosci.arizona.edu/Faculty/Dornhaus/courses/materials/papers/Proulx%20Promislow%20Phillips%20networks%20ecol%20evol.pdf | archivedate=2011-08-15 }}</ref> The analysis of biological networks with respect to human diseases has led to the field of [[network medicine]].<ref>{{cite journal | last1 = Barabási | first1 = A. L. | last2 = Gulbahce | first2 = N. | last3 = Loscalzo | first3 = J. | year = 2011 | title = Network medicine: a network-based approach to human disease | url = | journal = Nature Reviews Genetics | volume = 12 | issue = 1| pages = 56–68 | doi=10.1038/nrg2918 | pmid=21164525 | pmc=3140052}}</ref><ref>{{Cite journal|last=Habibi|first=Iman|last2=Emamian|first2=Effat S.|last3=Abdi|first3=Ali|date=2014-10-07|title=Advanced Fault Diagnosis Methods in Molecular Networks|journal=PLOS ONE|volume=9|issue=10|pages=e108830|doi=10.1371/journal.pone.0108830|issn=1932-6203|pmc=4188586|pmid=25290670|bibcode=2014PLoSO...9j8830H}}</ref>
A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web. Biological networks provide a mathematical representation of connections found in ecological, evolutionary, and physiological studies, such as neural networks. The analysis of biological networks with respect to human diseases has led to the field of network medicine.
生物网络是应用于生物系统的任何网络。网络是任何系统的子单位，连接成一个整体，如物种单位连接成一个整体的食物网。生物网络提供了在生态学、进化学和生理学研究中发现的联系的数学表示，例如神经网络。与人类疾病相关的生物网络分析引领了网络医学领域的发展。
==Network biology and bioinformatics==
Complex biological systems may be represented and analyzed as computable networks. For example, ecosystems can be modeled as networks of interacting species or a protein can be modeled as a network of amino acids. Breaking a protein down farther, [[amino acids]] can be represented as a network of connected [[atom]]s, such as [[carbon]], [[nitrogen]], and [[oxygen]]. [[vertex (graph theory)|Nodes]] and [[vertex (graph theory)|edges]] are the basic components of a network. Nodes represent units in the network, while edges represent the interactions between the units. Nodes can represent a wide array of biological units, from individual organisms to individual neurons in the brain. Two important properties of a network are [[vertex (graph theory)|degree]] and [[betweenness centrality]]. Degree (or connectivity, a distinct usage from that used in [[Connectivity (graph theory)|graph theory]]) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network.<ref name="Proulx">{{cite journal |author= Proulx, S.R. |title= Network thinking in ecology and evolution |journal= Trends in Ecology and Evolution |year= 2005 |volume= 20 |issue= 6 |pages= 345–353 |doi=10.1016/j.tree.2005.04.004 |pmid=16701391|display-authors=etal}}</ref> Nodes with high betweenness essentially serve as bridges between different portions of the network (i.e. interactions must pass through this node to reach other portions of the network). In social networks, nodes with high degree or high betweenness may play important roles in the overall composition of a network.
Complex biological systems may be represented and analyzed as computable networks. For example, ecosystems can be modeled as networks of interacting species or a protein can be modeled as a network of amino acids. Breaking a protein down farther, amino acids can be represented as a network of connected atoms, such as carbon, nitrogen, and oxygen. Nodes and edges are the basic components of a network. Nodes represent units in the network, while edges represent the interactions between the units. Nodes can represent a wide array of biological units, from individual organisms to individual neurons in the brain. Two important properties of a network are degree and betweenness centrality. Degree (or connectivity, a distinct usage from that used in graph theory) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network. Nodes with high betweenness essentially serve as bridges between different portions of the network (i.e. interactions must pass through this node to reach other portions of the network). In social networks, nodes with high degree or high betweenness may play important roles in the overall composition of a network.
复杂的生物系统可以用可计算网络来表示和分析。例如，生态系统可以被模拟为相互作用的物种网络，或者蛋白质可以被模拟为氨基酸网络。进一步分解蛋白质，氨基酸可以表示为一个由相互连接的原子组成的网络，如碳、氮和氧。节点和边是网络的基本组成部分。节点表示网络中的单元，边表示单元之间的相互作用。节点可以代表一系列广泛的生物单元，从单个的生物体到大脑中单个的神经元。网络的两个重要性质是度和中心性。度(或连通性，一个不同于图论的用法)是连接一个节点的边的数量，而介于两者之间是衡量一个节点在网络中的中心位置。具有高中间性的节点本质上充当网络不同部分之间的桥梁(即。交互必须通过这个节点才能到达网络的其他部分)。在社会网络中，高度或高度介于两者之间的节点可能在网络的整体组成中发挥重要作用。
As early as the 1980s, researchers started viewing [[DNA]] or [[genome]]s as the dynamic storage of a language system with precise computable finite [[state (computer science)|states]] represented as a [[finite state machine]].<ref>{{cite book |author= Searls, D. |title= Artificial intelligence and molecular biology |publisher= MIT Press |year= 1993 |location= Cambridge, MA}}</ref> Recent [[complex system]]s research has also suggested some far-reaching commonality in the organization of information in problems from biology, [[computer science]], and [[physics]], such as the [[Bose–Einstein condensate]] (a special state of matter).<ref>{{cite journal |author1=Bianconi, G. |author2=Barabasi A. |lastauthoramp=yes |title= Bose-Einstein condensation in complex networks |journal= Phys. Rev. Lett. |year= 2001 |volume= 86 |issue= 24 |pages= 5632–5635 |doi=10.1103/physrevlett.86.5632|pmid=11415319 |arxiv=cond-mat/0011224|bibcode=2001PhRvL..86.5632B|hdl=2047/d20000696 }}</ref>
As early as the 1980s, researchers started viewing DNA or genomes as the dynamic storage of a language system with precise computable finite states represented as a finite state machine. Recent complex systems research has also suggested some far-reaching commonality in the organization of information in problems from biology, computer science, and physics, such as the Bose–Einstein condensate (a special state of matter).
早在20世纪80年代，研究人员就开始将 DNA 或基因组视为一个语言系统的动态存储，其精确的可计算有限状态表示为一个有限状态机。最近的复杂系统研究还表明，在生物学、计算机科学和物理学等问题的信息组织方面存在一些意义深远的共性，例如玻色-爱因斯坦凝聚态(一种特殊的物质状态)。
Bioinformatics has increasingly shifted its focus from individual [[gene]]s, proteins, and [[search algorithm]]s to large-scale networks often denoted as [[omics|-omes]] such as [[biome]], [[interactome]], [[genome]] and [[proteome]]. Such theoretical studies have revealed that biological networks share many features with other networks such as the [[Internet]] or [[social network]]s, e.g. their [[network topology]].
Bioinformatics has increasingly shifted its focus from individual genes, proteins, and search algorithms to large-scale networks often denoted as -omes such as biome, interactome, genome and proteome. Such theoretical studies have revealed that biological networks share many features with other networks such as the Internet or social networks, e.g. their network topology.
生物信息学的重点已经从单个基因、蛋白质和搜索算法逐渐转移到大规模网络，这些网络通常被称为生物组、交叉组、基因组和蛋白质组。这些理论研究揭示了生物网络与其他网络如互联网或社交网络有许多共同特征，例如:。他们的网络拓扑。
==Networks in biology==
===Protein–protein interaction networks===
{{main article|interactome}}
Many [[protein–protein interaction]]s (PPIs) in a cell form ''protein interaction networks'' (PINs) where proteins are ''nodes'' and their interactions are ''edges''.<ref>{{Cite journal|last=Habibi|first=Iman|last2=Emamian|first2=Effat S.|last3=Abdi|first3=Ali|date=2014-01-01|title=Quantitative analysis of intracellular communication and signaling errors in signaling networks|journal=BMC Systems Biology|volume=8|pages=89|doi=10.1186/s12918-014-0089-z|issn=1752-0509|pmc=4255782|pmid=25115405}}</ref> PINs are the most intensely analyzed networks in biology. There are dozens of PPI detection methods to identify such interactions. The [[Y2H|yeast two-hybrid system]] is a commonly used experimental technique for the study of binary interactions.<ref>{{cite journal |author= Mashaghi, A. |title= Investigation of a protein complex network |journal= European Physical Journal |year= 2004 |volume= 41 |issue= 1 |pages= 113–121 |doi=10.1140/epjb/e2004-00301-0|display-authors=etal|arxiv= cond-mat/0304207|bibcode= 2004EPJB...41..113M}}</ref>
Many protein–protein interactions (PPIs) in a cell form protein interaction networks (PINs) where proteins are nodes and their interactions are edges. PINs are the most intensely analyzed networks in biology. There are dozens of PPI detection methods to identify such interactions. The yeast two-hybrid system is a commonly used experimental technique for the study of binary interactions.
许多蛋白质-蛋白质相互作用(ppi)在细胞中形成蛋白质相互作用网络(pin) ，其中蛋白质是节点，它们的相互作用是边缘。个人识别码是生物学中分析最深入的网络。有几十种 PPI 检测方法来识别这种相互作用。酵母双杂交系统是研究二元相互作用的常用实验技术。
Recent studies have indicated conservation of molecular networks through deep evolutionary time.<ref>{{cite journal |author= Sharan, R. |title= Conserved patterns of protein interaction in multiple species |journal= Proceedings of the National Academy of Sciences of the United States of America |year= 2005 |volume= 102 |issue= 6 |pages= 1974–1979 |doi=10.1073/pnas.0409522102|pmid= 15687504 |display-authors=etal|pmc= 548573|bibcode= 2005PNAS..102.1974S}}</ref> Moreover, it has been discovered that proteins with high degrees of connectedness are more likely to be essential for survival than proteins with lesser degrees.<ref>{{cite journal |author= Jeong, H. |title= Lethality and centrality in protein networks |journal= Nature |year= 2001 |volume= 411 |issue= 6833 |pages= 41–42 |doi=10.1038/35075138 |pmid=11333967|display-authors=etal|bibcode= 2001Natur.411...41J |arxiv= cond-mat/0105306 }}</ref> This suggests that the overall composition of the network (not simply interactions between protein pairs) is important for the overall functioning of an organism.
Recent studies have indicated conservation of molecular networks through deep evolutionary time. Moreover, it has been discovered that proteins with high degrees of connectedness are more likely to be essential for survival than proteins with lesser degrees. This suggests that the overall composition of the network (not simply interactions between protein pairs) is important for the overall functioning of an organism.
