Genomic signatures of immune system aging
The functional decline of the immune system with aging, i.e., immunosenescence, has been associated with increased disease susceptibility, infections, and poor response to treatments and vaccination in elderly. However, we have yet to discover which genes, enhancers and regulatory interactions in which immune cells can explain the functional decline of immune functions with aging. In collaboration with the Banchereau Lab we work towards uncovering chromatin signatures of human immune system aging and to quantify the clinical implications of these signatures.
Epigenomic data mining
Capturing the dynamics of epigenomic patterns is essential to understand how gene expression patterns are established and maintained in healthy human cells, and how they are disrupted by pathologies. However, discovering these patterns and interpreting their biological meaning is a significant computational challenge. My research group tackles this challenge by developing innovative tools to integrate diverse data sources (ChIA-PET, ATAC-seq, RNA-seq), since intricate regulatory interactions and diverse regulatory elements cannot be inferred from a single data type. We develop machine learning models or network mining algorithms to integrate and interpret genomics data under the light of data accumulated in public repositories.
Genomic and genetics of T2D
In collaboration with the Stitzel lab we are studying genomic and epigenomic profiles in human islets and changes in these profiles associated with Type-2-Diabetes (T2D). For this we profile epigenomes and transcriptomes of human islet samples from healthy and diabetic individuals. We develop computational pipelines to integrate diverse genomics data along with the genetic information to uncover to what extent islet functions and responses are genetically modulated.