出版社: Chapman and Hall/CRC
副标题: Design Principles of Biological Circuits
出版年: 200677
页数: 320
定价: USD 62.95
装帧: Paperback
ISBN: 9781584886426
内容简介 · · · · · ·
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The text avoids specialist terms, focusing instead on several wellstudied biological systems that...
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The text avoids specialist terms, focusing instead on several wellstudied biological systems that concisely demonstrate key principles. "An Introduction to Systems Biology: Design Principles of Biological Circuits" builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
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视角独特，值得深入阅读
> 更多书评 2篇

Cynosure (我是一只橘)
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to ...20160927 20:15
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to reconfigure and adapt to new confitions may be one force that helps to maintain modular structure in biological systems. 这有点到哲学层面的味道 。 simplicity level 1: the structural simplicity associated with modularity and the small number of network motifs that make up the networks. 。 simplicity level 2: be able to treat regulatory circuits with simplified mathematical models(the dynamics of transcription circuits) that capture the essence of the behavior and have a certain degree of universality. 也就是说： 把the dynamics of transcription circuits)表示为：ODE/PDE 把molecular details(proteins data)表示为：ODE/PDE的系数(或者说是参数) 。 Integral feedback can be shown in many cases to be a unique solution to the problem of robust adaptation in the context of engineering control theory. 。 modularity,即模块和模块之间相互独立，这类似于数学上的正交分解。 modularity的目的是为了模块可以重复使用：用已有的若干模块的组合去解决新的问题。（模块之间尽可能相互独立） 正交分解的目的是为了找出线性无关的基向量（或基函数），用这些基向量（或基函数）的线性组合去表示问题空间。 modularity和正交分解都可以看作是把复杂问题转化为稍微简单一些的问题。
回应 20160927 20:15 
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulat...
20110226 03:21
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulatory graph, evolutionarily conserved edges preserve fitness to the organism. Autoregulation, including positive and negative autoregulations, are overrepresented in E.coli transcription network. Parameters of such autoregulation are under natural selection. Negative repression efficiently and robustly lock the gene into steadystate expression. Presence of such repression reduces cellcell variation. Positive autoregulation is slower than unregulated gene. Such slow dynamics can be useful in relatively long developmental processes.
回应 20110226 03:21 
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
20110222 18:29
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
回应 20110222 18:29 
Appendix C  Graph Properties of Transcription Networks sparse connectivity: Transcription networks are sparse, since ratio of existing edges and theoretical upper limit of edges << 1. Typically, less than 0.1% of possible edges are found in the network. degree distribution: Typically mean degree is 2 to 10 edges/node. Outdegree distribution can be approximately described as a power law,... (4回应)
20110213 06:54
Appendix C  Graph Properties of Transcription Networks sparse connectivity: Transcription networks are sparse, since ratio of existing edges and theoretical upper limit of edges << 1. Typically, less than 0.1% of possible edges are found in the network. degree distribution: Typically mean degree is 2 to 10 edges/node. Outdegree distribution can be approximately described as a power law, i.e. P(k) ~ k^(r), with r ~ 1 to 2. Transcription network often have many transcription factors regulate a few genes, fewer nodes that regulate tens of genes, and even fewer global regulators that regulate hundreds of genes. Global regulators usually respond to key environmental signal to control large ensembles of genes, e.g. bacteria CRP to glucose starvation, RpoS respond to general stress. Indegree distribution instead resembles compact distribution such as Poisson distribution. This may correspond in part to physical limitation that promoters are short in simple organisms. In more complex organisms, DNA looping action can increase the number of input transcription factors to a given gene. Higher organisms often display larger indegrees than microorganisms, accommodating the complex computational needed during development. motifs: Clustering coefficient C is the average number of triangles that a node participates in. Feedforward loop (a type of triangle) is generally overrepresented in motifs of sensory transcription networks. The major contribution to the clustering coefficient therefore stems from feedforward loops. This pattern appears to be selected due to its function, such as filtering and response acceleration. Generally, it appears that global statistical properties of biological network such as degree sequences and cluster sequences are the result of selection working on the detailed circuit patterns in each individual system. Different networks have different selection constraints, which must be understood in order to understand their graphical properties. modularity: Network modularity is the degree to which it can be separated into nearly independent subnetworks. A measure of modularity is proposed by Newman and Girvan, 2004 and 2005. The rationale of this modularity measure is that: a good partition of a network into modules must comprise many withinmodular edges and as few as possible betweenmodule edges. This is achieved by maximizing a modularity measure Q.