近年来的研究表明，分子网络在深层进化过程中是守恒的。此外，已经发现高连通性的蛋白质比低连通性的蛋白质更有可能是生存所必需的。这表明网络的整体组成(不仅仅是蛋白质对之间的相互作用)对于有机体的整体功能是重要的。
===Gene regulatory networks (DNA–protein interaction networks)===
{{main article| Gene regulatory network}}
The activity of genes is regulated by [[transcription factors]], proteins that typically bind to [[DNA]]. Most transcription factors bind to multiple binding sites in a [[genome]]. As a result, all cells have complex [[gene regulatory networks]]. For instance, the [[human genome]] encodes on the order of 1,400 DNA-binding transcription factors that regulate the expression of more than 20,000 human genes.<ref>{{cite journal |author= Vaquerizas, J.-M. |title= A census of human transcription factors: function, expression and evolution |journal= Nature Reviews Genetics |year= 2009 |volume= 10 |issue= 4 |pages= 252–263 |pmid= 19274049 |doi=10.1038/nrg2538|display-authors=etal}}</ref> Technologies to study gene regulatory networks include [[ChIP-chip]], [[ChIP-seq]], [[CliP-seq]], and others.
The activity of genes is regulated by transcription factors, proteins that typically bind to DNA. Most transcription factors bind to multiple binding sites in a genome. As a result, all cells have complex gene regulatory networks. For instance, the human genome encodes on the order of 1,400 DNA-binding transcription factors that regulate the expression of more than 20,000 human genes. Technologies to study gene regulatory networks include ChIP-chip, ChIP-seq, CliP-seq, and others.
基因的活性受转录因子调节，转录因子是典型的与 DNA 结合的蛋白质。大多数转录因子与基因组中的多个结合位点结合。因此，所有的细胞都有复杂的基因调控网络。例如，人类基因组编码1400个 dna 结合转录因子，调节超过20000个人类基因的表达。研究基因调控网络的技术包括 ChIP-chip、 ChIP-seq、 CliP-seq 等。
===Gene co-expression networks (transcript–transcript association networks)===
{{main article| Gene co-expression networks}}
Gene co-expression networks can be interpreted as association networks between variables that measure transcript abundances. These networks have been used to provide a systems biologic analysis of DNA microarray data, RNA-seq data, miRNA data etc.
Gene co-expression networks can be interpreted as association networks between variables that measure transcript abundances. These networks have been used to provide a systems biologic analysis of DNA microarray data, RNA-seq data, miRNA data etc.
基因共同表达网络可以解释为变量之间的关联网络，衡量转录丰度。这些网络已经被用于提供 DNA 微阵列数据、 RNA-seq 数据、 miRNA 数据等的系统生物学分析。
[[Weighted correlation network analysis|weighted gene co-expression network analysis]] is widely used to identify co-expression modules and intramodular hub genes. Co-expression modules may correspond to cell types or pathways. Highly connected intramodular hubs can be interpreted as representatives of their respective module.
weighted gene co-expression network analysis is widely used to identify co-expression modules and intramodular hub genes. Co-expression modules may correspond to cell types or pathways. Highly connected intramodular hubs can be interpreted as representatives of their respective module.
加权基因共表达网络分析被广泛应用于鉴定共表达模块和模块内核心基因。共表达模块可能对应于细胞类型或通路。高度连接的模块内集线器可以解释为其各自模块的代表。
===Metabolic networks===
{{main article|metabolic network}}
The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by [[enzymes]]. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called [[metabolic network]]. It is possible to use network analyses to infer how selection acts on metabolic pathways.<ref name="Proulx" />
The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways.
活细胞中的化合物通过生物化学反应相互连接，将一种化合物转化为另一种化合物。这些反应是由酶催化的。因此，一个细胞中的所有化合物都是一个复杂的生物化学反应网络的一部分，这个网络被称为代谢网络。使用网络分析来推断选择如何影响代谢途径是可能的。
===Signaling networks===
{{main article|Cell signaling}}
Signals are transduced within cells or in between cells and thus form complex signaling networks. For instance, in the [[MAPK/ERK pathway]] is transduced from the cell surface to the cell nucleus by a series of protein–protein interactions, phosphorylation reactions, and other events. Signaling networks typically integrate [[interactome|protein–protein interaction networks]], [[gene regulatory networks]], and [[metabolic network]]s.
Signals are transduced within cells or in between cells and thus form complex signaling networks. For instance, in the MAPK/ERK pathway is transduced from the cell surface to the cell nucleus by a series of protein–protein interactions, phosphorylation reactions, and other events. Signaling networks typically integrate protein–protein interaction networks, gene regulatory networks, and metabolic networks.
信号在细胞内或细胞之间传递，从而形成复杂的信号网络。例如，MAPK/ERK 通路通过一系列蛋白质-蛋白质相互作用、磷酸化反应和其他事件从细胞表面传递到细胞核。信号网络通常整合蛋白质-蛋白质相互作用网络、基因调控网络和代谢网络。
===Neuronal networks===
{{main article| Biological neural network}}
The complex interactions in the [[brain]] make it a perfect candidate to apply network theory. [[Neuron]]s in the brain are deeply connected with one another and this results in complex networks being present in the structural and functional aspects of the brain.<ref>{{cite journal |author1=Bullmore, E. |author2=O. Sporns |lastauthoramp=yes |title= Complex brain networks: graph theoretical analysis of structural and functional systems |journal= Nature Reviews Neuroscience |year= 2009 |volume= 10 |issue= 3 |pages= 186–198 |doi=10.1038/nrn2575 |pmid=19190637}}</ref> For instance, [[small-world network]] properties have been demonstrated in connections between cortical areas of the primate brain<ref>{{cite journal |author= Stephan, K.E. |title= Computational analysis of functional connectivity between areas of primate cerebral cortex |journal= [[Philosophical Transactions of the Royal Society B]]|year= 2000 |volume= 355 |issue= 1393 |pages= 111–126 |doi=10.1098/rstb.2000.0552|pmid= 10703047 |display-authors=etal|pmc= 1692715}}</ref> or during swallowing in humans.<ref>{{Cite journal|date=2016-12-01|title=Functional connectivity patterns of normal human swallowing: difference among various viscosity swallows in normal and chin-tuck head positions|journal=Brain Research|volume=1652|pages=158–169|doi=10.1016/j.brainres.2016.09.041|pmid=27693396|pmc=5102805|issn=0006-8993|last1=Jestrović|first1=Iva|last2=Coyle|first2=James L|last3=Perera|first3=Subashan|last4=Sejdić|first4=Ervin}}</ref> This suggests that cortical areas of the brain are not directly interacting with each other, but most areas can be reached from all others through only a few interactions.
The complex interactions in the brain make it a perfect candidate to apply network theory. Neurons in the brain are deeply connected with one another and this results in complex networks being present in the structural and functional aspects of the brain. For instance, small-world network properties have been demonstrated in connections between cortical areas of the primate brain or during swallowing in humans. This suggests that cortical areas of the brain are not directly interacting with each other, but most areas can be reached from all others through only a few interactions.
大脑中复杂的相互作用使其成为应用网络理论的完美候选者。大脑中的神经元彼此之间有着深刻的联系，这导致了大脑结构和功能方面的复杂网络。例如，灵长类动物大脑皮层区域之间的连接或者人类吞咽时的吞咽活动已经证明了小世界网络属性。这表明大脑皮层区域之间并不直接相互作用，但大部分区域可以通过少量的相互作用从所有其他区域到达。
===Food webs===
{{main article|Food web}}
All organisms are connected to each other through feeding interactions. That is, if a species eats or is eaten by another species, they are connected in an intricate [[food web]] of predator and prey interactions. The stability of these interactions has been a long-standing question in ecology.<ref>{{cite journal |author= MacArthur, R.H. |author-link= Robert MacArthur|title= Fluctuations in animal populations and a measure of community stability |journal= Ecology |year= 1955 |volume= 36 |issue= 3 |pages= 533–536 |doi=10.2307/1929601|jstor= 1929601}}</ref> That is to say, if certain individuals are removed, what happens to the network (i.e. does it collapse or adapt)? Network analysis can be used to explore food web stability and determine if certain network properties result in more stable networks. Moreover, network analysis can be used to determine how selective removals of species will influence the food web as a whole.<ref>{{cite journal |author= Dunne, J.A. |title= Network structure and biodiversity loss in food webs: robustness increases with connectance |journal= Ecology Letters |year= 2002 |volume= 5 |issue= 4 |pages= 558–567 |doi=10.1046/j.1461-0248.2002.00354.x|display-authors=etal}}</ref> This is especially important considering the potential species loss due to global climate change.
All organisms are connected to each other through feeding interactions. That is, if a species eats or is eaten by another species, they are connected in an intricate food web of predator and prey interactions. The stability of these interactions has been a long-standing question in ecology. That is to say, if certain individuals are removed, what happens to the network (i.e. does it collapse or adapt)? Network analysis can be used to explore food web stability and determine if certain network properties result in more stable networks. Moreover, network analysis can be used to determine how selective removals of species will influence the food web as a whole. This is especially important considering the potential species loss due to global climate change.
