Whole genome shotgun: modeling, optimization, assembly

个人简介(由申请人提供)：我是一名数学家，在美国攻读博士学位 加州大学伯克利分校。通过理论和计算， 包括大型软件开发，我解决了长期悬而未决的问题 在代数几何和纠错码领域。我已经长大了 对生物学的计算方面越来越感兴趣，并认识到 可以解决一些重要的和具有挑战性的生物学问题 使用我熟悉的数学工具。激动人心且富有成效 与怀特黑德研究所的研究人员的互动，包括 全基因组猎枪组装，证实了我对这一领域的热情 研究表明，我需要更深入、更正规的培训才能理解 这些问题的生物学背景。 我致力于再培训课程，这将丰富我的生物 背景和通过课程学习促进在基因组学领域的职业生涯 培训和研究经验。 这笔赠款将使我能够继续和扩展我在基本开放方面的工作 外地的问题，包括成本效益高和序列准确 获取和组装，跨物种基因组比对，以及通过 后者，基因和调控区域的有效定位，从而脱落 揭示了大量新的基因组数据。 我将在怀特黑德研究所开展我的工作，在那里，一个跨学科的 精神和激励的智力环境与尖端相结合 生产设施。埃里克·兰德博士将指导我的项目。他的背景和 研究兴趣使他非常适合指导我。他还赚到了 他的纯数学博士学位，并在界面上成功地工作 在纯数学和分子生物学以及基因组研究方面。我看着 期待加入他的团队，该团队将设计 老鼠的基因组，自己进行测序，并从中做出推断 关于人类和老鼠的基因组。

DESCRIPTION (provided by the applicant): I am a mathematician with a Ph.D. from the University of California at Berkeley. Through theory and computation, including large-scale software development, I solved longstanding open problems in the fields of algebraic geometry and error-correcting codes. I have grown increasingly interested in the computational aspects of biology and recognize that a number of important and challenging biological problems can be addressed using the mathematical tools I am familiar with. Stimulating and productive interactions with researchers at the Whitehead Institute, including work on whole genome shotgun assembly, have confirmed my enthusiasm for this area of research and revealed my need for deeper and more formal training to understand the biological context of these problems. I am committed to a course of retraining which will enrich my biological background and facilitate a career in genomics through coursework, on the job training, and research experience. The grant will enable me to continue and extend my work on fundamental open problems of the field, including cost-effective and accurate sequence acquisition and assembly, cross-species genomic alignment, and through the latter, effective location of genes and regulatory regions, thereby shedding light on vast riches of new genomic data. I will carry out my work at the Whitehead Institute, where an interdisciplinary spirit and stimulating intellectual environment meshes with a cutting-edge production facility. Dr. Eric Lander will direct my project. His background and research interests make him ideally suited to supervising me. He also earned his doctorate in pure mathematics and has worked successfully at the interface of pure mathematics and molecular biology as well as in genome research. I look forward to joining his team, which will design the sequencing and assembly of the mouse genome, do the sequencing itself, and from there make deductions about both the human and mouse genomes.