Enhanced proton therapy and better radiation treatment for cancer patients, a closer look at stem cells and protein complexes, targeted therapeutics, and ways to tag errors in massive medical databases are the winning ideas in this year’s Collaborative Advances in Biomedical Computing program.
Six Rice researchers and their Texas Medical Center collaborators will share seed grants totaling $550,000 provided by the John and Ann Doerr Fund for Computational Biomedicine. In 2006, the Doerrs, both alumni of the George R. Brown School of Engineering, gave $2.5 million to be distributed in grants over five years. The new awards represent the third round of funding.
The two-year grants, which took effect Jan. 1, encourage new projects that bridge computing information technology research at Rice and biomedical research at Rice and in the Texas Medical Center, with an eye toward their potential for external long-term funding. Rice’s Ken Kennedy Institute for Information Technology (K2I) administers the funding program.
“We’re excited about the collaborations being fostered by this generous gift from the Doerrs, who express with every dollar their confidence in the impact our researchers will have on the world,” said Jan Odegard, executive director of K2I. “We all recognize that advanced computing is critical to the progress of biomedical research and feel there’s no better way for that to happen than through collaborations between world-class researchers from Rice and the Texas Medical Center.”
The winning Rice faculty and their proposals:
Matthias Heinkenschloss, professor and chair of the Department of Computational and Applied Mathematics, will investigate improved computational tools for intensity-modulated proton therapy (IMPT) for cancer patients, which treats tumors in a way that minimizes damage to surrounding healthy tissue.
“To unlock the full potential of IMPT, substantially better computational methods for treatment planning are needed,” wrote Heinkenschloss. To that end, he and collaborators Pablo Yepes, a senior faculty fellow in physics and astronomy at Rice’s Bonner Nuclear Laboratory, and Xiaodong Zhang, an assistant professor in the Department of Radiation Physics at the University of Texas M.D. Anderson Cancer Center, are developing simulation and optimization tools for 3-D IMPT. They expect their approach to improve treatment and reduce treatment time, making proton therapy available to more patients.
Jianpeng Ma, a Rice professor in bioengineering with a joint appointment at Baylor College of Medicine (BCM), will investigate the role of particular polycomb group proteins (PcG) found to be abnormally elevated in cancer patients. PcGs also play a fundamental role in stem-cell maintenance.
Ma and collaborators Qinghua Wang, an assistant professor of biochemistry and molecular biology at BCM, and Jennifer West, Rice’s Isabel C. Cameron Professor in Bioengineering, will study computational DNA motif recognition to understand the regulatory mechanisms that differentiate stem cells and cancer cells from normal cells.
Yildiz Bayazitoglu, Rice’s Harry S. Cameron Professor in Mechanical Engineering, will use her grant to increase the speed and accuracy of simulations in photothermal cancer treatment. New therapies involve heating nanoparticles in a tumor with lasers to kill it without affecting surrounding tissue. Bayazitoglu wants to improve the accuracy of laser ablation through simulations to determine the proper temperature field before a procedure takes place, ultimately modeling specific treatments for many kinds of tumors.
Her collaborators include Andrew Meade, a Rice professor of mechanical engineering and civil and environmental engineering; Jason Stafford, assistant professor of imaging physics at M.D. Anderson; and Aysegul Sahin, director of the surgical pathology and breast pathology fellowship programs and a professor in the Department of Pathology at M.D. Anderson.
Luay Nakhleh, an assistant professor of computer science and of biochemistry and cell biology, will use targeted therapeutics and rational combination therapy to make personalized cancer treatment more effective.
Nakhleh, a bioinformatics specialist, will work with Prahlad Ram, an associate professor of systems biology at M.D. Anderson, to analyze and integrate large-scale “omics” (as in genomics and proteomics) data to identify effective combinations of drugs to treat cancers based on the specific genetic makeup of more than 50 breast cell lines.
Christopher Jermaine, an associate professor of computer science, will develop an algorithm to “learn” errors present in databases of electronic medical records and tag them as such. Jermaine and Elmer Bernstam, an associate professor at the University of Texas School of Health Information Sciences at Houston, hope to find error-tolerant answers when probing large amounts of warehoused medical data for clues to new treatments.
Lydia Kavraki, Rice’s Noah Harding Professor of Computer Science and a professor of bioengineering, will work to understand how complex macromolecular systems rearrange themselves to perform their functions. She and her collaborators will develop methods to find conformational pathways between different states of such systems. Ultimately, the goal is to improve the understanding of the functional mechanisms of higher levels of protein organization, such as viral shells. Understanding how viruses work is important as infection is a critical problem for cancer patients.
Her collaborators are Mark Moll, a research scientist in computer science at Rice; Wah Chiu, the Alvin Romansky Professor and director of the National Center for Macromolecular Imaging; and David Tweardy, professor of medicine and chief of the section of infectious diseases at BCM.