所有的生物都是通过食物的相互作用联系在一起的。也就是说，如果一个物种吃了另一个物种或被另一个物种吃了，它们就在一个复杂的捕食者和猎物相互作用的食物网中联系起来。这些相互作用的稳定性一直是生态学中的一个长期问题。也就是说，如果某些个体被移除，那么网络(即。它是崩溃还是适应) ？网络分析可以用来探索食物网的稳定性，并确定某些网络特性是否会导致更稳定的网络。此外，网络分析可以用来确定物种的选择性迁移将如何影响整个食物网。考虑到全球气候变化可能造成的物种损失，这一点尤其重要。
===Between-species interaction networks===
{{main article|social relation}}
In biology, pairwise interactions have historically been the focus of intense study. With the recent advances in [[network science]], it has become possible to scale up pairwise interactions to include individuals of many species involved in many sets of interactions to understand the structure and function of larger [[ecological network]]s.<ref>{{cite journal |author= Bascompte, J. |title= Disentangling the web of life |journal= Science |year= 2009 |volume=325 |issue= 5939 |pages= 416–419 |doi=10.1126/science.1170749 |pmid=19628856|bibcode=2009Sci...325..416B }}</ref> The use of [[Social network analysis|network analysis]] can allow for both the discovery and understanding how these complex interactions link together within the system’s network, a property which has previously been overlooked. This powerful tool allows for the study of various types of interactions (from [[competitive]] to [[cooperative]]) using the same general framework.<ref>{{cite journal |author= Krause, J. |title= Animal social networks: an introduction |journal= Behav. Ecol. Sociobiol. |year= 2009 |volume= 63 |issue= 7 |pages= 967–973 |doi=10.1007/s00265-009-0747-0|display-authors=etal}}</ref> For example, plant-[[pollinator]] interactions are mutually beneficial and often involve many different species of pollinators as well as many different species of plants. These interactions are critical to plant reproduction and thus the accumulation of resources at the base of the [[food chain]] for primary consumers, yet these interaction networks are threatened by [[Human impact on the environment|anthropogenic]] change. The use of network analysis can illuminate how [[pollination network]]s work and may in turn inform conservation efforts.<ref name="Memmott, J., et al. 2004 2605-261">{{cite journal |author= Memmott, J. |title= Tolerance of pollination networks to species extinctions |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2004 |volume= 271 |issue= 1557 |pages= 2605–261 |doi=10.1098/rspb.2004.2909|pmid= 15615687 |pmc= 1691904 |display-authors=etal}}</ref> Within pollination networks, nestedness (i.e., specialists interact with a subset of species that generalists interact with), redundancy (i.e., most plants are pollinated by many pollinators), and [[modularity (networks)|modularity]] play a large role in network stability.<ref name="Memmott, J., et al. 2004 2605-261"/><ref name="Olesen, J., et al. 2007 19891–19896">{{cite journal |author= Olesen, J. |title= The modularity of pollination networks |journal= PNAS |year= 2007 |volume= 104 |issue= 50 |pages= 19891–19896 |doi=10.1073/pnas.0706375104|pmid= 18056808 |pmc= 2148393 |display-authors=etal|bibcode= 2007PNAS..10419891O }}</ref> These network properties may actually work to slow the spread of disturbance effects through the system and potentially buffer the pollination network from anthropogenic changes somewhat.<ref name="Olesen, J., et al. 2007 19891–19896"/> More generally, the structure of species interactions within an ecological network can tell us something about the diversity, richness, and robustness of the network.<ref>{{cite journal |author= Campbell, V. |title= Experimental design and the outcome and interpretation of diversity-stability relations |journal= Oikos |year= 2011 |volume= 120 |issue= 3 |pages= 399–408 |doi=10.1111/j.1600-0706.2010.18768.x|display-authors=etal}}</ref> Researchers can even compare current constructions of species interactions networks with historical reconstructions of ancient networks to determine how networks have changed over time.<ref>{{cite journal |author= Lotze, H. |title= Historical changes in marine resources, food-web structure and ecosystem functioning in the Adriatic Sea, Mediterranean |journal= Ecosystems |year= 2011 |volume= 14 |issue= 2 |pages= 198–222 |doi=10.1007/s10021-010-9404-8|display-authors=etal}}</ref> Recent research into these complex species interactions networks is highly concerned with understanding what factors (e.g., diversity) lead to network stability.<ref>{{cite journal |author= Romanuk, T. |title= Maintenance of positive diversity-stability relations along a gradient of environmental stress |journal= PLoS ONE |year= 2010 |volume= 5 |issue= 4 |pages= e10378 |doi=10.1371/journal.pone.0010378|display-authors=etal |pmid=20436913 |pmc=2860506|bibcode=2010PLoSO...510378R }}</ref>
In biology, pairwise interactions have historically been the focus of intense study. With the recent advances in network science, it has become possible to scale up pairwise interactions to include individuals of many species involved in many sets of interactions to understand the structure and function of larger ecological networks. The use of network analysis can allow for both the discovery and understanding how these complex interactions link together within the system’s network, a property which has previously been overlooked. This powerful tool allows for the study of various types of interactions (from competitive to cooperative) using the same general framework. For example, plant-pollinator interactions are mutually beneficial and often involve many different species of pollinators as well as many different species of plants. These interactions are critical to plant reproduction and thus the accumulation of resources at the base of the food chain for primary consumers, yet these interaction networks are threatened by anthropogenic change. The use of network analysis can illuminate how pollination networks work and may in turn inform conservation efforts. Within pollination networks, nestedness (i.e., specialists interact with a subset of species that generalists interact with), redundancy (i.e., most plants are pollinated by many pollinators), and modularity play a large role in network stability. These network properties may actually work to slow the spread of disturbance effects through the system and potentially buffer the pollination network from anthropogenic changes somewhat. Researchers can even compare current constructions of species interactions networks with historical reconstructions of ancient networks to determine how networks have changed over time. Recent research into these complex species interactions networks is highly concerned with understanding what factors (e.g., diversity) lead to network stability.
在生物学中，成对相互作用历来是密集研究的焦点。随着网络科学的最新进展，已经有可能扩大成对的相互作用，以包括许多物种的个体参与多组相互作用，从而理解更大的生态网络的结构和功能。使用网络分析可以发现和理解这些复杂的交互如何在系统的网络中连接在一起，这是以前被忽视的属性。这个强大的工具允许使用相同的总体框架研究各种类型的交互(从竞争到合作)。例如，植物与传粉者之间的相互作用是互惠互利的，通常涉及许多不同种类的传粉者以及许多不同种类的植物。这些相互作用对植物生殖和初级消费者食物链底层的资源积累至关重要，然而这些相互作用网络受到人为变化的威胁。网络分析的使用可以说明授粉网络是如何工作的，反过来也可以为保护工作提供信息。在授粉网络中，内嵌性(即专家与多面手相互作用的物种子集相互作用)、冗余性(即大多数植物是由许多授粉者授粉的)和模块性在网络稳定性中扮演着重要角色。这些网络属性实际上可以减缓干扰效应通过系统的传播，并可能缓冲授粉网络的人为变化。研究人员甚至可以将物种相互作用网络的现有结构与古代网络的历史重建进行比较，以确定网络随着时间的推移是如何发生变化的。最近对这些复杂物种间相互作用网络的研究高度关注于理解什么因素(如多样性)导致网络的稳定性。
===Within-species interaction networks===
{{main article|social relation}}
Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level.<ref>{{cite journal |author= Croft, D.P |title= Social networks in the guppy (Poecilia reticulate) |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2004 |volume= 271 |issue= Suppl |pages= S516–S519 |doi=10.1098/rsbl.2004.0206|pmid= 15801620 |pmc= 1810091 |display-authors=etal}}</ref> One of the most attractive features of the network paradigm would be that it provides a single conceptual framework in which the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.) can be studied.<ref>{{Cite journal|last=Krause, Lusseau, James|first=Jens, David, Richard|date=1 May 2009|title=Animal social networks: an introduction|url=https://www.researchgate.net/publication/226996156_Animal_social_networks_An_introduction|journal=Behavioral Ecology and Sociobiology|volume=63|pages=967-973|doi=10.1007/s00265-009-0747-0|via=}}</ref>
Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level. One of the most attractive features of the network paradigm would be that it provides a single conceptual framework in which the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.) can be studied.
网络分析提供了量化个体之间关联的能力，这使得在物种和/或种群水平上推断整个网络的细节成为可能。网络范式最吸引人的特征之一是，它提供了一个单一的概念框架，其中动物的社会组织在所有层次(个人，二元，群体，人口)和所有类型的互动(攻击性，合作，性等。)可以研究。
Researchers interested in [[ethology]] across a multitude of taxa, from insects to primates, are starting to incorporate network analysis into their research. Researchers interested in social insects (e.g., ants and bees) have used network analyses to better understand division of labor, task allocation, and foraging optimization within colonies;<ref>{{cite journal |author= Dornhaus, A. |title= Benefits of recruitment in honey bees: Effects of ecology and colony size in an individual-based model |journal= Behavioral Ecology |year= 2006 |volume=17 |issue= 3 |pages= 336–344 |doi=10.1093/beheco/arj036|display-authors=etal|doi-access= free }}</ref><ref>{{cite journal |author= Linksvayer, T. |title= Developmental evolution in social insects: Regulatory networks from genes to societies |journal= Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |year= 2012 |volume=318 |issue= 3 |pages= 159–169 |doi=10.1002/jez.b.22001|pmid= 22544713 |display-authors=etal}}</ref><ref>{{cite journal |author= Mullen, R. |title= A review of ant algorithms |journal= Expert Systems with Applications |year= 2009 |volume=36 |issue= 6 |pages= 9608–9617 |doi=10.1016/j.eswa.2009.01.020|display-authors=etal}}</ref> Other researchers are interested in how certain network properties at the group and/or population level can explain individual level behaviors. Studies have demonstrated how animal social network structure can be influenced by factors ranging from characteristics of the environment to characteristics of the individual, such as developmental experience and personality. At the level of the individual, the patterning of social connections can be an important determinant of [[Fitness (biology)|fitness]], predicting both survival and reproductive success. At the population level, network structure can influence the patterning of ecological and evolutionary processes, such as [[frequency-dependent selection]] and disease and information transmission.<ref>{{Cite journal|last=Croft, Darden, Wey|first=Darren P., Safi K., Tina W.|date=2016|title=Current directions in animal social networks|url=https://www.researchgate.net/publication/310819524_Current_directions_in_animal_social_networks|journal=Current Opinion in Behavioral Sciences|volume=12|pages=52-58|doi=10.1016/j.cobeha.2016.09.001|via=|hdl=10871/23348|hdl-access=free}}</ref> For instance, a study on [[Wire-tailed manakin|wire-tailed manakins]] (a small passerine bird) found that a male’s [[degree (graph theory)|degree]] in the network largely predicted the ability of the male to rise in the social hierarchy (i.e. eventually obtain a territory and matings).<ref>{{cite journal |author= Ryder, T.B. |title= Social networks in the lek-mating wire-tailed manakin (''Pipra filicauda'') |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2008 |volume= 275 |issue= 1641 |pages= 1367–1374 |doi=10.1098/rspb.2008.0205 |pmid=18381257 |pmc=2602714|display-authors=etal}}</ref> In [[bottlenose dolphin]] groups, an individual’s degree and [[betweenness centrality]] values may predict whether or not that individual will exhibit certain behaviors, like the use of side flopping and upside-down lobtailing to lead group traveling efforts; individuals with high betweenness values are more connected and can obtain more information, and thus are better suited to lead group travel and therefore tend to exhibit these signaling behaviors more than other group members.<ref>{{cite journal |author= Lusseau, D. |title= Evidence for social role in a dolphin social network |journal= Evolutionary Ecology |year= 2007 |volume=21 |issue= 3 |pages= 357–366 |doi=10.1007/s10682-006-9105-0|arxiv= q-bio/0607048 }}</ref>
Researchers interested in ethology across a multitude of taxa, from insects to primates, are starting to incorporate network analysis into their research. Researchers interested in social insects (e.g., ants and bees) have used network analyses to better understand division of labor, task allocation, and foraging optimization within colonies; Other researchers are interested in how certain network properties at the group and/or population level can explain individual level behaviors. Studies have demonstrated how animal social network structure can be influenced by factors ranging from characteristics of the environment to characteristics of the individual, such as developmental experience and personality. At the level of the individual, the patterning of social connections can be an important determinant of fitness, predicting both survival and reproductive success. At the population level, network structure can influence the patterning of ecological and evolutionary processes, such as frequency-dependent selection and disease and information transmission. For instance, a study on wire-tailed manakins (a small passerine bird) found that a male’s degree in the network largely predicted the ability of the male to rise in the social hierarchy (i.e. eventually obtain a territory and matings). In bottlenose dolphin groups, an individual’s degree and betweenness centrality values may predict whether or not that individual will exhibit certain behaviors, like the use of side flopping and upside-down lobtailing to lead group traveling efforts; individuals with high betweenness values are more connected and can obtain more information, and thus are better suited to lead group travel and therefore tend to exhibit these signaling behaviors more than other group members.
