Statistical Mechanics of Biological Sequence Analysis

该奖项支持凝聚态物理学和生物学之间的理论研究和教育。 生物科学正在经历一场革命性的变革，部分原因是实验技术的出现，这些技术产生了大量的定量生物数据，这些数据需要转化为对生物系统的理解。PI将使用统计物理学工具开发新方法来预测新基因的位置和黏菌多头绒泡菌线粒体基因组中RNA编辑位点的位置。这种生物体编辑其信使RNA，使基因的翻译信使RNA序列不同于其基因组序列。这种RNA编辑导致传统基因预测技术的失败。新的转移矩阵算法意识到RNA编辑将识别基因，精确定位编辑位点，并阐明编辑机制的功能。这个项目可以用一个具有复杂能源景观的物理系统来描述。除了将物理思想应用于生物系统之外，这项跨学科的研究还通过开辟新的探索前沿和推进无序系统的统计物理来推进凝聚态物理学。该奖项支持本科和研究生教育。学生将学习凝聚态物理学和分子生物学的计算技术和概念。这有助于为现代劳动力提供训练有素的个人，他们的背景在生物学和定量物理科学方面都很强。通过生物物理学本科和研究生课程的发展，具有跨学科教育的学生基础将扩大到直接参与研究项目的个人之外。该项目还将产生用于解释定量生物数据的新算法。在研究过程中开发的算法将可供更广泛的材料研究和科学界使用。该奖项支持凝聚态物理学和生物学之间的理论研究和教育。 生物科学正在经历一场革命性的变革，部分原因是实验技术的出现，这些技术产生了大量的定量生物数据，这些数据需要转化为对生物系统的理解。这项研究的重点是发生在埃博拉病毒和人类等多种生物体中的RNA编辑。大多数基因被复制成信使RNA序列，然后被翻译成蛋白质。在表现出RNA编辑的生物体中，特殊的机制在信使RNA被翻译成蛋白质之前对其进行修饰。这使得识别导致特定蛋白质产生的基因变得复杂。它还提出了关于该过程如何工作以及为什么它如此可靠的有趣问题。PI将使用统计物理学工具开发新方法来预测新基因的位置和黏菌多头绒泡菌线粒体基因组中RNA编辑位点的位置。除了将物理思想应用于生物系统之外，这项跨学科的研究还通过开辟新的探索前沿和推进无序系统的统计物理来推进凝聚态物理学。该奖项支持本科和研究生教育。学生将学习凝聚态物理学和分子生物学的计算技术和概念。这有助于为现代劳动力提供训练有素的个人，他们的背景在生物学和定量物理科学方面都很强。通过生物物理学本科和研究生课程的发展，具有跨学科教育的学生基础将扩大到直接参与研究项目的个人之外。该项目还将产生用于解释定量生物数据的新算法。在研究过程中开发的算法将可供更广泛的材料研究和科学界使用。

This award supports theoretical research and education at the interface between condensed matter physics and biology. The biological sciences are undergoing a revolutionary change fueled in part by the emergence of experimental techniques that produce massive amounts of quantitative biological data that need to be transformed into understanding of biological systems. The PI will use statistical physics tools to develop new methods to predict the location of new genes and of RNA editing sites in the mitochondrial genome of the slime mold Physarum polycephalum. This organism edits its messenger RNAs so that the translated messenger RNA sequence of a gene differs from its genomic sequence. This RNA editing leads to a failure of conventional gene prediction techniques. New transfer matrix algorithms aware of RNA editing will identify genes, pinpoint editing sites, and shed light on the functioning of the editing machinery. This project can be described in terms of a physical system with a complex energy landscape. Beyond applying physical ideas to biological systems, this interdisciplinary research also advances condensed matter physics by opening new frontiers of inquiry and by advancing the statistical physics of disordered systems.This award supports education at the undergraduate and graduate levels. Students will learn computational techniques and concepts from condensed matter physics and molecular biology. This helps provide well-trained individuals for the modern workforce with a background that is at once strong in biology and quantitative physical science. Through the development of undergraduate and graduate courses in biophysics the base of students with an interdisciplinary education will be expanded beyond the individuals immediately involved in the research projects. The project will also yield new algorithms for the interpretation of quantitative biological data. Algorithms developed in the course of the research will be accessible to the broader materials research and scientific communities. %%%This award supports theoretical research and education at the interface between condensed matter physics and biology. The biological sciences are undergoing a revolutionary change fueled in part by the emergence of experimental techniques that produce massive amounts of quantitative biological data that need to be transformed into understanding of biological systems. This research focuses on RNA-editing which occurs in organisms as diverse as the Ebola virus and humans. Most genes are copied into messenger RNA sequences that are in turn translated into proteins. In organisms exhibiting RNA-editing, special machinery operates to modify the messenger RNA before it is translated into proteins. This complicates the identification of genes that result in the creation of specific proteins. It also raises interesting questions about how the process works and why it is so reliable. The PI will use statistical physics tools to develop new methods to predict the location of new genes and of RNA editing sites in the mitochondrial genome of the slime mold Physarum polycephalum. Beyond applying physical ideas to biological systems, this interdisciplinary research also advances condensed matter physics by opening new frontiers of inquiry and by advancing the statistical physics of disordered systems.This award supports education at the undergraduate and graduate levels. Students will learn computational techniques and concepts from condensed matter physics and molecular biology. This helps provide well-trained individuals for the modern workforce with a background that is at once strong in biology and quantitative physical science. Through the development of undergraduate and graduate courses in biophysics the base of students with an interdisciplinary education will be expanded beyond the individuals immediately involved in the research projects. The project will also yield new algorithms for the interpretation of quantitative biological data. Algorithms developed in the course of the research will be accessible to the broader materials research and scientific communities.***