Greater Boston
I am a 'wet-dry' biophysicist specialized in transcription factor biology. My research projects have combined experimental and computational methods to study the molecular interactions that regulate how transcription factors find their binding sites on nucleosomal DNA, as well as how cytokine genes respond to immunological stimuli and how mitotic checkpoint is sustained. I am interested in developing novel biomedical technologies based on molecular understanding and high-throughput data analysis.
Computational and biochemical research on Transcription Factors and Gene Regulation
Computational and Biochemical research on Transcription Factors and the Gene Regulation
Identification of human lineage specifiers by the comparative analysis of TF:DNA binding specificity data: I created and applied bioinformatic tools to study how transcription factors are recruited in different cellular contexts in vivo. My projects developed a glossary of intrinsic DNA binding specificity for human transcription factors, methods to construct matched genomic background sequences, tools to remove the bias induced by constitutive accessible regions in gene sequence analysis. These tools improves the identification of transcription factors binding within regulatory regions of the human genome, thereby enabling orthogonal analysis to refine candidate factors specifying a cellular phenotype and to identify the underlying genetic mechanisms of disease and mutations.
Genome wide analysis on the impact of topologically associating domains in gene regulation: I investigated topologically associated domains (TADs) and their regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions.
Molecular mechanisms controlling mitotic progression: I worked on the spindle assembly checkpoint (SAC) and its signaling pathway, the cellular machinery overseeing the distribution of chromosomes into the emerging daughter cells during cell division. My research was able to disprove the existing hypothesis that initial activation of the spindle assembly checkpoint released protein complex Mad2/CDC20 through experiments in living yeast cells. Instead, I found that the dimerization interface of Mad2 in CDC20/Mad2 is important for checkpoint signaling because it interacts with another checkpoint protein Mad3.
Modeling of cytokine activation in Lymphocytes during immunological response: I used computational and experimental methods to model cytokine activation in Lymphocytes in order to understand and control the coordinated programs of gene expression during cell differentiation. I described and predicted how cells of the mammalian immune system react to pathogens in a stochastic manner, and then I modulated the experimental system to mimic its description in mathematical terms.