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

Data structures and data types of object-oriented databases

Annotation of existing data is becoming a standard tool in many branches of e-science. Increasingly, databases are being built to receive annotation, and other tools are being developed to annotate existing databases. Annotation is becoming an important part of communication among scientists. In this paper we review various kinds of annotation systems and describe the importance of designing databases in such a way that they can receive annotation. This includes designing extensible databases and the need for some form of co-ordinate system for the attachment of annotations. 1 Annotation: adding to existing structure

Annotating scientific data: why it is important and why it is difficult

This chapter is motivated by the question “are there any clean mathematical principles behind the design of query languages?” One can hardly blame the reader of various recent standards for asking this question The authors try to sketch what such a mathematical framework could be One of the classifying principles they use extensively is that of languages being organised around type systems, with language primitives corresponding to constructors and deconstructors for each type There is some value in casting the concepts in as general a form as possible; hence the use of the language of category theory for describing them Once the semantic framework is discussed, the chapter presents a calculus, itself a language, that could be (and was) used as an internal representation for various user languages The discussion is relevant to all kinds of data models: relational, object-relational, object-oriented, and semi-structured

A Structural Approach to Query Language Design

Gray Code Gleanings

We study absolute and relative keys for XML, and investigate their associated decision problems. We argue that these keys are important to many forms of hierarchically structured data including XML documents. In contrast to other proposals of keys for XML, these keys can be reasoned about efficiently. We show that the (finite) satisfiability problem for these keys is trivial, and their (finite) implication problem is finitely axiomatizable and decidable in PTIME in the size of keys.

Peter Buneman

Papers

Data structures and data types of object-oriented databases

Annotating scientific data: why it is important and why it is difficult

A Structural Approach to Query Language Design

Gray Code Gleanings

Reasoning about keys for XML