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

本项目将在蛋白质网络水平上研究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，而且有助于针对疾病阶段的药物设计。本科生将参与研究。疾病进展的过程将被分析为一个类似事件时间表的结构，其中a)每个事件代表由一组蛋白质完成的疾病阶段，将用团和团状图进行分析，b)信号从一个阶段到下一个阶段的传递将使用二部和双部图进行分析，c)信号的强度将使用扩散核进行分析。这项研究的结果不仅有助于疾病的早期诊断，而且有助于针对疾病阶段的药物设计。该项目将通过在PI已经开发的课程中分配项目来解决拟议工作中的问题，将研究整合到本科课程中。该项目将在学年和夏季为本科生提供集中的短期项目研究经验。该项目还计划为初高中学生提供研究经验。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。为了提高学生的参与度，还计划开设暑期研修院。

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.