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

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

https://bioinformatics.cs.vt.edu/~easychair/HusonBryant_MBE_2006.pdf

Application of Phylogenetic Networks in Evolutionary Studies

DBpedia is a community effort to extract structured information from Wikipedia and to make this information available on the Web. DBpedia allows you to ask sophisticated queries against datasets derived from Wikipedia and to link other datasets on the Web to Wikipedia data. We describe the extraction of the DBpedia datasets, and how the resulting information is published on the Web for human-andmachine-consumption. We describe some emerging applications from the DBpedia community and show how website authors can facilitate DBpedia content within their sites. Finally, we present the current status of interlinking DBpedia with other open datasets on the Web and outline how DBpedia could serve as a nucleus for an emerging Web of open data.

/pdf/dbpedia-a-nucleus-for-a-web-of-open-data-64wla3p0zr.pdf

DBpedia: a nucleus for a web of open data

This collaboratively edited knowledgebase provides a common source of data for Wikipedia, and everyone else.

https://dl.acm.org/doi/pdf/10.1145/2629489

Wikidata: a free collaborative knowledgebase

Data integration is the problem of combining data residing at different sources, and providing the user with a unified view of these data. The problem of designing data integration systems is important in current real world applications, and is characterized by a number of issues that are interesting from a theoretical point of view. This document presents on overview of the material to be presented in a tutorial on data integration. The tutorial is focused on some of the theoretical issues that are relevant for data integration. Special attention will be devoted to the following aspects: modeling a data integration application, processing queries in data integration, dealing with inconsistent data sources, and reasoning on queries.

/pdf/data-integration-a-theoretical-perspective-58aesjvhuk.pdf

Data integration: a theoretical perspective

A characterisation of rigid circuit graphs

A Note on the Metric Properties of Trees

Curated databases in bioinformatics and other disciplines are the result of a great deal of manual annotation, correction and transfer of data from other sources. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its integrity and scientific value. General purpose database systems provide little support for tracking provenance, especially when data moves among databases. This paper investigates general-purpose techniques for recording provenance for data that is copied among databases. We describe an approach in which we track the user's actions while browsing source databases and copying data into a curated database, in order to record the user's actions in a convenient, queryable form. We present an implementation of this technique and use it to evaluate the feasibility of database support for provenance management. Our experiments show that although the overhead of a naive approach is fairly high, it can be decreased to an acceptable level using simple optimizations.

/pdf/provenance-management-in-curated-databases-4isw6dy49x.pdf

Provenance management in curated databases

We present a new principle for the development of database query languages that the primitive operations should be organized around types. Viewing a relational database as consisting of sets of records, this principle dectates that we should investigate separately operations for records and sets. There are two immediate advantages of this approach, which is partly inspired by basic ideas from category theoryl. First, it provides a language for structures in which record and set types may be freely combined: nested relations or complex objects. Second, the fundamental operations for sets are closely related to those for other “collection types” such as bags or lists, and this suggests how database languages may be uniformly extended to these new types. the most general operation on sets, that of structural recursion , is one in which not all programs are well-defined. In looking for limited forms of this operation that always give rise to well-defined operations, we find a number of close connection with exiting database languages, notably those developed for complex objects. Moreover, even though the general paradigm of structural recursion is shown to be no more expressive than one of the existing languages for complex objects, it possesses certain properties of uniformity that make it a better candidate for an efficient, practical language. Thus rather than developing query languages by extending, for example, relational calculus, we advocate a very powerful paradigm in which a number of well-known languages are to be found as natural sublanguages.

Principles of programming with complex objects and collection types

This paper presents structural recursion as the basis of the syntax and semantics of query languages for semistructured data and XML. We describe a simple and powerful query language based on pattern matching and show that it can be expressed using structural recursion, which is introduced as a top-down, recursive function, similar to the way XSL is defined on XML trees. On cyclic data, structural recursion can be defined in two equivalent ways: as a recursive function which evaluates the data top-down and remembers all its calls to avoid infinite loops, or as a bulk evaluation which processes the entire data in parallel using only traditional relational algebra operators. The latter makes it possible for optimization techniques in relational queries to be applied to structural recursion. We show that the composition of two structural recursion queries can be expressed as a single such query, and this is used as the basis of an optimization method for mediator systems. Several other formal properties are established: structural recursion can be expressed in first-order logic extended with transitive closure; its data complexity is PTIME; and over relational data it is a conservative extension of the relational calculus. The underlying data model is based on value equality, formally defined with bisimulation. Structural recursion is shown to be invariant with respect to value equality.

/pdf/unql-a-query-language-and-algebra-for-semistructured-data-30t17pkj8y.pdf

Peter Buneman

Papers

A characterisation of rigid circuit graphs

A Note on the Metric Properties of Trees

Provenance management in curated databases

Principles of programming with complex objects and collection types

UnQL: a query language and algebra for semistructured data based on structural recursion