Predictive modeling of genome structure

Posted on Posted in Research Projects

Mathematical models allow us to develop rich predictions from quantitative measurement.  This approach to date has been vastly more successful in physics than molecular biology, where models have enable us to predict the existence of fundamental particles long before they are detected in nature, or determine the mass of celestial bodies that we could never put on a scale and […]


Posted on Posted in Research Projects

Single molecule fluorescent in situ hybridization (FISH) is a powerful technique to label and count individual RNA molecules of a particular type inside a fixed cell or tissue.  It allows us to study the organization of RNAs within a cell and the organization of cell-types (classified by RNA expression) within a complex tissue or environment.  The ability to have precise […]

Visualizing cis-interactions in vivo

Posted on Posted in Research Projects

In order to study the 3D DNA structures which regulate contacts between cis-regulatory elements (CREs) and their target transcribed elements (TEs), we are developing a super-resolution imaging approaches capable of resolving tens to hundreds of individual CREs, TEs, and intervening sequence in single cells of sectioned embryonic tissue and cultured cells at better than 20 nm resolution. We are applying this approach […]

3D Genome Structure

Posted on Posted in Research Projects

Differences in gene expression arise due to differences in how accessible the sequence encoding a gene is to the transcription machinery of the cell. While we know much about the structure of DNA at small lengths scales (<1 kilobase) and at large length scales (whole chromosomes), we understand little about its organization at the intermediate scale of kilobases to megabases. […]

About me

Posted on Leave a commentPosted in Uncategorized

I am particularly interested at present in how the nanoscale spatial organization of chromatin is regulated during development to affect gene expression. Background I was a postdoc in Xiaowei Zhuang’s group at Harvard, where I studied gene regulation in animal development through super-resolution microscopy and deep sequencing. I conducted my Ph.D. research under Michael Levine at UC Berkeley, where I studied cis-regulatory […]