Researchers developing signal processing techniques to identify gut microbial biomarkers of colon cancer

NSF grant to study gut microbiome

A rendering of blood cells with one infected cell.


An interdisciplinary team of researchers at Texas A&M University has been awarded a Division of Computing and Communication Foundations grant by the National Science Foundation to develop a gut-microbial investigation model that can identify critical dietary risk factors that cause colorectal cancer. The three-year, $350,000 project is a direct outcome of Texas A&M Engineering Experiment Station’s Interdisciplinary Seed Grants for Strategic Initiatives, which provided initial funding to establish the collaborative research effort.

The project, titled “Minimum Mean Square Error Estimation and Control of Partially Observed Boolean Dynamical Systems with Applications in Metagenomics,” aims to develop and apply innovative signal processing techniques to uncover the complex interactions among microbes, human cells and their metabolic products in the gut. The project will produce innovative methods for estimation and control of processes that consist of the complex interactions of many switching elements, such as "presence" and "absence" of a particular microbial species in the gut, which are only indirectly observed through noisy biomedical assays.

“Our goal is to develop a signal processing framework that formalizes the interactions of the complex eco-system observed in the human gut such as the microbial communities and their interactions with the gut epithelial cells,” said Dr. Ulisses M. Braga-Neto, associate professor in the Department of Electrical and Computer Engineering at Texas A&M and the principal investigator of the project. “This framework will allow us to study the effects of nutritional supplementation on this complex eco-system in terms of changes in the microbial diversity and human gut gene expression in cell-signaling pathways.”

The project will provide life scientists with computational tools for biochemical pathway discovery as well as rational intervention design, as in optimal drug scheduling and diet modifications to treat human disease. The project will also provide training opportunities for undergraduate and graduate students, preparing them for highly interdisciplinary biomedical research.

Braga-Neto is assisted by an interdisciplinary collaborative team that includes Dr. Robert S. Chapkin, Distinguished Professor in the Department of Nutrition and Food Science at Texas A&M AgriLife; Dr. Arul Jayaraman, Ray B. Nesbitt Endowed Chair Professor in the Artie  McFerrin Department of Chemical Engineering;, Dr. Xiaoning Qian, assistant professor in the electrical and computer engineering department; and Dr. Ivan Ivanov, clinical associate professor of bioinformatics in the Department of Veterinary Physiology and Pharmacology. Dr. Johanna W. Lampe, associate division director of the Cancer Prevention Program in the Division of Public Health Sciences at the Fred Hutchinson Cancer Research Center is an external collaborator.