NSF Postdoctoral Fellowship in Biology for FY 2011

本行动资助2011年度美国国家科学基金会生物学博士后研究奖学金，生物学与数学和物理科学交叉。该奖学金为生物学和统计学交叉领域的研究员在主办实验室的研究和培训计划提供支持。罗里·罗尔夫斯的研究和培训计划的标题是“开发用于检查基因表达进化的统计工具”。该奖学金的主办机构是加州大学伯克利分校，赞助科学家是dr。Rasmus Nielsen和Sandrine Dudoit。对特定基因使用程度的调节，称为基因表达，已被认为是解释物种多样性的重要机制，但还没有建立一个严格的统计框架来模拟基因表达进化。本研究使用Ornstein-Uhlenbeck过程来建立基因表达进化的模型。它考虑了现有的系统发育，基因之间和物种之间的关系，限制基因表达的因素，以及最适合的表达水平。在证明了该模型的生物学和统计学有效性之后，该研究使用了一组哺乳动物基因表达的数据，通过新的RNA-Seq技术进行测量。对哺乳动物基因表达水平进化的具体假设进行了检验。例如，基于该模型，似然比检验确定人类大脑中表达的基因是否沿着人类物种谱系经历了快速的表达适应。目标是生成一个模型的开源软件包，以便在跨生物学学科的表达进化研究中广泛使用。培训目标包括加强科学合作以及开发和分发科学界可以广泛获得的工具。更广泛的影响包括通过与科学媒体和公共博物馆合作，向公众宣传物种差异的根本原因。教育拓展包括在K-12学校和社区大学设计和教授一门课程。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2011, Intersections of Biology and Mathematical and Physical Sciences. The fellowship supports a research and training plan in a host laboratory for the Fellow at the intersection of biology and statistics. The title of the research and training plan for this fellowship to Rori Rohlfs is "Developing statistical tools to examine the evolution of gene expression." The host institution for this fellowship is the University of California, Berkeley, and the sponsoring scientists are Drs. Rasmus Nielsen and Sandrine Dudoit.The regulation of the degree to which a particular gene is used, called gene expression, has been proposed as an important mechanism explaining much of species diversity yet a rigorous statistical framework that models gene expression evolution has not yet been established. This research uses the Ornstein-Uhlenbeck process to build a model of the evolution of gene expression. It takes into account the existing phylogeny, relationships between genes and between species, factors limiting constraints on gene expression, and an optimally fit expression level. After demonstrating the model's biological and statistical validity, the research uses a data set of mammalian gene expression, as measured with new RNA-Seq technology. Specific hypotheses regarding the evolution of gene expression levels in mammals are tested. For instance, based on the model, the likelihood ratio test determines if genes expressed in human brain are undergoing rapid expression adaptation along the human species lineage. A goal is to produce an open source software package of the model for broad use in studies of expression evolution across biological disciplines.Training goals include strengthening scientific collaborations and developing and distributing tools that will be accessible widely to the scientific community. Broader impacts include outreach to the public through collaborations with science media and public museums on the underlying causes of differences between species. Educational outreach includes designing and teaching a course at K-12 schools and community colleges.