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

Semistructured databases are treated as dynamically typed: they come equipped with no independent schema or type system to constrain the data. Query languages that are designed for semistructured data, even when used with structured data, typically ignore any type information that may be present. The consequences of this are what one would expect from using a dynamic type system with complex data: fewer guarantees on the correctness of applications. For example, a query that would cause a type error in a statically typed query language will return the empty set when applied to a semistructured representation of the same data.

Much semistructured data originates in structured data. A semistructured representation is useful when one wants to add data that does not conform to the original type or when one wants to combine sources of different types. However, the deviations from the prescribed types are often minor, and we believe that a better strategy than throwing away all type information is to preserve as much of it as possible. We describe a system of untagged union types that can accommodate variations in structure while still allowing a degree of static type checking.

A novelty of this system is that it involves non-trivial equivalences among types, arising from a law of distributivity for records and unions: a value may be introduced with one type (e.g., a record containing a union) and used at another type (a union of records). We describe programming and query language constructs for dealing with such types, prove the soundness of the type system, and develop algorithms for subtyping and typechecking.

/pdf/union-types-for-semistructured-data-14ivoirptg.pdf

Union Types for Semistructured Data

A deterministic model for semistructured data

Annotation is some form of data that is added to an existing database. It could be additional data that for whatever reason cannot be stored in the original database, or it could be some form of metadata such as comments, probabilities, timestamps that are not normally regarded part of the basic database design. It has recently been observed that, in order to determine how annotations should be propagated through database queries, we need to have some structure on them. Although various forms of annotation have been considered in some detail, each form has been considered in isolation.In this paper we consider what happens when different forms of annotation are combined. We show that there are many cases in which annotations, for quite natural reasons, depend on one another. What is the appropriate structure to place on such annotations? We provide a method for combining different forms and provide a normal form which is useful in deciding whether two or more combined annotations are equivalent.

/pdf/combining-dependent-annotations-for-relational-algebra-347dvod6zn.pdf

Combining dependent annotations for relational algebra

Information concerning the origin of data (that is, its provenance) is important in many areas, especially scientific recordkeeping. Currently, provenance information must be maintained explicitly, by added effort of the database maintainer. Since such maintenance is tedious and error-prone, it is desirable to provide support for provenance in the database system itself. In order to provide such support, however, it is important to provide a clear explanation of the behavior and meaning of existing database operations, both queries and updates, with respect to provenance. In this paper we take the view that a query or update implicitly defines a provenance mapping linking components of the output to the originating components in the input. Our key result is that the proposed semantics are expressively complete relative to natural classes of queries that explicitly manipulate provenance.

/pdf/on-the-expressiveness-of-implicit-provenance-in-query-and-3akfynotvn.pdf

On the expressiveness of implicit provenance in query and update languages

Central features of object-oriented programming are method inheritance and data abstraction attained through hierarchical organization of classes. Recent studies show that method inheritance can be nicely supported by ML style type inference when extended to labeled records. This is based on the fact that a function that selects a field ƒ of a record can be given a polymorphic type that enables it to be applied to any record which contains a field ƒ. Several type systems also provide data abstraction through abstract type declarations. However, these two features have not yet been properly integrated in a statically checked polymorphic type system.This paper proposes a static type system that achieves this integration in an ML-like polymorphic language by adding a class construct that allows the programmer to build a hierarchy of classes connected by multiple inheritance declarations. Moreover, classes can be parameterized by types allowing “generic” definitions. The type correctness of class declarations is statically checked by the type system. The type system also infers a principal scheme for any type correct program containing methods and objects defined in classes.

Peter Buneman

Papers

Union Types for Semistructured Data

A deterministic model for semistructured data

Combining dependent annotations for relational algebra

On the expressiveness of implicit provenance in query and update languages

Static type inference for parametric classes