抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Complex networks arise in a wide range of biological and sociotechnical systems. Epidemic spreading is central to our understanding of dynamical processes in complex networks, and is of interest to physicists, mathematicians, epidemiologists, and computer and social scientists. This review presents the main results and paradigmatic models in infectious disease modeling and generalized social contagion processes.

Epidemic processes in complex networks

A great variety of systems in nature, society and technology -- from the web of sexual contacts to the Internet, from the nervous system to power grids -- can be modeled as graphs of vertices coupled by edges The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems In many cases, however, the edges are not continuously active As an example, in networks of communication via email, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts In some cases, edges are active for non-negligible periods of time: eg, the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks

Temporal Networks

Communications of the ACM (CACM for short, not the best sounding acronym around) is the ACM’s flagship magazine. Started in 1957, CACM is handy for keeping up to date on current research being carried out across all topics of computer science and realworld applications. CACM has had an illustrious past with many influential pieces of work and debates started within its pages. These include Hoare’s presentation of the Quicksort algorithm; Rivest, Shamir and Adleman’s description of the first publickey cryptosystem RSA; and Dijkstra’s famous letter against the use of GOTO. In addition to the print edition, which is released monthly, there is a fantastic website (http://cacm.acm. org/) that showcases not only the most recent edition but all previous CACM articles as well, readable online as well as downloadable as a PDF. In addition, the website lets you browse for articles by subject, a handy feature if you want to focus on a particular topic. CACM is really essential reading. Pretty much guaranteed to contain content that is interesting to anyone, it keeps tabs on the latest in computer science. It is a valuable asset for us students, who tend to delve deep into a particular area of CS and forget everything that is happening around us. — Daniel Gooch U ndergraduate research is like a box of chocolates: You never know what kind of project you will get. That being said, there are still a few things you should know to get the most out of the experience.

Communications of the ACM

https://www.linkgroup.hu/docs/13PharmTher.pdf

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review

Connections in complex networks are inherently fluctuating over time and exhibit more dimensionality than analysis based on standard static graph measures can capture. Here, we introduce the concepts of temporal paths and distance in time-varying graphs. We define as temporal small world a time-varying graph in which the links are highly clustered in time, yet the nodes are at small average temporal distances. We explore the small-world behavior in synthetic time-varying networks of mobile agents and in real social and biological time-varying systems.

/pdf/small-world-behavior-in-time-varying-graphs-3oj3v0615h.pdf

Small-world behavior in time-varying graphs.

Temporal networks, i.e., networks in which the interactions among a set of elementary units change over time, can be modelled in terms of time-varying graphs, which are time-ordered sequences of graphs over a set of nodes. In such graphs, the concepts of node adjacency and reachability crucially depend on the exact temporal ordering of the links. Consequently, all the concepts and metrics proposed and used for the characterisation of static complex networks have to be redefined or appropriately extended to time-varying graphs, in order to take into account the effects of time ordering on causality. In this chapter we discuss how to represent temporal networks and we review the definitions of walks, paths, connectedness and connected components valid for graphs in which the links fluctuate over time. We then focus on temporal node-node distance, and we discuss how to characterise link persistence and the temporal small-world behaviour in this class of networks. Finally, we discuss the extension of classic centrality measures, including closeness, betweenness and spectral centrality, to the case of time-varying graphs, and we review the work on temporal motifs analysis and the definition of modularity for temporal graphs.

Graph Metrics for Temporal Networks

The study of influential members of human networks is an important research question in social network analysis. However, the current state-of-the-art is based on static or aggregated representation of the network topology. We argue that dynamically evolving network topologies are inherent in many systems, including real online social and technological networks: fortunately the nature of these systems is such that they allow the gathering of large quantities of finegrained temporal data on interactions amongst the network members.In this paper we propose novel temporal centrality metrics which take into account such dynamic interactions over time. Using a real corporate email dataset we evaluate the important individuals selected by means of static and temporal analysis taking two perspectives: firstly, from a semantic level, we investigate their corporate role in the organisation; and secondly, from a dynamic process point of view, we measure information dissemination and the role of information mediators. We find that temporal analysis provides a better understanding of dynamic processes and a more accurate identification of important people compared to traditional static methods.

/pdf/analysing-information-flows-and-key-mediators-through-2l0qxx3e33.pdf

Analysing information flows and key mediators through temporal centrality metrics

The analysis of social and technological networks has attracted a lot of attention as social networking applications and mobile sensing devices have given us a wealth of real data. Classic studies looked at analysing static or aggregated networks, i.e., networks that do not change over time or built as the results of aggregation of information over a certain period of time. Given the soaring collections of measurements related to very large, real network traces, researchers are quickly starting to realise that connections are inherently varying over time and exhibit more dimensionality than static analysis can capture.In this paper we propose new temporal distance metrics to quantify and compare the speed (delay) of information diffusion processes taking into account the evolution of a network from a local and global view. We show how these metrics are able to capture the temporal characteristics of time-varying graphs, such as delay, duration and time order of contacts (interactions), compared to the metrics used in the past on static graphs. As a proof of concept we apply these techniques to two classes of time-varying networks, namely connectivity of mobile devices and e-mail exchanges.

/pdf/temporal-distance-metrics-for-social-network-analysis-34wiqzabg9.pdf

Temporal distance metrics for social network analysis

The analysis of social and technological networks has attracted a lot of attention as social networking applications and mobile sensing devices have given us a wealth of real data. Classic studies looked at analysing static or aggregated networks, i.e., networks that do not change over time or built as the results of aggregation of information over a certain period of time. Given the soaring collections of measurements related to very large, real network traces, researchers are quickly starting to realise that connections are inherently varying over time and exhibit more dimensionality than static analysis can capture.In this paper we propose new temporal distance metrics to quantify and compare the speed (delay) of information diffusion processes taking into account the evolution of a network from a global view. We show how these metrics are able to capture the temporal characteristics of time-varying graphs, such as delay, duration and time order of contacts (interactions), compared to the metrics used in the past on static graphs. We also characterise network reachability with the concepts of in- and out-components. Then, we generalise them with a global perspective by defining temporal connected components. As a proof of concept we apply these techniques to two classes of time-varying networks, namely connectivity of mobile devices and interactions on an online social network.

/pdf/characterising-temporal-distance-and-reachability-in-mobile-4dyivkvhln.pdf

John Tang

Papers

Small-world behavior in time-varying graphs.

Graph Metrics for Temporal Networks

Analysing information flows and key mediators through temporal centrality metrics

Temporal distance metrics for social network analysis

Characterising temporal distance and reachability in mobile and online social networks