从昆虫到灵长类动物，研究人员对动物行为学感兴趣，并开始将网络分析纳入他们的研究中。对社会性昆虫(如蚂蚁和蜜蜂)感兴趣的研究人员利用网络分析来更好地理解群体内的分工、任务分配和觅食优化; 其他研究人员则对群体和/或种群水平的某些网络特性如何解释个体水平的行为感兴趣。研究表明，动物的社会网络结构是如何受到从环境特征到个体特征，如发展经验和人格等因素的影响。在个体层面上，社会联系的模式可能是适应性的一个重要决定因素，预测生存和繁殖的成功。在种群水平上，网络结构可以影响生态和进化过程的模式，如频率依赖性选择和疾病及信息传递。例如，一项针对线尾 manakins (一种小型雀形目鸟)的研究发现，雄性网络中的学位在很大程度上预测了雄性在社会等级中上升的能力(即,。最终获得领地和交配)。在宽吻海豚群体中，个体的程度和中介中心性价值观可以预测个体是否会表现出某些行为，比如使用侧翻和倒挂龙虾来领导团队旅行; 中介价值观较高的个体相互联系更多，可以获得更多信息，因此更适合领导团队旅行，因此比其他团队成员更容易表现出这些信号传递行为。
[[Social network analysis]] can also be used to describe the social organization within a species more generally, which frequently reveals important proximate mechanisms promoting the use of certain behavioral strategies. These descriptions are frequently linked to ecological properties (e.g., resource distribution). For example, network analyses revealed subtle differences in the group dynamics of two related equid [[fission-fusion society|fission-fusion]] species, [[Grevy’s zebra]] and [[onager]]s, living in variable environments; Grevy’s zebras show distinct preferences in their association choices when they fission into smaller groups, whereas onagers do not.<ref>{{cite journal |author= Sundaresan, S. |title= Network metrics reveal differences in social organization between two fission-fusion species, Grevy's zebra and onager |journal= Oecologia |year= 2007 |volume= 151 |issue= 1 |pages= 140–149 |doi=10.1007/s00442-006-0553-6|pmid= 16964497 |display-authors=etal|bibcode= 2007Oecol.151..140S }}</ref> Similarly, researchers interested in primates have also utilized network analyses to compare social organizations across the diverse [[primate]] order, suggesting that using network measures (such as [[centrality]], [[assortativity]], [[modularity (networks)|modularity]], and betweenness) may be useful in terms of explaining the types of social behaviors we see within certain groups and not others.<ref>{{cite journal |author1=Kasper, C. |author2=Voelkl, B. |title= A social network analysis of primate groups |journal= Primates |year= 2009 |volume= 50 |issue=4 |pages= 343–356 |doi=10.1007/s10329-009-0153-2|pmid=19533270 }}</ref>
Social network analysis can also be used to describe the social organization within a species more generally, which frequently reveals important proximate mechanisms promoting the use of certain behavioral strategies. These descriptions are frequently linked to ecological properties (e.g., resource distribution). For example, network analyses revealed subtle differences in the group dynamics of two related equid fission-fusion species, Grevy’s zebra and onagers, living in variable environments; Grevy’s zebras show distinct preferences in their association choices when they fission into smaller groups, whereas onagers do not. Similarly, researchers interested in primates have also utilized network analyses to compare social organizations across the diverse primate order, suggesting that using network measures (such as centrality, assortativity, modularity, and betweenness) may be useful in terms of explaining the types of social behaviors we see within certain groups and not others.
社会网络分析也可以用来更广泛地描述一个物种内的社会组织，它经常揭示促进某些行为策略的使用的重要的近似机制。这些描述经常与生态属性(例如，资源分配)联系在一起。例如，网络分析揭示了生活在变化环境中的两个相关的等分裂融合物种——格雷维斑马和骑驴——的群体动力学的细微差异; 格雷维斑马在分裂为较小的群体时，在关联选择上表现出明显的偏好，而骑驴则不然。同样，对灵长类动物感兴趣的研究人员也利用网络分析来比较不同灵长类动物的社会组织，这表明使用网络测量(如集中性、协调性、模块性和介于性)可能有助于解释我们在某些群体中看到的社会行为类型，而不是其他群体。
Finally, social network analysis can also reveal important fluctuations in animal behaviors across changing environments. For example, network analyses in female [[chacma baboon]]s (''Papio hamadryas ursinus'') revealed important dynamic changes across seasons which were previously unknown; instead of creating stable, long-lasting social bonds with friends, baboons were found to exhibit more variable relationships which were dependent on short-term contingencies related to group level dynamics as well as environmental variability.<ref>{{cite journal |author= Henzi, S. |title= Cyclicity in the structure of female baboon social networks |journal= Behavioral Ecology and Sociobiology |year= 2009 |volume= 63 |issue= 7 |pages= 1015–1021 |doi=10.1007/s00265-009-0720-y|display-authors=etal}}</ref> Changes in an individual's social network environment can also influence characteristics such as 'personality': for example, social spiders that huddle with bolder neighbours tend to increase also in boldness.<ref>{{cite journal |author= Hunt, ER. |title= Social interactions shape individual and collective personality in social spiders |journal= Proceedings of the Royal Society B |year= 2018 |volume= 285 |issue= 1886 |pages= 20181366 |doi=10.1098/rspb.2018.1366|pmid= 30185649 |pmc= 6158534 |display-authors=etal}}</ref> This is a very small set of broad examples of how researchers can use network analysis to study animal behavior. Research in this area is currently expanding very rapidly, especially since the broader development of animal borne tags and [[computer vision]] that can be used to automate the collection of social associations.<ref>{{Cite journal|last=Krause J, Krause S, Arlinghaus R, Psorakis I, Roberts S, Rutz C|first=|date=2013|title=Reality mining of animal social systems.|url=https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reality-mining-of-animal-social-systems(570e21d0-527e-4275-8926-c4b479c55ee4).html|journal=Trends in Ecology and Evolution|volume=28|pages=541-551|doi=10.1016/j.tree.2013.06.002|via=}}</ref> Social network analysis is a valuable tool for studying animal behavior across all animal species, and has the potential to uncover new information about animal behavior and social ecology that was previously poorly understood.
Finally, social network analysis can also reveal important fluctuations in animal behaviors across changing environments. For example, network analyses in female chacma baboons (Papio hamadryas ursinus) revealed important dynamic changes across seasons which were previously unknown; instead of creating stable, long-lasting social bonds with friends, baboons were found to exhibit more variable relationships which were dependent on short-term contingencies related to group level dynamics as well as environmental variability. Changes in an individual's social network environment can also influence characteristics such as 'personality': for example, social spiders that huddle with bolder neighbours tend to increase also in boldness. This is a very small set of broad examples of how researchers can use network analysis to study animal behavior. Research in this area is currently expanding very rapidly, especially since the broader development of animal borne tags and computer vision that can be used to automate the collection of social associations. Social network analysis is a valuable tool for studying animal behavior across all animal species, and has the potential to uncover new information about animal behavior and social ecology that was previously poorly understood.
最后，社会网络分析还可以揭示动物行为在不断变化的环境中的重要波动。例如，对雌性沙卡马狒狒(Papio hamadryas ursinus)的网络分析揭示了以前未知的跨季节的重要动态变化; 结果发现，狒狒与朋友之间没有建立稳定、持久的社会联系，而是表现出更多的变化关系，这些关系依赖于与群体层面动态以及环境变化有关的短期偶然事件。个体社交网络环境的变化也会影响个体的性格特征，例如，与胆大的邻居挤在一起的社交蜘蛛也会更加大胆。这只是研究人员如何利用网络分析来研究动物行为的一小部分广泛的例子。这一领域的研究目前正在迅速扩展，特别是随着动物身上的标签和计算机视觉技术的广泛发展，这些技术可以用来自动收集社会关系。社会网络分析是研究所有动物物种的动物行为的一个有价值的工具，并且有可能发现以前鲜为人知的关于动物行为和社会生态的新信息。
==See also==
* [[List of omics topics in biology]]
* [[Biological network inference]]
* [[Applied Statistics]]
* [[Biostatistics]]
* [[Computational Biology]]
* [[Systems biology]]
* [[Weighted correlation network analysis]]
* [[Interactome]]
* [[Network medicine]]
== External links ==
* [http://www.nettab.org Network Tools and Applications in Biology] (NETTAB) workshops.
==References==
{{Reflist}}
==Books==
*E. Estrada, "The Structure of Complex Networks: Theory and Applications", Oxford University Press, 2011, {{ISBN|978-0-199-59175-6}}
*J. Krause, R. James, D. Franks, D. Croft, "Animal Social Networks", Oxford University Press, 2015, {{ISBN|978-0199679041}}
==External links==
* [https://web.archive.org/web/20110920220214/http://www.networkbio.org/ Networkbio.org], The site of the series of Integrative Network Biology (INB) meetings. For the 2012 event also see www.networkbio.org
* [http://networkbiology.org Networkbiology.org], NetworkBiology wiki site.
* [http://www.lindinglab.org LindingLab.org], Technical University of Denmark (DTU) studies Network Biology and Cellular Information Processing, and is also organizing the Denmark branch of the annual "[http://www.lindinglab.org/events ''Integrative Network Biology and Cancer'']" symposium series.
* [http://nrnb.org NRNB.org], The National Resource for Network Biology. A US National Institute of Health (NIH) Biomedical Technology Research Center dedicated to the study of biological networks.
*[http://networkrepository.com/asn.php Network Repository] The first interactive data and network data repository with real-time visual analytics.
*[https://bansallab.github.io/asnr/ Animal Social Network Repository(ASNR)] The first multi-taxonomic repository that collates 790 social networks from more than 45 species, including those of mammals, reptiles, fish, birds, and insects
*[http://konect.uni-koblenz.de/networks/ KONECT – Koblenz network collection.]
