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

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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.