Whole genome shotgun: modeling, optimization, assembly

描述（由申请人提供）：我是一名数学家，拥有博士学位。从 位于伯克利的加州大学。通过理论和计算， 包括大规模软件开发，我解决了长期存在的问题， 在代数几何和纠错码领域。我已经成长 对生物学的计算方面越来越感兴趣， 许多重要的和具有挑战性的生物学问题可以被解决， 使用我熟悉的数学工具。的刺激和富有成效 与怀特黑德研究所研究人员的互动，包括以下工作 全基因组鸟枪组装，证实了我对这一领域的热情， 研究，并揭示了我需要更深入，更正式的培训，以了解 这些问题的生物学背景。 我决心参加一个再培训课程，这将丰富我的生物学知识。 背景和促进基因组学的职业生涯，通过课程，在工作中 培训和研究经验。 这笔赠款将使我能够继续和扩大我的工作，基本开放 该领域的问题，包括成本效益和准确的序列 获取和组装，跨物种基因组比对，并通过 后者，基因和调控区的有效定位，从而脱落 新基因组数据的巨大财富。 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的 生产设施。埃里克·兰德博士将指导我的项目。他的背景和 他的研究兴趣使他非常适合指导我。他还赢得了 他的纯数学博士学位，并已成功地在接口 在纯数学和分子生物学以及基因组研究中的重要性。我看起来 期待加入他的团队，他们将设计 老鼠的基因组，自己做测序，然后从那里做出推论 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.