BBS Faculty Member - Jeffrey Moffitt

Jeffrey Moffitt

Assistant Professor

Boston Children's Hospital
Warren Alpert Building, WA-149E
200 Longwood Avenue
Boston, MA 02115
Visit my lab page here.

in situ single-cell transcriptomic techniques offer the exciting ability to characterize gene expression within single cells in their native tissue context. With these technologies, it is possible to discover different types and states of cells in essentially any tissue in any organism while simultaneously mapping the spatial and functional organization of these cells. Our laboratory adopts, improves, and innovates new approaches to in situ single-cell 'omics, and we use these novel approaches to understand a range of biological systems. Our primary focus is to understand the spatial organization of the gut microbiome and the host gut and, in turn, to understand how this spatial organization modulates the mechanisms by which the host senses and shapes the composition and activity of the microbiome and by which the microbiome remodels many different aspects of host physiology.

Last Update: 8/2/2018


For a complete listing of publications click here.



Chen, K.H., Boettiger, A.N., Moffitt, J.R., Wang, S., Zhuang, X., “Spatially Resolved, Highly Multiplexed RNA Profiling in Single Cells,” Science 348, aaa6090 (2015). PMC4662681

Moffitt, J.R., Pandey, S., Boettiger, A.N., Wang, S., Zhuang, X., “Spatial Organization Shapes the Turnover of a Bacterial Transcriptome,” eLife 5, 213065 (2016). PMC4874777

Moffitt, J.R., Hao, J., Wang, G., Chen, K.H., Babcock, H.P., Zhuang, X., “High-Throughput Single-Cell Gene-Expression Profiling with Multiplexed Error-Robust Fluorescence in situ Hybridization,” PNAS 113, 11046 (2016). PMC5047202

Moffitt, J.R., Hao, J., Bambah-Mukku, D., Lu, T., Dulac, C., Zhuang, X., “High-Performance Multiplexed Fluorescence in situ Hybridization in Culture and Tissue with Matrix Imprinting and Clearing,” PNAS 113, 14456 (2016). PMC5167177

Wang, G., Moffitt, J.R., Zhuang, X., “Multiplexed Imaging of High-Density Libraries of RNAs with MERFISH and Expansion Microscopy,” Scientific Reports 8, 4847 (2018). PMC5859009

Emanuel, G., Moffitt, J.R., Zhuang, X., “High-Throughput, Image-Based Screening of Genetic Variant Libraries,” Nature Methods, doi:10.1038/nmeth.4495; 1159-1162 (2017). PMC5958624

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