A list of publications can also be found on pubmed and google scholar.

†Contributed Equally, *Corresponding Author


The emerging landscape of spatial profiling technologies

Moffitt, J.R., Lundberg, E., Heyn, H.

Nature Reviews Genetics doi: (2022)


Cell segmentation in imaging-based spatial transcriptomics

Petukhov, V., Xu, R.J., Soldatov, R.A., Cadinu, P., Khodosevich, K., Moffitt, J.R., Kharchenko, P.V.

Nature Biotechnology doi: (2021)


MAFG-driven astrocytes promote CNS inflammation

Wheeler, M.A., Clark, I.C., Tjon, E.C., Li, Z., Zandee, S.E.J., Couturier, C.P., Watson, B.R., Scalisi, G., Alkwai, S., Rothhammer, V., Rotem, A., Heyman, J.A., Thaploo, S., Sanmarco, L.M., Ragoussis, J., Weitz, D.A., Petrecca, K., Moffitt, J.R., Becher, B., Antel, J.P., Prat, A., Quintana, F.J.

Nature 578 593 (2020)

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

Kagan, J., Moritz, R., Mazurchuk, R., Lee, J.H., Kharchenko, P., Rozenblatt-Rosen, O., Ruppin, E., Edfors, F., Ginty, F., Goltsev, Y., Wells, J., LaCava, J., Rieseterer, J., Germain, R., Shi, T., Chee, M., Budnik, B., Yates, J., Chait, B., Moffitt, J.R., Smith, R., Srivastava, S.

Journal of Proteome Research 19 1900 (2020)

Spatial organization of the transcriptome in individual neurons

Wang, G., Ang C.-E., Fan, J., Wang, A., Moffitt, J.R., Zhuang, X.

bioRxiv (2020)

Prior Publications


Multiplexed Detection of RNA using MERFISH and Branched DNA Amplification

Xia, C., Babcock, H., *Moffitt, J.R., *Zhuang, X.

Scientific Reports 9 7721 (2019)

bioRxiv (2018)


Molecular, Spatial and Functional Single-Cell Profiling of the Hypothalamic Preoptic Region

†Moffitt, J.R., †Bambah-Mukku, D., Eichhorn, S.E., Vaughn, E., Shekhar, K., Perez, J.D., Rubinstein, N.D., Hao, J., Regev, A., Dulac, C. Zhuang, X.

Science eaau5324 (2018)

Multiplexed Imaging of High-Density Libraries of RNAs with MERFISH and Expansion Microscopy

Wang, G., Moffitt, J.R., Zhuang, X.

Scientific Reports 8, 4847 (2018).


High-Throughput, Image-Based Screening of Genetic Variant Libraries

Emanuel, G., *Moffitt, J.R., *Zhuang, X.

Nature Methods 14, 1159-1162 (2017)


High-Performance Multiplexed Fluorescence in situ Hybridization in Culture and Tissue with Matrix Imprinting and Clearing

†Moffitt, J.R., †Hao, J., Bambah-Mukku, D., Lu, T., Dulac, C., Zhuang, X.

PNAS 113, 14456-14461 (2016)

High-Throughput Single-Cell Gene-Expression Profiling with Multiplexed Error-Robust Fluorescence in situ Hybridization

*†Moffitt, J.R., †Hao, J., †Wang, G., Chen, K.H., Babcock, H.P., *Zhuang, X.

PNAS 113, 11046-11051 (2016)

Spatial Organization of Chromatin Domains and Compartments in Single Chromosomes

Wang, S., Su, J.H., Beliveau, B., Bintu, B., Moffitt, J.R., Wu, C., Zhuang, X.

Science 353, 598-602 (2016)

Spatial Organization Shapes the Turnover of a Bacterial Transcriptome

Moffitt, J.R., Pandey, S., Boettiger, A.N., Wang, S., Zhuang, X.

eLife 5, 213065 (2016)

RNA Imaging with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH)

*Moffitt, J.R., *Zhuang, X.

Methods in Enzymology 572, 1-49 (2016)

Super-Resolution Imaging Reveals Distinct Chromatin Folding for Different Epigenetic States

Boettiger, A.N., Bintu, B., Moffitt, J.R., Wang, S., Beliveau, B., Fudenberg, G., Imakaev, M., Mirny, L.A., Wu, C., Zhuang, X.

Nature 529, 418-422 (2016)


Spatially Resolved, Highly Multiplexed RNA Profiling in Single Cells

†Chen, K.H., †Boettiger, A.N., †Moffitt, J.R., Wang, S., Zhuang, X.

Science 348, aaa6090 (2015)


Characterization and Development of Photoactivatable Fluorescent Proteins for Single-Molecule-Based Superresolution Imaging

Wang S., Moffitt, J.R., Dempsey, G.T., Xie, X.S., Zhuang, X.

PNAS 111, 8452-8457 (2014)

Simultaneous Dual-Color 3D STED Microscopy

Osseforth, C., Moffitt, J.R., Schermelleh, L., Michaelis J.