[[Category:Biological techniques and tools]]
Category:Biological techniques and tools
类别: 生物技术和工具
[[Category:Bioinformatics]]
Category:Bioinformatics
类别: 生物信息学
[[Category:Systems biology]]
Category:Systems biology
分类: 系统生物学
[[Category:Networks]]
Category:Networks
类别: 网络
<noinclude>
<small>This page was moved from [[wikipedia:en:Biological network]]. Its edit history can be viewed at [[生物网络/edithistory]]</small></noinclude>
[[Category:待整理页面]]
{{Network Science}}
{{refimprove|date=October 2011}}
A '''biological network''' is any [[network science|network]] that applies to [[biological system]]s. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole [[food web]]. Biological networks provide a [[graph theory|mathematical representation]] of connections found in [[ecological network|ecological]], [[phylogenetic network|evolutionary]], and [[physiological]] studies, such as [[neural networks]].<ref name="Proulx05">{{cite journal | last1=Proulx | first1=S. R. | last2=Promislow | first2=D. E. L. | last3=Phillips | first3=P. C. | title=Network thinking in ecology and evolution | journal=Trends in Ecology and Evolution | volume=20 | issue=6 | pages=345–353 | year=2005 | doi=10.1016/j.tree.2005.04.004 | url=http://eeb19.biosci.arizona.edu/Faculty/Dornhaus/courses/materials/papers/Proulx%20Promislow%20Phillips%20networks%20ecol%20evol.pdf | pmid=16701391 | url-status=dead | archiveurl=https://web.archive.org/web/20110815122330/http://eeb19.biosci.arizona.edu/Faculty/Dornhaus/courses/materials/papers/Proulx%20Promislow%20Phillips%20networks%20ecol%20evol.pdf | archivedate=2011-08-15 }}</ref> The analysis of biological networks with respect to human diseases has led to the field of [[network medicine]].<ref>{{cite journal | last1 = Barabási | first1 = A. L. | last2 = Gulbahce | first2 = N. | last3 = Loscalzo | first3 = J. | year = 2011 | title = Network medicine: a network-based approach to human disease | url = | journal = Nature Reviews Genetics | volume = 12 | issue = 1| pages = 56–68 | doi=10.1038/nrg2918 | pmid=21164525 | pmc=3140052}}</ref><ref>{{Cite journal|last=Habibi|first=Iman|last2=Emamian|first2=Effat S.|last3=Abdi|first3=Ali|date=2014-10-07|title=Advanced Fault Diagnosis Methods in Molecular Networks|journal=PLOS ONE|volume=9|issue=10|pages=e108830|doi=10.1371/journal.pone.0108830|issn=1932-6203|pmc=4188586|pmid=25290670|bibcode=2014PLoSO...9j8830H}}</ref>
A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web. Biological networks provide a mathematical representation of connections found in ecological, evolutionary, and physiological studies, such as neural networks. The analysis of biological networks with respect to human diseases has led to the field of network medicine.
生物网络是应用于生物系统的任何网络。网络是任何系统的子单位，连接成一个整体，如物种单位连接成一个整体的食物网。生物网络提供了在生态学、进化学和生理学研究中发现的联系的数学表示，例如神经网络。与人类疾病相关的生物网络分析引领了网络医学领域的发展。
==Network biology and bioinformatics==
Complex biological systems may be represented and analyzed as computable networks. For example, ecosystems can be modeled as networks of interacting species or a protein can be modeled as a network of amino acids. Breaking a protein down farther, [[amino acids]] can be represented as a network of connected [[atom]]s, such as [[carbon]], [[nitrogen]], and [[oxygen]]. [[vertex (graph theory)|Nodes]] and [[vertex (graph theory)|edges]] are the basic components of a network. Nodes represent units in the network, while edges represent the interactions between the units. Nodes can represent a wide array of biological units, from individual organisms to individual neurons in the brain. Two important properties of a network are [[vertex (graph theory)|degree]] and [[betweenness centrality]]. Degree (or connectivity, a distinct usage from that used in [[Connectivity (graph theory)|graph theory]]) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network.<ref name="Proulx">{{cite journal |author= Proulx, S.R. |title= Network thinking in ecology and evolution |journal= Trends in Ecology and Evolution |year= 2005 |volume= 20 |issue= 6 |pages= 345–353 |doi=10.1016/j.tree.2005.04.004 |pmid=16701391|display-authors=etal}}</ref> Nodes with high betweenness essentially serve as bridges between different portions of the network (i.e. interactions must pass through this node to reach other portions of the network). In social networks, nodes with high degree or high betweenness may play important roles in the overall composition of a network.
Complex biological systems may be represented and analyzed as computable networks. For example, ecosystems can be modeled as networks of interacting species or a protein can be modeled as a network of amino acids. Breaking a protein down farther, amino acids can be represented as a network of connected atoms, such as carbon, nitrogen, and oxygen. Nodes and edges are the basic components of a network. Nodes represent units in the network, while edges represent the interactions between the units. Nodes can represent a wide array of biological units, from individual organisms to individual neurons in the brain. Two important properties of a network are degree and betweenness centrality. Degree (or connectivity, a distinct usage from that used in graph theory) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network. Nodes with high betweenness essentially serve as bridges between different portions of the network (i.e. interactions must pass through this node to reach other portions of the network). In social networks, nodes with high degree or high betweenness may play important roles in the overall composition of a network.
复杂的生物系统可以用可计算网络来表示和分析。例如，生态系统可以被模拟为相互作用的物种网络，或者蛋白质可以被模拟为氨基酸网络。进一步分解蛋白质，氨基酸可以表示为一个由相互连接的原子组成的网络，如碳、氮和氧。节点和边是网络的基本组成部分。节点表示网络中的单元，边表示单元之间的相互作用。节点可以代表一系列广泛的生物单元，从单个的生物体到大脑中单个的神经元。网络的两个重要性质是度和中心性。度(或连通性，一个不同于图论的用法)是连接一个节点的边的数量，而介于两者之间是衡量一个节点在网络中的中心位置。具有高中间性的节点本质上充当网络不同部分之间的桥梁(即。交互必须通过这个节点才能到达网络的其他部分)。在社会网络中，高度或高度介于两者之间的节点可能在网络的整体组成中发挥重要作用。
As early as the 1980s, researchers started viewing [[DNA]] or [[genome]]s as the dynamic storage of a language system with precise computable finite [[state (computer science)|states]] represented as a [[finite state machine]].<ref>{{cite book |author= Searls, D. |title= Artificial intelligence and molecular biology |publisher= MIT Press |year= 1993 |location= Cambridge, MA}}</ref> Recent [[complex system]]s research has also suggested some far-reaching commonality in the organization of information in problems from biology, [[computer science]], and [[physics]], such as the [[Bose–Einstein condensate]] (a special state of matter).<ref>{{cite journal |author1=Bianconi, G. |author2=Barabasi A. |lastauthoramp=yes |title= Bose-Einstein condensation in complex networks |journal= Phys. Rev. Lett. |year= 2001 |volume= 86 |issue= 24 |pages= 5632–5635 |doi=10.1103/physrevlett.86.5632|pmid=11415319 |arxiv=cond-mat/0011224|bibcode=2001PhRvL..86.5632B|hdl=2047/d20000696 }}</ref>
As early as the 1980s, researchers started viewing DNA or genomes as the dynamic storage of a language system with precise computable finite states represented as a finite state machine. Recent complex systems research has also suggested some far-reaching commonality in the organization of information in problems from biology, computer science, and physics, such as the Bose–Einstein condensate (a special state of matter).
早在20世纪80年代，研究人员就开始将 DNA 或基因组视为一个语言系统的动态存储，其精确的可计算有限状态表示为一个有限状态机。最近的复杂系统研究还表明，在生物学、计算机科学和物理学等问题的信息组织方面存在一些意义深远的共性，例如玻色-爱因斯坦凝聚态(一种特殊的物质状态)。
Bioinformatics has increasingly shifted its focus from individual [[gene]]s, proteins, and [[search algorithm]]s to large-scale networks often denoted as [[omics|-omes]] such as [[biome]], [[interactome]], [[genome]] and [[proteome]]. Such theoretical studies have revealed that biological networks share many features with other networks such as the [[Internet]] or [[social network]]s, e.g. their [[network topology]].
Bioinformatics has increasingly shifted its focus from individual genes, proteins, and search algorithms to large-scale networks often denoted as -omes such as biome, interactome, genome and proteome. Such theoretical studies have revealed that biological networks share many features with other networks such as the Internet or social networks, e.g. their network topology.
生物信息学的重点已经从单个基因、蛋白质和搜索算法逐渐转移到大规模网络，这些网络通常被称为生物组、交叉组、基因组和蛋白质组。这些理论研究揭示了生物网络与其他网络如互联网或社交网络有许多共同特征，例如:。他们的网络拓扑。
==Networks in biology==
===Protein–protein interaction networks===
{{main article|interactome}}
Many [[protein–protein interaction]]s (PPIs) in a cell form ''protein interaction networks'' (PINs) where proteins are ''nodes'' and their interactions are ''edges''.<ref>{{Cite journal|last=Habibi|first=Iman|last2=Emamian|first2=Effat S.|last3=Abdi|first3=Ali|date=2014-01-01|title=Quantitative analysis of intracellular communication and signaling errors in signaling networks|journal=BMC Systems Biology|volume=8|pages=89|doi=10.1186/s12918-014-0089-z|issn=1752-0509|pmc=4255782|pmid=25115405}}</ref> PINs are the most intensely analyzed networks in biology. There are dozens of PPI detection methods to identify such interactions. The [[Y2H|yeast two-hybrid system]] is a commonly used experimental technique for the study of binary interactions.<ref>{{cite journal |author= Mashaghi, A. |title= Investigation of a protein complex network |journal= European Physical Journal |year= 2004 |volume= 41 |issue= 1 |pages= 113–121 |doi=10.1140/epjb/e2004-00301-0|display-authors=etal|arxiv= cond-mat/0304207|bibcode= 2004EPJB...41..113M}}</ref>
Many protein–protein interactions (PPIs) in a cell form protein interaction networks (PINs) where proteins are nodes and their interactions are edges. PINs are the most intensely analyzed networks in biology. There are dozens of PPI detection methods to identify such interactions. The yeast two-hybrid system is a commonly used experimental technique for the study of binary interactions.
许多蛋白质-蛋白质相互作用(ppi)在细胞中形成蛋白质相互作用网络(pin) ，其中蛋白质是节点，它们的相互作用是边缘。个人识别码是生物学中分析最深入的网络。有几十种 PPI 检测方法来识别这种相互作用。酵母双杂交系统是研究二元相互作用的常用实验技术。
Recent studies have indicated conservation of molecular networks through deep evolutionary time.<ref>{{cite journal |author= Sharan, R. |title= Conserved patterns of protein interaction in multiple species |journal= Proceedings of the National Academy of Sciences of the United States of America |year= 2005 |volume= 102 |issue= 6 |pages= 1974–1979 |doi=10.1073/pnas.0409522102|pmid= 15687504 |display-authors=etal|pmc= 548573|bibcode= 2005PNAS..102.1974S}}</ref> Moreover, it has been discovered that proteins with high degrees of connectedness are more likely to be essential for survival than proteins with lesser degrees.<ref>{{cite journal |author= Jeong, H. |title= Lethality and centrality in protein networks |journal= Nature |year= 2001 |volume= 411 |issue= 6833 |pages= 41–42 |doi=10.1038/35075138 |pmid=11333967|display-authors=etal|bibcode= 2001Natur.411...41J |arxiv= cond-mat/0105306 }}</ref> This suggests that the overall composition of the network (not simply interactions between protein pairs) is important for the overall functioning of an organism.
