RUI: Quartet-Based Approaches to Phylogenomics

RUI：基于四重奏的系统基因组学方法

• 批准号: 1616186
• 负责人: Joseph Rusinko
• 金额: $ 18万
• 依托单位: Hobart and William Smith Colleges
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616186&HistoricalAwards=false
• 关键词: RUI; Quartet; Based; Approaches; Phylogenomics

A modernization of the mathematical and statistical tools used to uncover the evolutionary history of life on earth is required to keep pace with the rapid expansion in the availability of genetic data. Moreover, different segments of genetic information can tell conflicting evolutionary histories about a collection of organisms. This project develops mathematical tools for reconstructing the evolutionary history of large collections of organisms, and for constructing a single tree that encapsulates the conflicting stories told by different pieces of the genome. Ten undergraduate students, many recruited from groups underrepresented in STEM fields at this primarily undergraduate institution, will be trained in techniques at the intersection of mathematics, statistics, and biology that are required for the algorithmic developments. Most methods of super-tree or species tree reconstruction rely on accurately reconstructed gene trees. In practice, however, most inferred gene trees used in these reconstructions do contain errors. By identifying and explicitly accounting for gene tree estimation error, this project will improve algorithms for super-tree and species tree reconstruction. Alternative approaches for which species trees are reconstructed without dependence on the prior estimation of gene trees will also be developed.

用来揭示地球上生命进化史的数学和统计工具需要现代化，以跟上可获得的遗传数据的快速增长的步伐。此外，遗传信息的不同部分可以告诉人们关于一组有机体的相互冲突的进化史。该项目开发了数学工具，用于重建大型生物体集合的进化史，并构建一棵树，封装不同基因组片段讲述的相互冲突的故事。十名本科生将接受算法开发所需的数学、统计学和生物学交叉技术方面的培训，其中许多人是从这所以本科为主的院校STEM领域代表性较低的群体中招募的。大多数超树或物种树的重建方法都依赖于准确重建的基因树。然而，在实践中，这些重建中使用的大多数推断的基因树确实包含错误。通过识别和显式解释基因树估计误差，该项目将改进超树和物种树重建算法。还将开发另一种方法，在不依赖于基因树的先前估计的情况下重建物种树。

项目成果

Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods

• DOI: 10.1109/tcbb.2016.2638911
• 发表时间: 2018-05-01
• 期刊: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
• 影响因子: 4.5
• 作者: Davidson, Ruth;Lawhorn, MaLyn;Weber, Noah
• 通讯作者: Weber, Noah

H-Representation of the Kimura-3 Polytope for the $m$-Claw Tree

$m$-爪树的 Kimura-3 多胞体的 H 表示

• DOI: 10.1137/15m1051890
• 发表时间: 2017
• 期刊: SIAM Journal on Discrete Mathematics
• 影响因子: 0.8
• 作者: Mauhar, Marie;Rusinko, Joseph;Vernon, Zoe
• 通讯作者: Vernon, Zoe