Federal Grant Award Summary

Boston University Medical Campus received a $449,625 Project Grant from the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training program (CFDA 93.859), effective June 1, 2026 through March 31, 2031. Under the direction of Dr. Chao Zhang, a computational biologist, the award funds development of a deep learning framework to discover temporal changes in host-microbiome interactions. The project delivers two primary products: (1) a novel microorganism identification pipeline utilizing deep learning methods to replace traditional alignment-based approaches for identifying microbiota from sequencing data, incorporating statistical methods to assess microbial abundance while minimizing false positives and enabling contamination detection applicable to retrospective analyses of large-scale studies; and (2) a deep learning-based analytical method to evaluate associations between microbiome composition or metabolic functions and host molecular features such as transcriptomics data.

This five-year initiative addresses critical gaps in microbiome research by providing computational tools and methodologies that overcome existing technical challenges in multi-omics data integration. The framework enables efficient microbiome analysis across diverse disease contexts, including infectious diseases such as Helicobacter pylori-associated gastric cancer and Mycobacterium tuberculosis infection, thereby facilitating broader investigation of host-microbiome interactions in large consortium studies previously limited by sample access and analytical constraints.