Just prior to their participation in the November 2018 Supercomputing Conference (SC18) in Dallas, the Lyda Hill Department of Bioinformatics at UT Southwestern Medical Center hosted its first annual hackathon, U-Hack Med. The hackathon included participants ranging in age and experience from high school students to industry professionals and college professors around the country. The two-day event focused mainly on computer-based solutions for the most pervasive problems facing clinical researchers and health care providers today.

Within the span of 26 hours, the group of data and computer scientists would write over 10,000 lines of code to address these pressing issues. Venkat Malladi, M.S., Director of Bioinformatics Core Facility described the importance of the event as an opportunity to “…showcase what we’re doing at UT Southwestern, and around the Dallas and Fort Worth area… I think it is really showcasing the diversity of the types of research we have.”

While much of the research produced by UT Southwestern focuses on basic science research, Malladi explained that there is still a need for ways to address problems in the field of clinical research. One of the ways bioinformatics researchers are attempting to do this is to use datasets produced by UT Southwestern researchers and provide useful applications of the information. Malladi further explained, “We wanted to break down the silos at UT Southwestern and promote interdepartmental research and we were able to make progress towards that goal through this event. It is also a way to highlight career paths for undergraduate and graduate students in the greater Dallas-Fort Worth area.”

Above the hush of the room, a steady rhythm of keystrokes could be heard as participants furiously typed away at their keyboards. One group seemed to be a bit livelier than the others, who were intensely focused on their computer screens. Bo Li, Ph.D., who is an assistant professor at UT Southwestern Medical Center, was excited to guide his team on a mission to develop a simple blood test which could predict cancer. Li explained, “The goal of our research is to find diagnostic, prognostic or even therapeutic options for cancer patients, and to identify cancer associated T cells.”

He went on to explain that their methods would eventually lead to the development of equipment for non-invasive early detection in cancer patients. Dr. Li excitedly shared that his lab has already had some success with preliminary applications in research focused on patients with breast cancer. Other projects included the use of virtual reality to simulate deep-learning, and the use of progression images to predict the likelihood that a tumor will spread from its original location – a project that went on to win the award for best use of visualization.

“We wanted to break down the silos at UT Southwestern and promote interdepartmental research and we were able to make progress towards that goal through this event.”

Venkat Malladi, M.S., Director of Bioinformatics Core Facility

The overall winners of the event took home the Lyda Hill award, which was rated by feasibility, clinical application, innovation, and “wow factor.” Team members working on this project focused their sights on developing artificial neural networks that could predict ECMO-related neurological injuries in post-operative patients. Extracorporeal membrane oxygenation (ECMO) is the use of a machine to provide oxygen to blood and remove carbon dioxide gas, all while bypassing the heart; the blood is then warmed and pumped back into the patient. The team’s solution showed that the artificial neural network can forecast complications due to a patient’s exposure to ECMO therapy during a stay in an intensive care unit. This can help doctors determine a plan of care and whether a patient should receive ECMO therapy.

Community Support

“While medicine continues to rapidly evolve, one fact remains the same – our community’s continuing investment brings needed momentum forward. It is my hope U-Hack Med will build on that investment and catalyze even more progress and impact for North Texas.”

Kathleen M. Gibson, President and CEO, Southwestern Medical Foundation

Founded in the Spring of 2015 with an extraordinary contribution from the Lyda Hill Foundation, the Lyda Hill Department of Bioinformatics offers students a state-of-the-art environment in which to work side by side with faculty to meet the informatics challenge in biomedicine – to detect, learn, and project patterns among increasingly higher-dimensional data sets. It is without a doubt one of the most salient examples of philanthropy at work in the Dallas area, showing how our community’s generosity catalyzes progress in medicine.

Kathleen Gibson, President and CEO of Southwestern Medical Foundation, expressed these sentiments in saying, “While medicine continues to rapidly evolve, one fact remains the same – our community’s continuing investment brings needed momentum forward. It is my hope U-Hack Med will build on that investment and catalyze even more progress and impact for North Texas.”

Gaudenz Danuser, Ph.D., Professor and Chair of the Lyda Hill Department of Bioinformatics, described the implications of the results as having great potential for the medical community. “The outcome of this event has been beyond my greatest expectation. Of the 12 projects, 8 to 10 emerged from the two-day hackathon with actionable outcomes. The clinical projects in particular did very well. We can now collaborate further with these teams to continue developing and polishing their solutions to the point of bringing these innovations to the patient bedside.”


Congratulations to all the winners and teams that competed!

Lyda Hill Award: Team 6: ML Predictive Scoring for Neurological Injury in Pediatric Heart-Lung Bypass (ECMO) Patients

  • Neel Shah and Abdelaziz Farhat, UTSW Pediatric Critical Care
  • Jeon Lee, UTSW Bioinformatics Core Facility
  • Rafe McBeth, UTSW Medical Physics Resident
  • Ziheng Wang, UT Dallas UTD PhD candidate and Research Assistant in Mechanical Engineering

Best Use of Visualization Award: Team 8: Differentiation of Metastatic Potential in Melanoma Cells

  • Andrew Jamieson, UT Southwestern Medical Center
  • Elizabeth Zou, Massachusetts Institute of Technology
  • Colin Brochtrup, University of Texas at Dallas
  • Mahmoud Elgenedy, University of Texas at Dallas
  • Stephan Dawetwyler, UT Southwestern Medical Center

Most Out of the Box Award: Team 4: Simulating Molecular Dynamics of Potential Drug Target Regions

  • Milo Lin, UT Southwestern Medical Center
  • Mike Trenfield, UT Southwestern Medical Center
  • Milo Lin, UT Southwestern Medical Center
  • John Yoo, University of Texas at Dallas
  • Umberto Ciri, University of Texas at Dallas
  • Kevin Nguyen, UT Southwestern Medical Center

Best Desk-to-Bedside Award: Team 1: Machine Learning to Distinguish T-Cell Receptor Subregions

  • Bo Li, UT Southwestern Medical Center
  • Coby Herford, University of Texas at Dallas
  • Dat Ngo, University of Texas at Dallas
  • Sean Kennedy, University of Texas at Dallas
  • Calvin Ross, University of Texas at Dallas
  • Yingfei Chen, UT Southwestern Medical Center

Most Likely to Become a Start-Up Award: Team 12: ML Algorithm for Staging of Liver Disease

  • Murat Can Çobanoğlu, UT Southwestern Medical Center
  • Xiaoxian Jing, Southern Methodist University
  • Meyer Zinn, St. Mark’s School of Texas
  • Siddarth Agarwal, University of Texas at Arlington
  • Kevin VanHorn, University of Texas at Dallas
  • Michael Dannunzio, University of Texas at Dallas

Next Sci-Fi Blockbuster Award (Highest Wow Factor Score): Team 3: Learning Models in Virtual Reality

  • Murat Can Çobanoǧlu, UT Southwestern Medical Center
  • Xiaoxian Jing, Southern Methodist University
  • Meyer Zinn, St. Mark’s School of Texas
  • Siddharth Agarwal, University of Texas at Arlington
  • Kevin VanHorn, University of Texas at Dallas
  • Michael Dannunzio, University of Texas at Dallas

Click here to view the full U-HACK MED outcomes Learn more about how our community established this innovative department