CAREER: Analysis, Construction and Visualization of 3D Genome Structures

这个项目将研究基因组的三维(3D)结构。三维基因组结构是研究基因组折叠、基因组功能和空间基因调控的关键，但与一维(1D)线性基因组相比，它还没有得到很好的研究。这个职业项目的主要目标是设计和开发基于接触的计算方法，使用由基因组构象捕获技术和下一代DNA测序产生的染色体接触(交互)数据来分析、构建和可视化基因组的3D结构。研究数据、方法和工具将为开发两门新的生物信息学课程提供材料，这两门课程整合了计算优化、分子结构建模、基因组测序和基因组注释。该项目的成功完成将产生一套新的计算方法和生物信息学工具来分析、构建和可视化3D基因组结构。这些方法和工具将促进在空间背景下对基因组结构、功能和基因调控的研究，这将在后基因组时代现代生物科学的几乎所有方面都有广泛的应用。研究部分将产生一套丰富的新数据和方法，以培训K1-12、本科生、研究生和博士后。这两门生物信息学新课程的广泛推广，将丰富生物信息学、计算生物学、计算机科学、大规模约束优化、分子结构建模等课程。有关该项目的更多信息，请访问：http://www.cs.missouri.edu/~chengji/nsf_career.html.。

This project will investigate the three-dimensional (3D) structures of genomes. A 3D genome structure is critical for studying genome folding, genome function, and spatial gene regulation, but it has not been well studied in comparison with a one-dimensional (1D) linear genome. The main goal of this CAREER project is to design and develop contact-based computational methods to analyze, construct, and visualize 3D structures of genomes using chromosomal contact (interaction) data generated by genome conformation capturing techniques and next-generation DNA sequencing. The research data, methods and tools will provide materials to develop two new bioinformatics courses, integrating computational optimization, molecular structure modeling, genome sequencing, and genome annotation. The successful completion of this project will produce a set of novel computational methods and bioinformatics tools to analyze, construct, and visualize 3D genome structures. The methods and tools will boost the study of genome structure, function, and gene regulation in the spatial context, which will have broad applications in almost every aspect of modern biological sciences in the post-genomic era. The research component will generate a rich set of new data and methods to train K1-12, undergraduate, graduate and postdoctoral students. The wide dissemination of the two new bioinformatics courses will enrich the curriculum of bioinformatics, computational biology, computer science, large-scale constrained optimization, and molecular structure modeling. More information about the project is available at: http://www.cs.missouri.edu/~chengji/nsf_career.html.