Research Projects
Computational Immunology
T cells are key components of immune responses against viruses and recognize viral molecules by binding to them with their T cell receptors (TCRs). My group is building computational tools to predict what TCRs can bind to using a combination of sequence and protein structure methods. Recently, we published one of the first peer-reviewed approaches to predict the specificity of TCRs.
Our method is called SwarmTCR and uses swarm intelligence (an AI-based approach) to predict TCR specificity for a variety of viral antigens. With increasing amounts of data and novel computational methods it should soon be possible to accurately predict what an individual’s immune system can recognize.
This will open new avenues for personalized vaccines, cancer immunotherapy, and other transformative treatments within the Precision Medicine paradigm.
Activities & Outcomes
- Received $384,000 in NIH grants/subcontracts
- Published over seven articles in top bioinformatics and immunology journals
- Two MS theses and one PhD thesis completed
- One PhD student and one MS student currently working on this project
Key Faculty and Collaborators
- Dario Ghersi, M.D, Ph.D.
Food System: Access, Technology & Education
Addressing food insecurity requires a comprehensive approach that recognizes the complex factors contributing to this global challenge. Presently, our food system prioritizes productivity and profit over people and planet, which has resulted in disproportionate environmental damage, health issues, and food insecurity for marginalized communities, including women, children, immigrants, indigenous populations, and people of color.
Our project’s vision is to build an innovation hub that will leverage local resources and integrate evolving technologies to dismantle food apartheid and break the barriers that currently exist in our food system so that access to healthy food is not determined by zip code.
Our strategic and collaborative approach to addressing inequities in access to healthy food holds the key to alleviating health disparities in marginalized populations.
Activities & Outcomes
- The solutions we build through the hub have the opportunity to impact both local and global food insecurity
- A: Workforce & community building
- B: Self-sustaining research & education integration
- C: Community-Centered R&D Impacts
Key Faculty and Collaborators
- Dhundy R. Bastola, Ph.D.
- Ada-Rhodes Shorts, Ph.D.
Digital Health Information System & Patient Empowerment
Values-driven decision-making is especially crucial for patients living with multiple chronic disease, including cancer, due to the complex treatment choices involved. Navigating through the maze of medical information with limited medical knowledge can be a daunting task.
To overcome these challenges and assist patients partner with their doctor in healthcare decision making, patients’ empowerment is essential. Unfortunately, trust issues relating to the sources informing patient decision making can hinder patient empowerment.
Recent advances in ML/AI enable us to develop a reliable intelligent information system that will assist patients with relevant medical information, tailor health education, and support decision-making process alongside their doctor. By untangling the web of factors influencing patient choices, we aim to develop a safe, efficient, and point-of-care information system that truly empowers patients to make informed decisions aligned with their values and priorities.
Activities & Outcomes
- Digital healthcare innovation
- Improve Health outcome and quality of life
- Empower patients
- Development of patientcentered care model
- Define key dimensions of patient empowerment
Key Faculty and Collaborators
- Dhundy R. Bastola, Ph.D.
- Joel Elson, Ph.D.
- Christian Haas, Ph.D.
NU Center for Biomedical Informatics Research & Innovation (CBIRI)
The mission of the center is to serve as a coordination and communication vehicle for biomedical informatics (BMI) educational and research activities, and resources; build new collaborations pertinent to both academia and industry by horizontal integration of BMI expertise, resources, and users under one umbrella organization, and to facilitate effective utilization of BMI resources and expertise in the realms of all types of health research.
Activities & Outcomes
- Biomedical Informatics has been an integral part of basic, clinical and public health research across the University of Nebraska campuses since the 1990s
- Over $175 million awarded in the last five years
- UNO College of IS&T is a national leader in bioinformatics education
- Access to BMI scientists, students, technology & data
Key Faculty and Collaborators
- Co-Director, Ann Fruhling, Ph.D.
- Co-Director, Babu Guda, Ph.D.
- Hesham Ali, Ph.D.
- Kiran Bastola, Ph.D.
- Martina Clarke, Ph.D.
- Kate Cooper, Ph.D.
- Dario Ghersi, M.D, Ph.D.
Software Tool Support for Bioengineering Innovation
As the world wide web grows rapidly, a text corpus is becoming increased online at an incredible rate. Managing a corpus of documents is critical for many areas of science, industry, and culture. For example, bioengineering researchers, who study a new generation of advanced materials, frequently need to identify and understand a comprehensive body of literature describing an association between material features of interest. However, there is no inspection technique to help such researchers who need to make critical decisions based on their understanding of a corpus of documents.
In this research, we present a text visualization approach which extracts and visualizes topic models regarding bioengineering document collections, systematically discovering hidden thematic structures in a collection of documents.
Activities & Outcomes
- *Publication - COMPSAC 21, Information'23
- *Student Support - 1 MS thesis, GRACA 20
- Funding - NSF EPSCoR 19 with $1.25M to UNO of $6M
- *Software tool demo at the DDMD workshop 20, 21, a topic visualization model for discovering hidden thematic structures in a corpus of documents
* Only includes Dr. Song's contributions
Key Faculty and Collaborators
- Pavathi Chundi, Ph.D. (Co-PI)
- Pei-Chi Huang, Ph.D.