4回应 20110213 06:54

Cynosure (我是一只橘)
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to ...20160927 20:15
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to reconfigure and adapt to new confitions may be one force that helps to maintain modular structure in biological systems. 这有点到哲学层面的味道 。 simplicity level 1: the structural simplicity associated with modularity and the small number of network motifs that make up the networks. 。 simplicity level 2: be able to treat regulatory circuits with simplified mathematical models(the dynamics of transcription circuits) that capture the essence of the behavior and have a certain degree of universality. 也就是说： 把the dynamics of transcription circuits)表示为：ODE/PDE 把molecular details(proteins data)表示为：ODE/PDE的系数(或者说是参数) 。 Integral feedback can be shown in many cases to be a unique solution to the problem of robust adaptation in the context of engineering control theory. 。 modularity,即模块和模块之间相互独立，这类似于数学上的正交分解。 modularity的目的是为了模块可以重复使用：用已有的若干模块的组合去解决新的问题。（模块之间尽可能相互独立） 正交分解的目的是为了找出线性无关的基向量（或基函数），用这些基向量（或基函数）的线性组合去表示问题空间。 modularity和正交分解都可以看作是把复杂问题转化为稍微简单一些的问题。
回应 20160927 20:15 
Nirvana.Viaje (游标卡尺不估读)
2.4, p15p21 dY/dt = \beta  \alpha Y (2.10) 最简单的一阶常微分方程，通解为指数函数乘以某系数，分离变量两端积分便得： => dY = (\beta  \alpha Y) => \int dY = \int (\beta  \alpha Y)dt 用Y_st为初值条件确定系数： => Y(t) = Y_st e^(st) (2.12) 上式利用t接近零时e^0=1 Taylor近似即得： Y~\beta t (2.15) Ex2.3, p18 习题2.3像是常数变易法解了个形如y'＋P(x)·y ＝ Q(x)的一阶常微 ref:  常数变...20110207 12:11
2.4, p15p21 dY/dt = \beta  \alpha Y (2.10) 最简单的一阶常微分方程，通解为指数函数乘以某系数，分离变量两端积分便得： => dY = (\beta  \alpha Y) => \int dY = \int (\beta  \alpha Y)dt 用Y_st为初值条件确定系数： => Y(t) = Y_st e^(st) (2.12) 上式利用t接近零时e^0=1 Taylor近似即得： Y~\beta t (2.15) Ex2.3, p18 习题2.3像是常数变易法解了个形如y'＋P(x)·y ＝ Q(x)的一阶常微 ref:  常数变易法  http://www.cnblogs.com/lookof/archive/2009/01/06/1370065.html  欢迎参加系统生物学导论  Uri Alon组本页讨论： http://www.douban.com/group/topic/17439561/
回应 20110207 12:11 
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
20110222 18:29
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
回应 20110222 18:29 
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulat...
20110226 03:21
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulatory graph, evolutionarily conserved edges preserve fitness to the organism. Autoregulation, including positive and negative autoregulations, are overrepresented in E.coli transcription network. Parameters of such autoregulation are under natural selection. Negative repression efficiently and robustly lock the gene into steadystate expression. Presence of such repression reduces cellcell variation. Positive autoregulation is slower than unregulated gene. Such slow dynamics can be useful in relatively long developmental processes.
回应 20110226 03:21

Cynosure (我是一只橘)
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to ...20160927 20:15
CH1 。 CH12 Every time the goal changes, these modules need only be rewired in order to satisfy the new goal. If the goal stops changing for a sufficient length of time, the networks in the simulation begin to lose modularity and evolve toward a nonmodular design, a design that is typically more optimal(e.g. uses fewer components). 这与软件开发和软件优化的思想如出一辄！ 。 Thus, the ability to reconfigure and adapt to new confitions may be one force that helps to maintain modular structure in biological systems. 这有点到哲学层面的味道 。 simplicity level 1: the structural simplicity associated with modularity and the small number of network motifs that make up the networks. 。 simplicity level 2: be able to treat regulatory circuits with simplified mathematical models(the dynamics of transcription circuits) that capture the essence of the behavior and have a certain degree of universality. 也就是说： 把the dynamics of transcription circuits)表示为：ODE/PDE 把molecular details(proteins data)表示为：ODE/PDE的系数(或者说是参数) 。 Integral feedback can be shown in many cases to be a unique solution to the problem of robust adaptation in the context of engineering control theory. 。 modularity,即模块和模块之间相互独立，这类似于数学上的正交分解。 modularity的目的是为了模块可以重复使用：用已有的若干模块的组合去解决新的问题。（模块之间尽可能相互独立） 正交分解的目的是为了找出线性无关的基向量（或基函数），用这些基向量（或基函数）的线性组合去表示问题空间。 modularity和正交分解都可以看作是把复杂问题转化为稍微简单一些的问题。
回应 20160927 20:15 
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulat...
20110226 03:21
Evolution can be fast. Mutations can occur at a comparatively high rate. A single bacterium in 10ml culture grows and divides to reach saturation of 10^10 cells in less than a day. Since mutation rate is 10^(9) per basepair per generation, up to saturation, the bacterial population reach 10 mutation per basepair. If we treat mutation as randomized force, which abolishes edges in gene regulatory graph, evolutionarily conserved edges preserve fitness to the organism. Autoregulation, including positive and negative autoregulations, are overrepresented in E.coli transcription network. Parameters of such autoregulation are under natural selection. Negative repression efficiently and robustly lock the gene into steadystate expression. Presence of such repression reduces cellcell variation. Positive autoregulation is slower than unregulated gene. Such slow dynamics can be useful in relatively long developmental processes.