Recent studies have indicated conservation of molecular networks through deep evolutionary time. Moreover, it has been discovered that proteins with high degrees of connectedness are more likely to be essential for survival than proteins with lesser degrees. This suggests that the overall composition of the network (not simply interactions between protein pairs) is important for the overall functioning of an organism.
近年来的研究表明，分子网络在深层进化过程中是守恒的。此外，已经发现高连通性的蛋白质比低连通性的蛋白质更有可能是生存所必需的。这表明网络的整体组成(不仅仅是蛋白质对之间的相互作用)对于有机体的整体功能是重要的。
===Gene regulatory networks (DNA–protein interaction networks)===
{{main article| Gene regulatory network}}
The activity of genes is regulated by [[transcription factors]], proteins that typically bind to [[DNA]]. Most transcription factors bind to multiple binding sites in a [[genome]]. As a result, all cells have complex [[gene regulatory networks]]. For instance, the [[human genome]] encodes on the order of 1,400 DNA-binding transcription factors that regulate the expression of more than 20,000 human genes.<ref>{{cite journal |author= Vaquerizas, J.-M. |title= A census of human transcription factors: function, expression and evolution |journal= Nature Reviews Genetics |year= 2009 |volume= 10 |issue= 4 |pages= 252–263 |pmid= 19274049 |doi=10.1038/nrg2538|display-authors=etal}}</ref> Technologies to study gene regulatory networks include [[ChIP-chip]], [[ChIP-seq]], [[CliP-seq]], and others.
The activity of genes is regulated by transcription factors, proteins that typically bind to DNA. Most transcription factors bind to multiple binding sites in a genome. As a result, all cells have complex gene regulatory networks. For instance, the human genome encodes on the order of 1,400 DNA-binding transcription factors that regulate the expression of more than 20,000 human genes. Technologies to study gene regulatory networks include ChIP-chip, ChIP-seq, CliP-seq, and others.
基因的活性受转录因子调节，转录因子是典型的与 DNA 结合的蛋白质。大多数转录因子与基因组中的多个结合位点结合。因此，所有的细胞都有复杂的基因调控网络。例如，人类基因组编码1400个 dna 结合转录因子，调节超过20000个人类基因的表达。研究基因调控网络的技术包括 ChIP-chip、 ChIP-seq、 CliP-seq 等。
===Gene co-expression networks (transcript–transcript association networks)===
{{main article| Gene co-expression networks}}
Gene co-expression networks can be interpreted as association networks between variables that measure transcript abundances. These networks have been used to provide a systems biologic analysis of DNA microarray data, RNA-seq data, miRNA data etc.
Gene co-expression networks can be interpreted as association networks between variables that measure transcript abundances. These networks have been used to provide a systems biologic analysis of DNA microarray data, RNA-seq data, miRNA data etc.
基因共同表达网络可以解释为变量之间的关联网络，衡量转录丰度。这些网络已经被用于提供 DNA 微阵列数据、 RNA-seq 数据、 miRNA 数据等的系统生物学分析。
[[Weighted correlation network analysis|weighted gene co-expression network analysis]] is widely used to identify co-expression modules and intramodular hub genes. Co-expression modules may correspond to cell types or pathways. Highly connected intramodular hubs can be interpreted as representatives of their respective module.
weighted gene co-expression network analysis is widely used to identify co-expression modules and intramodular hub genes. Co-expression modules may correspond to cell types or pathways. Highly connected intramodular hubs can be interpreted as representatives of their respective module.
加权基因共表达网络分析被广泛应用于鉴定共表达模块和模块内核心基因。共表达模块可能对应于细胞类型或通路。高度连接的模块内集线器可以解释为其各自模块的代表。
===Metabolic networks===
{{main article|metabolic network}}
The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by [[enzymes]]. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called [[metabolic network]]. It is possible to use network analyses to infer how selection acts on metabolic pathways.<ref name="Proulx" />
The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways.
活细胞中的化合物通过生物化学反应相互连接，将一种化合物转化为另一种化合物。这些反应是由酶催化的。因此，一个细胞中的所有化合物都是一个复杂的生物化学反应网络的一部分，这个网络被称为代谢网络。使用网络分析来推断选择如何影响代谢途径是可能的。
===Signaling networks===
{{main article|Cell signaling}}
Signals are transduced within cells or in between cells and thus form complex signaling networks. For instance, in the [[MAPK/ERK pathway]] is transduced from the cell surface to the cell nucleus by a series of protein–protein interactions, phosphorylation reactions, and other events. Signaling networks typically integrate [[interactome|protein–protein interaction networks]], [[gene regulatory networks]], and [[metabolic network]]s.
Signals are transduced within cells or in between cells and thus form complex signaling networks. For instance, in the MAPK/ERK pathway is transduced from the cell surface to the cell nucleus by a series of protein–protein interactions, phosphorylation reactions, and other events. Signaling networks typically integrate protein–protein interaction networks, gene regulatory networks, and metabolic networks.
信号在细胞内或细胞之间传递，从而形成复杂的信号网络。例如，MAPK/ERK 通路通过一系列蛋白质-蛋白质相互作用、磷酸化反应和其他事件从细胞表面传递到细胞核。信号网络通常整合蛋白质-蛋白质相互作用网络、基因调控网络和代谢网络。
===Neuronal networks===
{{main article| Biological neural network}}
The complex interactions in the [[brain]] make it a perfect candidate to apply network theory. [[Neuron]]s in the brain are deeply connected with one another and this results in complex networks being present in the structural and functional aspects of the brain.<ref>{{cite journal |author1=Bullmore, E. |author2=O. Sporns |lastauthoramp=yes |title= Complex brain networks: graph theoretical analysis of structural and functional systems |journal= Nature Reviews Neuroscience |year= 2009 |volume= 10 |issue= 3 |pages= 186–198 |doi=10.1038/nrn2575 |pmid=19190637}}</ref> For instance, [[small-world network]] properties have been demonstrated in connections between cortical areas of the primate brain<ref>{{cite journal |author= Stephan, K.E. |title= Computational analysis of functional connectivity between areas of primate cerebral cortex |journal= [[Philosophical Transactions of the Royal Society B]]|year= 2000 |volume= 355 |issue= 1393 |pages= 111–126 |doi=10.1098/rstb.2000.0552|pmid= 10703047 |display-authors=etal|pmc= 1692715}}</ref> or during swallowing in humans.<ref>{{Cite journal|date=2016-12-01|title=Functional connectivity patterns of normal human swallowing: difference among various viscosity swallows in normal and chin-tuck head positions|journal=Brain Research|volume=1652|pages=158–169|doi=10.1016/j.brainres.2016.09.041|pmid=27693396|pmc=5102805|issn=0006-8993|last1=Jestrović|first1=Iva|last2=Coyle|first2=James L|last3=Perera|first3=Subashan|last4=Sejdić|first4=Ervin}}</ref> This suggests that cortical areas of the brain are not directly interacting with each other, but most areas can be reached from all others through only a few interactions.
The complex interactions in the brain make it a perfect candidate to apply network theory. Neurons in the brain are deeply connected with one another and this results in complex networks being present in the structural and functional aspects of the brain. For instance, small-world network properties have been demonstrated in connections between cortical areas of the primate brain or during swallowing in humans. This suggests that cortical areas of the brain are not directly interacting with each other, but most areas can be reached from all others through only a few interactions.
大脑中复杂的相互作用使其成为应用网络理论的完美候选者。大脑中的神经元彼此之间有着深刻的联系，这导致了大脑结构和功能方面的复杂网络。例如，灵长类动物大脑皮层区域之间的连接或者人类吞咽时的吞咽活动已经证明了小世界网络属性。这表明大脑皮层区域之间并不直接相互作用，但大部分区域可以通过少量的相互作用从所有其他区域到达。
===Food webs===
{{main article|Food web}}
All organisms are connected to each other through feeding interactions. That is, if a species eats or is eaten by another species, they are connected in an intricate [[food web]] of predator and prey interactions. The stability of these interactions has been a long-standing question in ecology.<ref>{{cite journal |author= MacArthur, R.H. |author-link= Robert MacArthur|title= Fluctuations in animal populations and a measure of community stability |journal= Ecology |year= 1955 |volume= 36 |issue= 3 |pages= 533–536 |doi=10.2307/1929601|jstor= 1929601}}</ref> That is to say, if certain individuals are removed, what happens to the network (i.e. does it collapse or adapt)? Network analysis can be used to explore food web stability and determine if certain network properties result in more stable networks. Moreover, network analysis can be used to determine how selective removals of species will influence the food web as a whole.<ref>{{cite journal |author= Dunne, J.A. |title= Network structure and biodiversity loss in food webs: robustness increases with connectance |journal= Ecology Letters |year= 2002 |volume= 5 |issue= 4 |pages= 558–567 |doi=10.1046/j.1461-0248.2002.00354.x|display-authors=etal}}</ref> This is especially important considering the potential species loss due to global climate change.
All organisms are connected to each other through feeding interactions. That is, if a species eats or is eaten by another species, they are connected in an intricate food web of predator and prey interactions. The stability of these interactions has been a long-standing question in ecology. That is to say, if certain individuals are removed, what happens to the network (i.e. does it collapse or adapt)? Network analysis can be used to explore food web stability and determine if certain network properties result in more stable networks. Moreover, network analysis can be used to determine how selective removals of species will influence the food web as a whole. This is especially important considering the potential species loss due to global climate change.
