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

The purpose of this thesis is to investigate a type system for databases and object-oriented programming and to design a statically typed programming language for these applications. Such a language should ideally have a static type system that supports: (1) polymorphism and static type inference, (2) rich data structures and operations to represent various data models for databases including the relational model and more recent complex object models, (3) central features of object-oriented programming including user definable class hierarchies, multiple inheritance, and data abstraction, (4) the notion of extents and object-identities for object-oriented databases. Without a proper formalism, it is not obvious that the construction of such a type system is possible. This thesis attempts to construct one such formalism and proposes a programming language that uniformly integrate all of the above features.
The specific contributions of this thesis include: (1) A simple semantics for ML polymorphism and axiomatization of the equational theory of ML. (2) A uniform generalization of the relational model to arbitrary complex database objects that are constructed by labeled records, labeled variants, finite sets and recursive definition. (3) A framework for semantics of types for complex database objects. (4) The notion of conditional typing schemes that extends Milner's typing scheme for ML to a wide range of complex structures and operations. (5) A formulation of the notion of classes and inheritance in an ML style static type system. (6) The notion of views that enable us to represent object-oriented databases in an ML style static type system. (7) A proposal of a polymorphic programming language, Machiavelli, for databases and object-oriented programming with static type inference. In addition to the above technical contributions, a prototype implementation of Machiavelli that embodies most of the features presented in this thesis has been done in Standard ML of New Jersey.

/pdf/a-study-of-semantics-types-and-languages-for-databases-and-51bgen7b5l.pdf

A study of semantics, types and languages for databases and object-oriented programming

Functional programming and databases

Wikis have proved enormously successful as a means to collaborate in the creation and publication of textual information. At the same time, a large number of curated databases have been developed through collaboration for the dissemination of structured data in specific domains, particularly bioinformatics. We demonstrate a general-purpose platform for collaborative data management, DBWiki, designed to achieve the best of both worlds. Our system not only facilitates the collaborative creation of a database; it also provides features not usually provided by database technology such as versioning, provenance tracking, citability, and annotation. In our demonstration we will show how DBWiki makes it easy to create, correct, discuss and query structured data, placing more power in the hands of users while managing tedious details of data curation automatically.

/pdf/dbwiki-a-structured-wiki-for-curated-data-and-collaborative-zsrvop4f7a.pdf

DBWiki: a structured wiki for curated data and collaborative data management

Functional programming systems, although they have nice theoretical properties and elegant implementations, have failed to make any significant impact in the practical world of applications programming. We shall describe a simple FP system for databases that is gaining considerable practical use as an interface language for complex database management systems. Not only does it provide a concise formalism for database queries but the implementation, which is done by a lazy evaluator, in many cases produces more efficient queries than conventional query systems because it reduces the amount of i/o. We also suggest that the implementation technique may be more generally applicable to FP systems.

A practical functional programming system for databases

Provenance, or records of the origin, context, custody, derivation or other historical information about a (digital) object, has recently become an important research topic in a number of areas, particularly databases. However, there has been little interaction between researchers across subdisciplines of computer science working on related problems. This article reports on a workshop on Principles of Provenance held in Edinburgh, Scotland in November 2007, which facilitated interaction among researchers working on provenance in databases, security, information retrieval, Semantic Web, and software engineering settings, as well as developers and database administrators who are currently working with provenance in practice, or foresee the need to do so in the near future.

Peter Buneman

Papers

A study of semantics, types and languages for databases and object-oriented programming

Functional programming and databases

DBWiki: a structured wiki for curated data and collaborative data management

A practical functional programming system for databases

Report on the Principles of Provenance Workshop