Dr. Paul Blainey 

Associate Professor of Biological Engineering,
Massachusetts Institute of Technology
Broad Institute of Harvard and MIT 

 

Read more about Dr. Paul Blainey at https://be.mit.edu/directory/paul-blainey.

 

• Integrated sample prep for highly deployable genomics. Readout by next-generation sequencing (NGS) no longer limits throughput for many project types, but clinical applications demand low input quantities and streamlined workflows. To meet this demand, we developed a family of lab-on-a-chip microfluidic systems to realize major advances in real-world throughput, cost, and sensitivity by integrating entire sample preparation workflows from crude biological samples for whole genome shotgun and RNA-sequencing at the micro-scale, including direct-from-cells capability.
• High quality single cell genome sequencing. Microfluidics and whole-genome amplification are enabling single-cell genomics. At the same time, these technologies limit single-cell genomic studies by imposing cost and complexity (microfluidics) and limiting data quality (whole-genome amplification).Here I will present two new methods for single-cell genome analysis, one that requires no microfluidics or specialized equipment for direct single-cell genome amplification and another that leverages culture-based amplification rather than biochemical amplification to enable precise study of de novo mutations in single human cells.
• New scalable chemical and genomic screening technology. Droplet microfluidics methods are dramatically increasing the throughput of single-cell genomics assays. However, such methods have not yet impacted drug discovery due to small molecule crosstalk between droplets, particularly for more hydrophobic drug-like molecules. I will describe a new platform for processing and tracking tens of thousands of droplets in parallel that prevents crosstalk of small hydrophobic solutes. Beyond sequencing naturally occurring nucleic acids, functional genomics applies artificial genome perturbation and phenotype determination to identify gene functions. In forward genetic screens, efficient pooled methods for genome-wide screening are now popular, but require physical separation of selected cells for readout by amplicon sequencing. Many disease processes are characterized by complex cellular phenotypes that are best analyzed by high-content imaging assays. Here we present work using in-situ sequencing to combine major advantages of pooled approaches with high content imaging assays.

Bio

Paul Blainey is a core member of the Broad Institute of MIT and Harvard and an associate professor in the Department of Biological Engineering at MIT. An expert in microanalysis systems for studies of individual molecules and cells, Blainey is applying this technology to advance understanding of DNA-protein interaction, evolutionary processes, and functional differences between cells. The Blainey group develops and translates microfluidic, chemical, imaging, and sequencing approaches to make high-throughput quantitative biology routine – including single-cell analysis. Such capabilities will allow scientists to determine the genomic sequences from organisms that have not been successfully cultured in the lab and examine genetic differences on a cell-to-cell basis, driving new insights into fundamental aspects of cell function and evolution. Blainey seeks to empower researchers to obtain new types of information about biological specimens and integrate different types of information, such as imaging data and next-generation sequencing-based data. He holds a B.S. in chemistry and B.A. in mathematics from the University of Washington. He earned a Ph.D. in physical chemistry from Harvard University, where he studied how proteins interact with DNA with Xiaoliang Sunney Xie and Greg Verdine. He then completed postdoctoral research at Stanford University in the laboratory of Stephen Quake, where he pioneered novel optofluidic methods to perform single-cell microbial sequencing.