所有的生物都是通过食物的相互作用联系在一起的。也就是说，如果一个物种吃了另一个物种或被另一个物种吃了，它们就在一个复杂的捕食者和猎物相互作用的食物网中联系起来。这些相互作用的稳定性一直是生态学中的一个长期问题。也就是说，如果某些个体被移除，那么网络(即。它是崩溃还是适应) ？网络分析可以用来探索食物网的稳定性，并确定某些网络特性是否会导致更稳定的网络。此外，网络分析可以用来确定物种的选择性迁移将如何影响整个食物网。考虑到全球气候变化可能造成的物种损失，这一点尤其重要。
===Between-species interaction networks===
{{main article|social relation}}
In biology, pairwise interactions have historically been the focus of intense study. With the recent advances in [[network science]], it has become possible to scale up pairwise interactions to include individuals of many species involved in many sets of interactions to understand the structure and function of larger [[ecological network]]s.<ref>{{cite journal |author= Bascompte, J. |title= Disentangling the web of life |journal= Science |year= 2009 |volume=325 |issue= 5939 |pages= 416–419 |doi=10.1126/science.1170749 |pmid=19628856|bibcode=2009Sci...325..416B }}</ref> The use of [[Social network analysis|network analysis]] can allow for both the discovery and understanding how these complex interactions link together within the system’s network, a property which has previously been overlooked. This powerful tool allows for the study of various types of interactions (from [[competitive]] to [[cooperative]]) using the same general framework.<ref>{{cite journal |author= Krause, J. |title= Animal social networks: an introduction |journal= Behav. Ecol. Sociobiol. |year= 2009 |volume= 63 |issue= 7 |pages= 967–973 |doi=10.1007/s00265-009-0747-0|display-authors=etal}}</ref> For example, plant-[[pollinator]] interactions are mutually beneficial and often involve many different species of pollinators as well as many different species of plants. These interactions are critical to plant reproduction and thus the accumulation of resources at the base of the [[food chain]] for primary consumers, yet these interaction networks are threatened by [[Human impact on the environment|anthropogenic]] change. The use of network analysis can illuminate how [[pollination network]]s work and may in turn inform conservation efforts.<ref name="Memmott, J., et al. 2004 2605-261">{{cite journal |author= Memmott, J. |title= Tolerance of pollination networks to species extinctions |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2004 |volume= 271 |issue= 1557 |pages= 2605–261 |doi=10.1098/rspb.2004.2909|pmid= 15615687 |pmc= 1691904 |display-authors=etal}}</ref> Within pollination networks, nestedness (i.e., specialists interact with a subset of species that generalists interact with), redundancy (i.e., most plants are pollinated by many pollinators), and [[modularity (networks)|modularity]] play a large role in network stability.<ref name="Memmott, J., et al. 2004 2605-261"/><ref name="Olesen, J., et al. 2007 19891–19896">{{cite journal |author= Olesen, J. |title= The modularity of pollination networks |journal= PNAS |year= 2007 |volume= 104 |issue= 50 |pages= 19891–19896 |doi=10.1073/pnas.0706375104|pmid= 18056808 |pmc= 2148393 |display-authors=etal|bibcode= 2007PNAS..10419891O }}</ref> These network properties may actually work to slow the spread of disturbance effects through the system and potentially buffer the pollination network from anthropogenic changes somewhat.<ref name="Olesen, J., et al. 2007 19891–19896"/> More generally, the structure of species interactions within an ecological network can tell us something about the diversity, richness, and robustness of the network.<ref>{{cite journal |author= Campbell, V. |title= Experimental design and the outcome and interpretation of diversity-stability relations |journal= Oikos |year= 2011 |volume= 120 |issue= 3 |pages= 399–408 |doi=10.1111/j.1600-0706.2010.18768.x|display-authors=etal}}</ref> Researchers can even compare current constructions of species interactions networks with historical reconstructions of ancient networks to determine how networks have changed over time.<ref>{{cite journal |author= Lotze, H. |title= Historical changes in marine resources, food-web structure and ecosystem functioning in the Adriatic Sea, Mediterranean |journal= Ecosystems |year= 2011 |volume= 14 |issue= 2 |pages= 198–222 |doi=10.1007/s10021-010-9404-8|display-authors=etal}}</ref> Recent research into these complex species interactions networks is highly concerned with understanding what factors (e.g., diversity) lead to network stability.<ref>{{cite journal |author= Romanuk, T. |title= Maintenance of positive diversity-stability relations along a gradient of environmental stress |journal= PLoS ONE |year= 2010 |volume= 5 |issue= 4 |pages= e10378 |doi=10.1371/journal.pone.0010378|display-authors=etal |pmid=20436913 |pmc=2860506|bibcode=2010PLoSO...510378R }}</ref>
In biology, pairwise interactions have historically been the focus of intense study. With the recent advances in network science, it has become possible to scale up pairwise interactions to include individuals of many species involved in many sets of interactions to understand the structure and function of larger ecological networks. The use of network analysis can allow for both the discovery and understanding how these complex interactions link together within the system’s network, a property which has previously been overlooked. This powerful tool allows for the study of various types of interactions (from competitive to cooperative) using the same general framework. For example, plant-pollinator interactions are mutually beneficial and often involve many different species of pollinators as well as many different species of plants. These interactions are critical to plant reproduction and thus the accumulation of resources at the base of the food chain for primary consumers, yet these interaction networks are threatened by anthropogenic change. The use of network analysis can illuminate how pollination networks work and may in turn inform conservation efforts. Within pollination networks, nestedness (i.e., specialists interact with a subset of species that generalists interact with), redundancy (i.e., most plants are pollinated by many pollinators), and modularity play a large role in network stability. These network properties may actually work to slow the spread of disturbance effects through the system and potentially buffer the pollination network from anthropogenic changes somewhat. Researchers can even compare current constructions of species interactions networks with historical reconstructions of ancient networks to determine how networks have changed over time. Recent research into these complex species interactions networks is highly concerned with understanding what factors (e.g., diversity) lead to network stability.
在生物学中，成对相互作用历来是密集研究的焦点。随着网络科学的最新进展，已经有可能扩大成对的相互作用，以包括许多物种的个体参与多组相互作用，从而理解更大的生态网络的结构和功能。使用网络分析可以发现和理解这些复杂的交互如何在系统的网络中连接在一起，这是以前被忽视的属性。这个强大的工具允许使用相同的总体框架研究各种类型的交互(从竞争到合作)。例如，植物与传粉者之间的相互作用是互惠互利的，通常涉及许多不同种类的传粉者以及许多不同种类的植物。这些相互作用对植物生殖和初级消费者食物链底层的资源积累至关重要，然而这些相互作用网络受到人为变化的威胁。网络分析的使用可以说明授粉网络是如何工作的，反过来也可以为保护工作提供信息。在授粉网络中，内嵌性(即专家与多面手相互作用的物种子集相互作用)、冗余性(即大多数植物是由许多授粉者授粉的)和模块性在网络稳定性中扮演着重要角色。这些网络属性实际上可以减缓干扰效应通过系统的传播，并可能缓冲授粉网络的人为变化。研究人员甚至可以将物种相互作用网络的现有结构与古代网络的历史重建进行比较，以确定网络随着时间的推移是如何发生变化的。最近对这些复杂物种间相互作用网络的研究高度关注于理解什么因素(如多样性)导致网络的稳定性。
===Within-species interaction networks===
{{main article|social relation}}
Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level.<ref>{{cite journal |author= Croft, D.P |title= Social networks in the guppy (Poecilia reticulate) |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2004 |volume= 271 |issue= Suppl |pages= S516–S519 |doi=10.1098/rsbl.2004.0206|pmid= 15801620 |pmc= 1810091 |display-authors=etal}}</ref> One of the most attractive features of the network paradigm would be that it provides a single conceptual framework in which the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.) can be studied.<ref>{{Cite journal|last=Krause, Lusseau, James|first=Jens, David, Richard|date=1 May 2009|title=Animal social networks: an introduction|url=https://www.researchgate.net/publication/226996156_Animal_social_networks_An_introduction|journal=Behavioral Ecology and Sociobiology|volume=63|pages=967-973|doi=10.1007/s00265-009-0747-0|via=}}</ref>
Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level. One of the most attractive features of the network paradigm would be that it provides a single conceptual framework in which the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.) can be studied.
网络分析提供了量化个体之间关联的能力，这使得在物种和/或种群水平上推断整个网络的细节成为可能。网络范式最吸引人的特征之一是，它提供了一个单一的概念框架，其中动物的社会组织在所有层次(个人，二元，群体，人口)和所有类型的互动(攻击性，合作，性等。)可以研究。
Researchers interested in [[ethology]] across a multitude of taxa, from insects to primates, are starting to incorporate network analysis into their research. Researchers interested in social insects (e.g., ants and bees) have used network analyses to better understand division of labor, task allocation, and foraging optimization within colonies;<ref>{{cite journal |author= Dornhaus, A. |title= Benefits of recruitment in honey bees: Effects of ecology and colony size in an individual-based model |journal= Behavioral Ecology |year= 2006 |volume=17 |issue= 3 |pages= 336–344 |doi=10.1093/beheco/arj036|display-authors=etal|doi-access= free }}</ref><ref>{{cite journal |author= Linksvayer, T. |title= Developmental evolution in social insects: Regulatory networks from genes to societies |journal= Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |year= 2012 |volume=318 |issue= 3 |pages= 159–169 |doi=10.1002/jez.b.22001|pmid= 22544713 |display-authors=etal}}</ref><ref>{{cite journal |author= Mullen, R. |title= A review of ant algorithms |journal= Expert Systems with Applications |year= 2009 |volume=36 |issue= 6 |pages= 9608–9617 |doi=10.1016/j.eswa.2009.01.020|display-authors=etal}}</ref> Other researchers are interested in how certain network properties at the group and/or population level can explain individual level behaviors. Studies have demonstrated how animal social network structure can be influenced by factors ranging from characteristics of the environment to characteristics of the individual, such as developmental experience and personality. At the level of the individual, the patterning of social connections can be an important determinant of [[Fitness (biology)|fitness]], predicting both survival and reproductive success. At the population level, network structure can influence the patterning of ecological and evolutionary processes, such as [[frequency-dependent selection]] and disease and information transmission.<ref>{{Cite journal|last=Croft, Darden, Wey|first=Darren P., Safi K., Tina W.|date=2016|title=Current directions in animal social networks|url=https://www.researchgate.net/publication/310819524_Current_directions_in_animal_social_networks|journal=Current Opinion in Behavioral Sciences|volume=12|pages=52-58|doi=10.1016/j.cobeha.2016.09.001|via=|hdl=10871/23348|hdl-access=free}}</ref> For instance, a study on [[Wire-tailed manakin|wire-tailed manakins]] (a small passerine bird) found that a male’s [[degree (graph theory)|degree]] in the network largely predicted the ability of the male to rise in the social hierarchy (i.e. eventually obtain a territory and matings).<ref>{{cite journal |author= Ryder, T.B. |title= Social networks in the lek-mating wire-tailed manakin (''Pipra filicauda'') |journal= [[Philosophical Transactions of the Royal Society B]] |year= 2008 |volume= 275 |issue= 1641 |pages= 1367–1374 |doi=10.1098/rspb.2008.0205 |pmid=18381257 |pmc=2602714|display-authors=etal}}</ref> In [[bottlenose dolphin]] groups, an individual’s degree and [[betweenness centrality]] values may predict whether or not that individual will exhibit certain behaviors, like the use of side flopping and upside-down lobtailing to lead group traveling efforts; individuals with high betweenness values are more connected and can obtain more information, and thus are better suited to lead group travel and therefore tend to exhibit these signaling behaviors more than other group members.<ref>{{cite journal |author= Lusseau, D. |title= Evidence for social role in a dolphin social network |journal= Evolutionary Ecology |year= 2007 |volume=21 |issue= 3 |pages= 357–366 |doi=10.1007/s10682-006-9105-0|arxiv= q-bio/0607048 }}</ref>
Researchers interested in ethology across a multitude of taxa, from insects to primates, are starting to incorporate network analysis into their research. Researchers interested in social insects (e.g., ants and bees) have used network analyses to better understand division of labor, task allocation, and foraging optimization within colonies; Other researchers are interested in how certain network properties at the group and/or population level can explain individual level behaviors. Studies have demonstrated how animal social network structure can be influenced by factors ranging from characteristics of the environment to characteristics of the individual, such as developmental experience and personality. At the level of the individual, the patterning of social connections can be an important determinant of fitness, predicting both survival and reproductive success. At the population level, network structure can influence the patterning of ecological and evolutionary processes, such as frequency-dependent selection and disease and information transmission. For instance, a study on wire-tailed manakins (a small passerine bird) found that a male’s degree in the network largely predicted the ability of the male to rise in the social hierarchy (i.e. eventually obtain a territory and matings). In bottlenose dolphin groups, an individual’s degree and betweenness centrality values may predict whether or not that individual will exhibit certain behaviors, like the use of side flopping and upside-down lobtailing to lead group traveling efforts; individuals with high betweenness values are more connected and can obtain more information, and thus are better suited to lead group travel and therefore tend to exhibit these signaling behaviors more than other group members.
