CAREER: Computational and Statistical Genomics of Gene Families

职业：基因家族的计算和统计基因组学

• 批准号: 0845494
• 负责人: Matthew Hahn
• 金额: $ 100.33万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2014-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0845494&HistoricalAwards=false
• 关键词: CAREER; Computational; Statistical; Genomics; Gene

(This award is funded through the American Recovery and Reinvestment Act of 2009: Public Law 111-5).This is a CAREER award to support the research of Dr. Matthew Hahn in the Department of Biology and School of Informatics at Indiana University. Dr. Hahn is a third-year, tenure-track Assistant Professor. Genome sequencing projects have revealed large and frequent changes between species in the size of gene families. These changes have been shown to be responsible for morphological, physiological, and behavioral differences between species, and to contribute to much of the genetic and genomic diversity we observe in nature. To further understand the importance of these changes, researchers must be able to understand the mechanisms and modes by which gene families evolve. Despite the growing body of data on gene families, until recently we lacked a statistical framework that would allow for inferences regarding gene family evolution among species. In earlier work from his dissertation research, Dr. Hahn proposed such a framework for studying gene family evolution, and showed that it could be used for hypothesis testing, inference of ancestral states, and estimation of gene duplication and deletion rates. This project will be developing novel statistical and computational methods for studying gene families, and examining the biological mechanisms underlying gene family evolution. This work is enabling more refined estimates of gene duplication and loss rates, and will provide new ways for detecting and studying whole genome duplications. Methods for studying gene families from low-coverage genomes will also be developed. Gene duplication can distribute paralogous genes across the genome. Locations of individual genes will allow study of both within-genome and between-genome dynamics of gene families. Lineages differ in their rates of gene turnover which raises the question of how these differences come about. This research is identifying the biological factors determining observed rate variation among lineages and among individual gene families. Dr. Hahn is developing new computational models and free software, which will be available at http://www.bio.indiana.edu/~hahnlab/.This research will contribute to many fields, including studies of gene and genome duplication to studies of gene regulation, transposable elements, genetic robustness, and RNA interference. As a part of his CAREER project, the PI is integrating knowledge from these diverse fields at high school, undergraduate, and graduate levels to inform biological reasoning and to create new lines of scientific inquiry. Further, the PI will prepare and implement a curriculum for students at a local technology-focused high school. This curriculum will integrate computers into the biology classroom by introducing the basic principles of programming alongside the basic principles of biology.

（该奖项是通过2009年的《美国复苏与再投资法》（American Recovery and Revistment Act）资助的：公法111-5）。这是一项职业奖，旨在支持印第安纳大学生物学和信息学系的Matthew Hahn博士的研究。 Hahn博士是三年级的任期助理教授。基因组测序项目揭示了基因家族大小的物种之间的巨大变化。这些变化已被证明是物种之间形态，生理和行为差异的原因，并为我们在自然界观察到的许多遗传和基因组多样性做出了贡献。为了进一步了解这些变化的重要性，研究人员必须能够理解基因家族发展的机制和模式。尽管关于基因家族的数据越来越多，但直到最近，我们仍缺乏一个统计框架，该框架可以推断出有关物种之间基因家族进化的推断。在他的论文研究中的早期工作中，哈恩博士提出了研究基因家族进化的框架，并表明它可以用于假设检验，祖先状态的推断以及基因重复和缺失率的估计。该项目将开发用于研究基因家族的新型统计和计算方法，并检查基因家族进化的生物学机制。这项工作正在实现对基因复制和损失率的更精致的估计，并将为检测和研究整个基因组重复提供新的方法。还将开发用于研究低覆盖基因组基因家族的方法。基因重复可以在整个基因组上分布寄生虫基因。单个基因的位置将允许研究基因家族的基因组和基因组之间的动力学。谱系的基因周转率有所不同，这提出了这些差异如何产生的问题。这项研究正在确定确定谱系和个体基因家族之间观察到的速率变化的生物学因素。 Hahn博士正在开发新的计算模型和免费软件，该软件将在http://www.bio.indiana.edu/~hahnlab/..hatiana.ide.edu/chahnlab/...this Research中提供许多领域，包括对基因和基因组重复的研究，以研究基因调控，基因调节，转移元素，遗传稳定性，遗传稳定性，RNA Interpertions和RNA Interpertions和RNA Interpertion。作为他职业生涯项目的一部分，PI正在整合高中，本科和研究生级别的这些不同领域的知识，以告知生物学推理并创建新的科学探究线。此外，PI将为当地以技术为重点的高中的学生准备和实施课程。该课程将通过将编程的基本原理与生物学的基本原理一起引入基本原理，将计算机整合到生物学课堂中。