Optics Express 22, 7028-7039 (2014)


Fast Compressed Sensing Analysis for Super-Resolution Imaging using L1-homotopy

†Babcock, H., †Moffitt, J.R., and Zhuang, X.

Optics Express 21, 28583-28596 (2013)

Robust Circadian Oscillations in Cyanobacteria Require Transcriptional Feedback Regulation

Teng, S., †Mukherji, S., †Moffitt, J.R., †de Buyl, S., and O’Shea, E. K.

Science 340, 737-740 (2013)

Statistical Analysis of Molecular Signal Recording

Glaser, J.I., Zamft, B.M., Marblestone, A.H., Moffitt, J.R., Tyo, K., Boyden, E.S., Church, G., and Kording, K.P.

PLOS Computational Biology 9, e1003145 (2013)


High Degree of Coordination and Division of Labor among Subunits in a Homomeric Ring ATPase

Chistol, G., Liu, S., Hetherington, C.L., Moffitt, J.R., Grimes, S., Jardine, P.J., and Bustamante, C.

Cell 151, 1017 (2012)

Lessons from Viral Packaging Motors

Hetherington, C. L., Chistol, G., Moffitt, J.R., and Bustamante, C.

in Comprehensive Biophysics, Ed. Goldman, Y., 4, 420 (2012)


Single-Base Pair Unwinding and Asynchronous RNA Release by the Hepatitis C Virus NS3 Helicase

Cheng, W., Arunajadai, S.G., Moffitt, J.R., Tinoco, I. Jr., and Bustamante, C.

Science 23, 1746 (2011)

Time Gating Improves the Spatial Resolution of STED Microscopy

*Moffitt, J.R., Osseforth, C., and *Michaelis, J.

Optics Express 19, 4242 (2011)


Mechanistic Constraints from the Substrate Concentration Dependence of Enzymatic Fluctuations

Moffitt, J.R., Chemla, Y.R., and Bustamante, C.

PNAS 107, 15739 (2010)

Methods in Statistical Kinetics

Moffitt, J.R., Chemla, Y.R., and Bustamante, C.

Methods in Enzymology 475, 221 (2010)

Mechanochemistry of a Viral DNA Packaging Motor

Yu, J., Moffitt, J.R., Hetherington, C.L., Bustamante, C., and Oster, G.

Journal of Molecular Biology 400, 186 (2010)


Substrate Interactions and Promiscuity in a Viral DNA Packaging Motor

†Aathavan, K., †Politzer, A.T., †Kaplan, A., †Moffitt, J.R., Chemla, Y.R., Grimes, S., Jardine, P.J., Anderson, D.L., and Bustamante, C.

Nature 461, 669 (2009)

Intersubunit Coordination in a Homomeric Ring ATPase

†Moffitt, J.R., †Chemla, Y.R., Aathavan, K., Grimes, S., Jardine, P.J., Anderson, D.L., and Bustamante, C.

Nature 457, 446 (2009)

DNA Based Molecular Motors

Michaelis, J., Muschielok, A., Andrecka, J., Kügel, W., and Moffitt, J.R.

Physics of Life 6, 250 (2009)

Viral Packaging: One Step at a Time

Bustamante, C. and Moffitt, J.R.

in Proceedings of the Nobel Symposium: Single Molecule Spectroscopy in Chemistry, Physics and Biology, Sånga Säby 96, 237 (2009)

Past, Present, and Future of Single-Molecule Studies of Transcription

Bustamante, C., and Moffitt, J.R.

in RNA polymerases as a molecular motors, Eds. Strict, T. and Buc, H., RSC (2009)


Exact Solutions for Kinetic Models of Macromolecular Dynamics

†Chemla, Y.R., †Moffitt, J.R., and Bustamante, C.

J. Chem. Phys. B 112, 6026 (2008)

Recent Advances in Optical Tweezers

Moffitt, J.R., Chemla, Y.R., Smith, S.B., and Bustamante, C.

Ann. Rev. Biochem. 77, 205 (2008)

High-Resolution Dual-Trap Optical Tweezers with Differential Detection

Bustamante, C., Chemla, Y.R., and Moffitt, J.R.

in Single-Molecule Techniques: A Laboratory Manual, Eds. Selvin, P.J. and Ha, T., CSHL (2008)


Differential Detection of Dual Traps Improves the Spatial Resolution of Optical Tweezers

†Moffitt, J.R., †Chemla, Y.R., Izhaky, D., and Bustamante, C.

PNAS 103, 9006 (2006)


Self-Erasing Perturbations of Abelian Sandpiles

Moffitt, J.R., Macdonald, P., Lindner, J.F.

Physical Review E 70, 016203 (2004)


System Level Implementation of Beam Position Monitors with Local Data Processing Capability for the Cornell Electron Storage Ring

Palmer, M.A., Dobbins, J.A., Rock, B.Y., Strohman, C.R., and Moffitt, J.R.

Proc. of the 2003 Part. Accel. Conf. 2473 (2003)

Copyright 2022

Jeffrey Moffitt