CAREER: RUI: NetDA -- Protein Network-Based Software for Disease Analysis Using Cliques, Bipartite Graphs, and Diffusion Kernels

这个项目将在蛋白质网络水平上调查和分析疾病进展的复杂现象。将开发一种软件工具NetDA(基于网络的疾病分析)，以了解疾病在不同阶段之间过渡时疾病进展的基本机制。这项研究的结果不仅有助于疾病的早期诊断，还将有助于针对疾病阶段的药物设计。本科生将参与这项研究。疾病进展过程将被分析为类似事件时间表的结构，其中a)由一组蛋白质完成的代表疾病阶段的每个事件将被用团和团状图来分析，b)信号从一个阶段到下一个阶段的转移将使用二部图和二部体图来分析，以及c)信号的强度将使用扩散核来分析。这项研究的结果不仅有助于疾病的早期诊断，还将有助于针对疾病阶段的药物设计。该项目将把研究整合到本科课程中，方法是在PI已经开发的课程中指定项目，以解决拟议工作中的问题。该项目将为本科生在学年和暑假期间使用有针对性的短期项目提供研究经验。该项目还计划为初中生提供研究经验。该项目还将开发方法，在图形的帮助下，向K-12学生介绍编程概念和生物信息学。还计划举办一个暑期学院，以提高学生的参与度。

This project will investigate and analyze the complex phenomena of disease progression at the protein network level. A software tool, NetDA (Network-based Disease Analysis) to understand the essential mechanisms of disease progression as transitions between disease stages will be developed. The outcome of this study will help not only in early diagnosis of a disease but also in drug design specific for a disease stage. Undergraduate students will be involved in the research.The process of disease progression will be analyzed as an event-schedule-like structure, where a) each event representing a disease stage completed by a group of proteins will be analyzed in terms of clique and clique-like graphs, b) transfer of signals from one stage to the next will be analyzed using bipartite and bipartite-like graphs, and c) the strength of signals will be analyzed using diffusion kernels. The outcome of this study will help not only in early diagnosis of a disease but also in drug design specific for a disease stage. The project will integrate research into the undergraduate curriculum by assigning projects, in courses already developed by the PI, to solve problems in the proposed work. The project will provide research experience for undergraduate students using focused short projects during both academic year and summer. There is also a plan for the project to provide research experience for middle and high school students. The project will also develop approaches to introduce K-12 students to programming concepts as well as bioinformatics with the help of graphics. A summer institute is also planned to enhance student participation.