回应 20110226 03:21 
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
20110222 18:29
While activation/repression graph reveals a qualitative dynamics of simple circuits, further consideration has to be done on separation of time scale of different cellular processes. For stable proteins, especially protein assuming static structural roles, which do not belong to response module to external signals, have a response time similar to that of a cell generation time.
回应 20110222 18:29 
Appendix C  Graph Properties of Transcription Networks sparse connectivity: Transcription networks are sparse, since ratio of existing edges and theoretical upper limit of edges << 1. Typically, less than 0.1% of possible edges are found in the network. degree distribution: Typically mean degree is 2 to 10 edges/node. Outdegree distribution can be approximately described as a power law,... (4回应)
20110213 06:54
Appendix C  Graph Properties of Transcription Networks sparse connectivity: Transcription networks are sparse, since ratio of existing edges and theoretical upper limit of edges << 1. Typically, less than 0.1% of possible edges are found in the network. degree distribution: Typically mean degree is 2 to 10 edges/node. Outdegree distribution can be approximately described as a power law, i.e. P(k) ~ k^(r), with r ~ 1 to 2. Transcription network often have many transcription factors regulate a few genes, fewer nodes that regulate tens of genes, and even fewer global regulators that regulate hundreds of genes. Global regulators usually respond to key environmental signal to control large ensembles of genes, e.g. bacteria CRP to glucose starvation, RpoS respond to general stress. Indegree distribution instead resembles compact distribution such as Poisson distribution. This may correspond in part to physical limitation that promoters are short in simple organisms. In more complex organisms, DNA looping action can increase the number of input transcription factors to a given gene. Higher organisms often display larger indegrees than microorganisms, accommodating the complex computational needed during development. motifs: Clustering coefficient C is the average number of triangles that a node participates in. Feedforward loop (a type of triangle) is generally overrepresented in motifs of sensory transcription networks. The major contribution to the clustering coefficient therefore stems from feedforward loops. This pattern appears to be selected due to its function, such as filtering and response acceleration. Generally, it appears that global statistical properties of biological network such as degree sequences and cluster sequences are the result of selection working on the detailed circuit patterns in each individual system. Different networks have different selection constraints, which must be understood in order to understand their graphical properties. modularity: Network modularity is the degree to which it can be separated into nearly independent subnetworks. A measure of modularity is proposed by Newman and Girvan, 2004 and 2005. The rationale of this modularity measure is that: a good partition of a network into modules must comprise many withinmodular edges and as few as possible betweenmodule edges. This is achieved by maximizing a modularity measure Q.
4回应 20110213 06:54
论坛 · · · · · ·
国内出了，并且是译本，还能看  来自Nirvana.Viaje  2 回应  20180716 
我也想要  来自健坤散人  4 回应  20100710 
0 有用 AppleLimeStd 20180715
有之前读“mathematical physiology”的经验，这本书读起来轻松多了。大量的生物网络和工程设计的类比很有意思，并且基本每个小部分都涉及到了一点哲学性的“为什么”的讨论。而这些类比只是为了让一些模型更容易被理解。最后几章逐渐上升到了一种对生物系统演化过程的“思考方式”，很值得琢磨。
0 有用 蓝鸢唯紫 20111009
讨论班之一，讲的不错很清楚，貌似很流行，国外很多网上讨论的~
0 有用 swq457080 20180113
分析了转录调控网络，新的观点包括响应时间、反馈回路、robustness等。对生物网络的进化规则有清晰的描述, 如costbenefit analysis 和 demand rules. 相当于硕士微电子和博士生信的一个统一
0 有用 lavie 20121202
读了一大半
0 有用 dliu201304 20140629
入门。
0 有用 AppleLimeStd 20180715
有之前读“mathematical physiology”的经验，这本书读起来轻松多了。大量的生物网络和工程设计的类比很有意思，并且基本每个小部分都涉及到了一点哲学性的“为什么”的讨论。而这些类比只是为了让一些模型更容易被理解。最后几章逐渐上升到了一种对生物系统演化过程的“思考方式”，很值得琢磨。
0 有用 swq457080 20180113
分析了转录调控网络，新的观点包括响应时间、反馈回路、robustness等。对生物网络的进化规则有清晰的描述, 如costbenefit analysis 和 demand rules. 相当于硕士微电子和博士生信的一个统一
0 有用 王兵 20161130
很喜欢的一本系统生物学书，而且有幸见到 Uri Alon 本人签名合影。
0 有用 [已注销] 20150508
a beautiful book~
0 有用 dliu201304 20140629
入门。