Paul Blainey, PhD



(617) 714-7320
Associate Professor of Biological Engineering


Prof. Blainey completed his undergraduate degrees in Mathematics and Chemistry at the University of Washington and a MA in Chemistry from Harvard University. Paul Blainey continued his doctoral studies in Physical Chemistry at Harvard University under the joint supervision of Profs. Xiaoliang Sunney Xie and Gregory L. Verdine. He held a postdoctoral appointment at Stanford University where he developed high-throughput microoptofluidic methods for whole-genome amplification of DNA from individual, uncultivated microbial cells in Prof. Stephen Quake’s laboratory. Paul joined MIT as an Assistant Professor of Biological Engineering in 2012.


Broadly, research in the Blainey group integrates new microfluidic, optical, and molecular tools for application in biology and medicine. We emphasize quantitative single-cell and single-molecule approaches, aiming to enable multiparametric studies with the power to reveal the workings of natural and engineered biological systems across a range of scales.

Research Areas: 

Honors & Awards: 

Burroughs Welcome Foundation Career Awards at the Scientific Interface, 2011
Agilent Early Career Investigator Award, 2014

Selected Publications:

Blainey, Paul C., Vito Graziano, Ana J. Pérez-Berná, William J. McGrath, Jane S Flint, Carmen San Martín, Sunney X Xie, and Walter F. Mangel. "Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: IV. viral proteinase slides along DNA to locate and process its substrates." J Biol Chem 288, no. 3 (2013): 2092-102.
Blainey, Paul C., Carlos E. Milla, David N. Cornfield, and Stephen R. Quake. "Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis." Sci Transl Med 4, no. 153 (2012): 153ra130.
Pamp, Sünje J., Eoghan D. Harrington, Stephen R. Quake, David A. Relman, and Paul C. Blainey. "Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)." Genome Res 22, no. 6 (2012): 1107-19.
Blainey, Paul C., and Stephen R. Quake. "Digital MDA for enumeration of total nucleic acid contamination." Nucleic Acids Res 39, no. 4 (2011): e19.
Blainey, Paul C., Guobin Luo, S C. Kou, Walter F. Mangel, Gregory L. Verdine, Biman Bagchi, and Sunney X Xie. "Nonspecifically bound proteins spin while diffusing along DNA." Nat Struct Mol Biol 16, no. 12 (2009): 1224-9.