Computational methods for decoding the DNA blueprints of molecular functionality

Yana Bromberg, Rutgers University
Host: Steven Salzberg

Precision medicine efforts propose leveraging complex molecular and medical data towards a better life. This ambitious objective requires advanced computational solutions. Here, however, deeper understanding will not simply diffuse from deeper machine learning, but from more insight into the details of molecular function and a mastery of applicable computational techniques.

My lab’s novel machine learning-based methods predict functional effects of genomic variants and leverage the identified patterns in functional changes to infer individual disease susceptibility. We have optimized our genome-to-disease mapping pipeline to both accommodate compute-resistant biologists and allow for custom variant scoring functions, feature selection, and machine learning techniques. We also built novel computational methods, including training the first general purpose language model for bacterial short-read DNA sequences, to be used in high-throughput functional profiling of microbiome data that can further elaborate on health and disease. Our purely computational work motivates new experimentally testable hypothesis regarding the biological mechanisms of disease. It also provides a potential means for earlier prognosis, more accurate diagnosis, and the development of better treatments.

Speaker Biography

Research in Yana Bromberg’s lab at Rutgers University is focused on designing machine learning, network analysis, and other computational techniques for the molecular functional annotation of genes, genomes, and metagenomes in the context of specific environments and diseases. The lab also studies evolution of life’s electron transfer reactions in Earth’s history and as potentially applicable to other planets. Dr. Bromberg received her Bachelor degrees in Biology and Computer Sciences from the State University of New York at Stony Brook and a Ph.D. in Biomedical Informatics from Columbia University. She is currently an Associate Professor at the Department of Biochemistry and Microbiology at Rutgers University. She also holds an adjunct position at the Department of Genetics at Rutgers and is a fellow of the Institute for Advanced Study at the Technical University of Munich, Germany. Dr. Bromberg is also the vice-president of the Board of Directors of the International Society for Computational Biology.