Collaborative Research: ABI Innovation: Quantifying and Exploiting the Structure of Phylogenetic Tree Space Through Network Analyses

合作研究：ABI创新：通过网络分析量化和利用系统发育树空间的结构

• 批准号: 1262476
• 负责人: Kyle Gallivan
• 金额: $ 25.6万
• 依托单位: Florida State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1262476&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Innovation; Quantifying

This project will develop a rich and flexible mathematical framework for quantifying the phylogenetic signal (i.e., the information about genealogical relationships among organisms) contained within big data sets of genome sequences. To quantify this signal, the relationships among different phylogenetic trees, or the branches in those trees, will be conceptualized as networks. The structure of these networks provides biologically meaningful information about the degree and causes of phylogenetic uncertainty and conflict. The newly developed framework will be implemented in publicly available software useable as a standalone application and as a webservice. In addition, the core functionality of the developed software will be closely integrated with other ongoing NSF-funded efforts to reconstruct and explore the Tree of Life (iPlant and the Open Tree of Life).This work will draw from expertise in evolutionary biology, computer science, and applied mathematics. Research activities will involve the direct contributions of both graduate and undergraduate researchers and software developers. Undergraduates will learn to code from graduate students in mentor-apprentice relationships. An undergraduate science communications student will develop a website illustrating phylogenetic principles and applied phylogenetic research, highlighting novel insights provided by the methods developed. Additionally, several in-person and remote training workshops will be held to introduce and familiarize researchers with newly developed tools. An ongoing computational biology seminar series targeted towards undergraduates will be held at Louisiana State University. The methods developed as part of this project will improve our ability to understand phylogenetic information, which is integral to a variety of applications in conservation, forensics, agriculture, and epidemiology. Updates on project progress and links to developed tools will be available at http://www.phyleauxgenetics.org/.

该项目将开发一个丰富而灵活的数学框架，用于量化基因组序列的大数据集中的系统发育信号（即有关生物体之间的家谱关系的信息）。 为了量化该信号，不同的系统发育树或这些树木中的分支之间的关系将被概念化为网络。 这些网络的结构提供了有关系统发育不确定性和冲突程度和原因的生物学意义信息。 新开发的框架将在可公开可用的软件中实现，可作为独立应用程序和Web服务。 此外，开发软件的核心功能将与其他正在进行的NSF资助的努力紧密整合，以重建和探索生命之树（iPlant和开放的生命之树）。这项工作将借鉴进化生物学，计算机科学和应用数学方面的专业知识。 研究活动将涉及研究生和本科研究人员和软件开发人员的直接贡献。 本科生将学会从指导批准关系的研究生那里进行编码。 一名本科科学传播专业的学生将开发一个网站，说明系统发育原理和应用系统发育研究，突出了开发方法提供的新颖见解。 此外，将举办几个面对面和远程培训研讨会，以介绍和熟悉研究人员新开发的工具。 持续的计算生物学研讨会系列针对本科生将在路易斯安那州立大学举行。 作为该项目的一部分开发的方法将提高我们了解系统发育信息的能力，这对于保护，取证，农业和流行病学是各种应用的组成部分。有关项目进度的更新和开发工具的链接将在http://www.phyleauxgenetics.org/上找到。