Statistical and high-throughput models of enhancer function and evolution

项目摘要 这份多元化副刊建议培训非裔美国人克里斯蒂安·伯恩斯先生 硕士研究生，研究比较基因组学和基因组生物学的现代方法。 非洲裔美国人在进化生物学中的代表性严重不足，而这 补充剂将帮助伯恩斯先生实现他进入顶级博士学位的目标 计划，并进一步发展他的职业生涯，成为一名R1大学的教员。我们的 主要目的是培训伯恩斯先生在基因组生物学方面的基本技能，包括长期阅读 基因组测序、组装、注释和比较分析。这次培训将 通过建立在PI实验室最新工作基础上的研究项目来完成 这揭示了转座元素(TE)丰度的显著差异 有亲缘关系的、神秘的画眉鸟种(龟科)。比克尼氏华盖线虫和微小华盖线虫 据估计，在距今仅15,000年前就出现了分歧，但展示了高达10%的 TE丰度的差异取决于TE亚族。这一项目将曝光李嘉诚。 燃烧到生物信息学的尖端方法，包括PacBio HiFi基因组 组装、组装质量评估、基因组比对、TE丰度和 注释和令人费解的分析。此项目与父建议书相关 因为众所周知增强子的起源和功能与TE之间的关系 增殖：脊椎动物基因组中的许多细胞被发现支持增强剂 在多种组织中的不同功能。父级提案的重点是理解 如何估计增强剂进化率的变化并将其与 通过高通量增强子分析发挥作用，这一补充将补充 目标2：探索TE扩散与母公司赠款之间可能存在的联系 新的增强子功能的起源。伯恩斯先生将接受深度辅导，重点是 对实现他的职业目标至关重要的四个方面：在科学领域找到自己的声音； 写作的重要性；获得技术技能；以及展望和规划 STEM的未来。这些研究和指导活动将共同加强 伯恩斯先生在进化生物学方面的职业前景，并为他配备持久的技术 和概念技能，使他能够实现他的职业目标。

Project Summary This diversity supplement proposes to train Mr. Christian Burns, an African American master’s student, in modern methods of comparative genomics and genome biology. African Americans are severely underrepresented in evolutionary biology and this supplement will assist Mr. Burns in reaching his goal of gaining admission to a top PhD program and furthering his career towards becoming a faculty at an R1 university. Our main Aim is to train Mr. Burns in basic skills in genome biology, including long-read genome sequencing, assembly, annotation and comparative analysis. This training will be accomplished through a research project building on recent work in the PI laboratory that revealed dramatic differences in transposable element (TE) abundance in two closely related, cryptic species of thrushes (family Turdidae). Catharus bicknelli and C. minimus are estimated to have diverged only ~15,000 years before present, yet exhibit up to 10% difference in TE abundance depending on the TE subfamily. This project will expose Mr. Burns to cutting-edge approaches in bioinformatics, including PacBio HiFi genome assembly, assembly quality assessment, genome alignment, TE abundance and annotation, and pangenome analysis. This project is related to the parent proposal because of the well-known relationship between enhancer origin and function and TE proliferation: many TEs in vertebrate genomes are discovered to underlie enhancers with diverse functions in multiple tissues. The parent proposal is focused on understanding how changes in evolutionary rate of enhancers can be estimated and tied to changes in function through high throughput enhancer assays, and this supplement will complement Aim 2 of the parent grant by exploring possible connections between TE proliferation and the origin of novel enhancer functions. Mr. Burns will receive in-depth mentoring focusing on four areas critical to achieving his career goals: Finding your voice in science; the importance of writing; acquisition of technical skills; and envisioning and planning for a future in STEM. Together these research and mentoring activities will strengthen the career prospects of Mr. Burns in evolutionary biology and equip him with lasting technical and conceptual skills to allow him to achieve his career goals.