- Myoungkyu Song, Ph.D. (UNO)
E-PACERR
A sense of community and knowledge of historical context is critical for trainees to understand the need for responsible research in bioinformatics. This project develops free online modules to enhance bioinformatics training in professionalism, reproducibility, and data and code sharing.
With this we build confidence in trainee ability to perform reproducible research, (2) support the bioinformatics research workforce, and (3) provide a piloted curriculum for other bioinformatics training programs to implement in their own educational settings.
Activities & Outcomes
- Funded NIH R25 grant (2021-2024)
- Name recognition for our BS Bioinformatics program
- Engagement with bioinformatics education research community
- MOOC on CanvasNet Summer 2024
- UNO Bioinformatics and BMI students supported
Key Faculty and Collaborators
- Kate Cooper, Ph.D.
- Dario Ghersi, M.D, Ph.D.
- Kiran Bastola, Ph.D.
Consumer Health Informatics
Food label literacy is associated with positive dietary and health behaviors, which are subsequently associated with lower risks for chronic disease. Trends in current literature suggest that the link between diet and human gut microbiome will play a major role in disease prevention through the field of precision nutrition.
The goal of this project is to support improved consumer understanding of food product labels by measuring of readability of ingredients lists, and to explore an ontological measure of the link between diet and microbiome.
Activities & Outcomes
- Submitted USDA NIFA grant ($750k), Summer '21
- One Journal publications, one submitted, one in-preparation
- One conference publication
- New course (one credit hour) offered J-session, Spring '21
- New area of interest to major health organizations (NIH, AMIA)
- Engagement with local collaborators with interest in diet and microbiome
Key Faculty and Collaborators
- Kate Cooper, Ph.D.
- Martina Clarke, Ph.D.
- Erin Bass, Ph.D.
- Jana Ponce, Ph.D. (UNMC)
Mobile Health for Sustainable Development
In this project, we investigate the ways in which the use mobile health applications can bring about improvements in the lives of people and their communities. Access to health information and healthcare is difficult. Many people just rely on which doctor's office is close and in their network.
Mobile health options have the ability to change this reality. Mobile health is more than just telehealth. It can be health monitoring apps for diabetes patients, portals linking health information, fitbit-like apps, and health and wellness apps that can help people target specific health goals. See: https://www.mhealthhelp.com/
Activities & Outcomes
- Addressing health inequities by mHealth SDOH resources
- Publications
- Impact: mHealth geolocation services to address social determinants of health
- Received $300,000 funding from NRI
Key Faculty and Collaborators
- Sajda Qureshi, Ph.D.
- John Windle, MD
- Martina Clarke, Ph.D.
- Timi Barone, Ph.D.
Shared Living Providers’ Documentation Burden
The goal of this study is to improve shared living providers (SLPs) clinical documentation experience by reducing the burden related to health information technology (HIT) use.
SLPs (henceforth, caregivers) are individuals that allow persons with intellectual and developmental disabilities (I/DD) to reside in their residential home while providing support in daily living activities and community integration.
To achieve this goal, we will explore caregivers’ perception of HIT-related documentation burden and its role in burnout. We will then identify information display needs and usability-related issues that arise when caregivers are using an electronic health record.
Activities & Outcomes
- This project examines administrative factors that may contribute to caregiver burnout
- Provide guidance for future decision-making
- To retain invaluable caregivers that support our community by providing services to individuals with I/DD
Key Faculty and Collaborators
- Martina A. Clarke, Ph.D., MSHI
- Lisa L. Neitzke, MD
- Kate M. Cooper, Ph.D.
IT for Development
Information Technology for Development at IS&T does: 1) Research into the effects of technology adoption and use on the economic, social and human development of people, businesses and communities; 2) Train students to conduct technology and training interventions with small businesses to measure their growth; 3) develop of tools to support the data collection and interventions; and 4) Apply research and training to improve the lives of people. This program involves projects such as Small Business Development: Opportunities and Challenges; Cloud computing for Small businesses; ICT Maturity: An Index for assessing a country’s capacity to grow through its ICT infrastructure and a Comparative Analysis of ICT adoption in China and the USA.
Activities & Outcomes
- Over 250 micro-enterprises studied
- Illustrate economic development
- Shows correlation between Information Technology interventions and business growth
- $250,000 funding from SBA
- $150,000 funding from NU Foundation
Key Faculty and Collaborators
- Sajda Qureshi, Ph.D.
- Peter Wolcott, Ph.D.
- Jason Xiong, Ph.D.
Establishing Appropriate Levels of Trust Between Patients, Physicians, and Information Sources
The project seeks to confront the pressing issue of trust within the healthcare sector, particularly under the shadow of increased targeting of healthcare workers and patients. This forward-thinking project aligns with the R&D trajectories of leading tech companies, aiming to provide breakthroughs beyond what is commercially available today.
Activities & Outcomes
- Supported by Nebraska Research Initiative (NRI)
- Provisional Patents and 2 New Invention Notifications
- Scholarly article: “Intelligent Systems for Patient Empowerment: A Focus on Trust”
Key Faculty and Collaborators
- Joel S. Elson, Ph.D.
- Kiran Bastola, Ph.D.