从昆虫到灵长类动物，研究人员对动物行为学感兴趣，并开始将网络分析纳入他们的研究中。对社会性昆虫(如蚂蚁和蜜蜂)感兴趣的研究人员利用网络分析来更好地理解群体内的分工、任务分配和觅食优化; 其他研究人员则对群体和/或种群水平的某些网络特性如何解释个体水平的行为感兴趣。研究表明，动物的社会网络结构是如何受到从环境特征到个体特征，如发展经验和人格等因素的影响。在个体层面上，社会联系的模式可能是适应性的一个重要决定因素，预测生存和繁殖的成功。在种群水平上，网络结构可以影响生态和进化过程的模式，如频率依赖性选择和疾病及信息传递。例如，一项针对线尾 manakins (一种小型雀形目鸟)的研究发现，雄性网络中的学位在很大程度上预测了雄性在社会等级中上升的能力(即,。最终获得领地和交配)。在宽吻海豚群体中，个体的程度和中介中心性价值观可以预测个体是否会表现出某些行为，比如使用侧翻和倒挂龙虾来领导团队旅行; 中介价值观较高的个体相互联系更多，可以获得更多信息，因此更适合领导团队旅行，因此比其他团队成员更容易表现出这些信号传递行为。
[[Social network analysis]] can also be used to describe the social organization within a species more generally, which frequently reveals important proximate mechanisms promoting the use of certain behavioral strategies. These descriptions are frequently linked to ecological properties (e.g., resource distribution). For example, network analyses revealed subtle differences in the group dynamics of two related equid [[fission-fusion society|fission-fusion]] species, [[Grevy’s zebra]] and [[onager]]s, living in variable environments; Grevy’s zebras show distinct preferences in their association choices when they fission into smaller groups, whereas onagers do not.<ref>{{cite journal |author= Sundaresan, S. |title= Network metrics reveal differences in social organization between two fission-fusion species, Grevy's zebra and onager |journal= Oecologia |year= 2007 |volume= 151 |issue= 1 |pages= 140–149 |doi=10.1007/s00442-006-0553-6|pmid= 16964497 |display-authors=etal|bibcode= 2007Oecol.151..140S }}</ref> Similarly, researchers interested in primates have also utilized network analyses to compare social organizations across the diverse [[primate]] order, suggesting that using network measures (such as [[centrality]], [[assortativity]], [[modularity (networks)|modularity]], and betweenness) may be useful in terms of explaining the types of social behaviors we see within certain groups and not others.<ref>{{cite journal |author1=Kasper, C. |author2=Voelkl, B. |title= A social network analysis of primate groups |journal= Primates |year= 2009 |volume= 50 |issue=4 |pages= 343–356 |doi=10.1007/s10329-009-0153-2|pmid=19533270 }}</ref>
Social network analysis can also be used to describe the social organization within a species more generally, which frequently reveals important proximate mechanisms promoting the use of certain behavioral strategies. These descriptions are frequently linked to ecological properties (e.g., resource distribution). For example, network analyses revealed subtle differences in the group dynamics of two related equid fission-fusion species, Grevy’s zebra and onagers, living in variable environments; Grevy’s zebras show distinct preferences in their association choices when they fission into smaller groups, whereas onagers do not. Similarly, researchers interested in primates have also utilized network analyses to compare social organizations across the diverse primate order, suggesting that using network measures (such as centrality, assortativity, modularity, and betweenness) may be useful in terms of explaining the types of social behaviors we see within certain groups and not others.
社会网络分析也可以用来更广泛地描述一个物种内的社会组织，它经常揭示促进某些行为策略的使用的重要的近似机制。这些描述经常与生态属性(例如，资源分配)联系在一起。例如，网络分析揭示了生活在变化环境中的两个相关的等分裂融合物种——格雷维斑马和骑驴——的群体动力学的细微差异; 格雷维斑马在分裂为较小的群体时，在关联选择上表现出明显的偏好，而骑驴则不然。同样，对灵长类动物感兴趣的研究人员也利用网络分析来比较不同灵长类动物的社会组织，这表明使用网络测量(如集中性、协调性、模块性和介于性)可能有助于解释我们在某些群体中看到的社会行为类型，而不是其他群体。
Finally, social network analysis can also reveal important fluctuations in animal behaviors across changing environments. For example, network analyses in female [[chacma baboon]]s (''Papio hamadryas ursinus'') revealed important dynamic changes across seasons which were previously unknown; instead of creating stable, long-lasting social bonds with friends, baboons were found to exhibit more variable relationships which were dependent on short-term contingencies related to group level dynamics as well as environmental variability.<ref>{{cite journal |author= Henzi, S. |title= Cyclicity in the structure of female baboon social networks |journal= Behavioral Ecology and Sociobiology |year= 2009 |volume= 63 |issue= 7 |pages= 1015–1021 |doi=10.1007/s00265-009-0720-y|display-authors=etal}}</ref> Changes in an individual's social network environment can also influence characteristics such as 'personality': for example, social spiders that huddle with bolder neighbours tend to increase also in boldness.<ref>{{cite journal |author= Hunt, ER. |title= Social interactions shape individual and collective personality in social spiders |journal= Proceedings of the Royal Society B |year= 2018 |volume= 285 |issue= 1886 |pages= 20181366 |doi=10.1098/rspb.2018.1366|pmid= 30185649 |pmc= 6158534 |display-authors=etal}}</ref> This is a very small set of broad examples of how researchers can use network analysis to study animal behavior. Research in this area is currently expanding very rapidly, especially since the broader development of animal borne tags and [[computer vision]] that can be used to automate the collection of social associations.<ref>{{Cite journal|last=Krause J, Krause S, Arlinghaus R, Psorakis I, Roberts S, Rutz C|first=|date=2013|title=Reality mining of animal social systems.|url=https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reality-mining-of-animal-social-systems(570e21d0-527e-4275-8926-c4b479c55ee4).html|journal=Trends in Ecology and Evolution|volume=28|pages=541-551|doi=10.1016/j.tree.2013.06.002|via=}}</ref> Social network analysis is a valuable tool for studying animal behavior across all animal species, and has the potential to uncover new information about animal behavior and social ecology that was previously poorly understood.
Finally, social network analysis can also reveal important fluctuations in animal behaviors across changing environments. For example, network analyses in female chacma baboons (Papio hamadryas ursinus) revealed important dynamic changes across seasons which were previously unknown; instead of creating stable, long-lasting social bonds with friends, baboons were found to exhibit more variable relationships which were dependent on short-term contingencies related to group level dynamics as well as environmental variability. Changes in an individual's social network environment can also influence characteristics such as 'personality': for example, social spiders that huddle with bolder neighbours tend to increase also in boldness. This is a very small set of broad examples of how researchers can use network analysis to study animal behavior. Research in this area is currently expanding very rapidly, especially since the broader development of animal borne tags and computer vision that can be used to automate the collection of social associations. Social network analysis is a valuable tool for studying animal behavior across all animal species, and has the potential to uncover new information about animal behavior and social ecology that was previously poorly understood.
最后，社会网络分析还可以揭示动物行为在不断变化的环境中的重要波动。例如，对雌性沙卡马狒狒(Papio hamadryas ursinus)的网络分析揭示了以前未知的跨季节的重要动态变化; 结果发现，狒狒与朋友之间没有建立稳定、持久的社会联系，而是表现出更多的变化关系，这些关系依赖于与群体层面动态以及环境变化有关的短期偶然事件。个体社交网络环境的变化也会影响个体的性格特征，例如，与胆大的邻居挤在一起的社交蜘蛛也会更加大胆。这只是研究人员如何利用网络分析来研究动物行为的一小部分广泛的例子。这一领域的研究目前正在迅速扩展，特别是随着动物身上的标签和计算机视觉技术的广泛发展，这些技术可以用来自动收集社会关系。社会网络分析是研究所有动物物种的动物行为的一个有价值的工具，并且有可能发现以前鲜为人知的关于动物行为和社会生态的新信息。
==See also==
* [[List of omics topics in biology]]
* [[Biological network inference]]
* [[Applied Statistics]]
* [[Biostatistics]]
* [[Computational Biology]]
* [[Systems biology]]
* [[Weighted correlation network analysis]]
* [[Interactome]]
* [[Network medicine]]
== External links ==
* [http://www.nettab.org Network Tools and Applications in Biology] (NETTAB) workshops.
==References==
{{Reflist}}
==Books==
*E. Estrada, "The Structure of Complex Networks: Theory and Applications", Oxford University Press, 2011, {{ISBN|978-0-199-59175-6}}
*J. Krause, R. James, D. Franks, D. Croft, "Animal Social Networks", Oxford University Press, 2015, {{ISBN|978-0199679041}}
==External links==
* [https://web.archive.org/web/20110920220214/http://www.networkbio.org/ Networkbio.org], The site of the series of Integrative Network Biology (INB) meetings. For the 2012 event also see www.networkbio.org
* [http://networkbiology.org Networkbiology.org], NetworkBiology wiki site.
* [http://www.lindinglab.org LindingLab.org], Technical University of Denmark (DTU) studies Network Biology and Cellular Information Processing, and is also organizing the Denmark branch of the annual "[http://www.lindinglab.org/events ''Integrative Network Biology and Cancer'']" symposium series.
* [http://nrnb.org NRNB.org], The National Resource for Network Biology. A US National Institute of Health (NIH) Biomedical Technology Research Center dedicated to the study of biological networks.
*[http://networkrepository.com/asn.php Network Repository] The first interactive data and network data repository with real-time visual analytics.
*[https://bansallab.github.io/asnr/ Animal Social Network Repository(ASNR)] The first multi-taxonomic repository that collates 790 social networks from more than 45 species, including those of mammals, reptiles, fish, birds, and insects
*[http://konect.uni-koblenz.de/networks/ KONECT – Koblenz network collection.]
[[Category:Biological techniques and tools]]
Category:Biological techniques and tools
类别: 生物技术和工具
[[Category:Bioinformatics]]
Category:Bioinformatics
类别: 生物信息学
[[Category:Systems biology]]
Category:Systems biology
分类: 系统生物学
[[Category:Networks]]
Category:Networks
类别: 网络
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