Michael Beer awarded $1.8 million grant from NIH

Michael Beer, an associate professor in the Department of Biomedical Engineering at Johns Hopkins University, has been awarded a $1.8 million grant from the National Institutes of Health as part of the Encyclopedia of DNA Elements Consortium.

Funded by the National Human Genome Research Institute, the ENCODE Project strives to catalog all the genes and regulatory elements — the parts of the genome that control whether genes are active or not — in humans and select model organisms.

It studies how DNA sequence between genes controls when and where genes are turned on, similar to dimmer switches. Mutations or variation within these control regions contribute to susceptibility for common human diseases.

The consortium consists of 18 funded groups, including six data generation groups, six functional validation groups, and six computational analysis groups. Beer has been awarded the grant as one of the computational analysis groups.

Beer’s research focuses on developing machine learning algorithms to sort through the large databases of ENCODE data to find specific molecular mechanisms for how these control regions function.

Being able to accurately identify cell-type specific enhancers from the ENCODE Consortium can be a challenge, says Beer. Beer and his group propose to “develop improved gkm-SVM models from ENCODE chromatin accessibility data and produce both genome wide and fine-scale maps of cell-specific enhancers and the core regulator binding sites within them.”

“We are excited to participate in this next phase of the ENCODE collaboration,” says Beer. “The ENCODE data sets are the best resource for training our algorithms to decode the regulatory DNA sequences which specify how enhancers control cell identity and differentiation.”

This project will contribute to the group’s understanding of regulatory element function and how sequence variation impacts a range of diseases such as autoimmune and neuropsychiatric disorders, cardiovascular disease, and increased susceptibility to specific types of cancer.

NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The NHGRI Extramural Research Program supports grants for research, and training and career development at sites nationwide. NHGRI plans to commit approximately $31.5 million to consortium projects over the next four years.