Moffitt Laboratory: Publications

                       PublicationsA list of publications can also be found on 
                            pubmed
                             and google scholar.
†Contributed Equally, *Corresponding Author

                    
Featured PapersA selection of highlights from our work

                       Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling†Cadinu, P., †Sivanathan, K.N., Misra, A., Xu, R.J., Mangani, D., Yang, E.,Rone, J.M., Tooley, K., Kye, Y.,
					   Bod, L., Geistlinger, L., Lee, T., Mertens, R.T., Ono, N., Wang, G., Sanmarco, L., Quintana, F.J., Anderson, A.C., Kuchroo, V.K., *Moffitt, J.R., *Nowarski, R.
Cell, In Press (2024)
bioRxiv (2023)

                       Spatial and temporal profiling of the complement system uncovered novel functions of the alternative complement pathway in brain developmentZhang, Y., Watson, B., Rattan, A., Lee, T., Chawla, S., Geistlinger, G., Guan, Y., Ma, M., Caldarone, B.J., Song, W., *Moffitt, J.R., *Carroll, M.C.
bioRxiv doi:  https://doi.org/10.1101/2023.11.22.568325 (2023)

                       The emerging landscape of spatial profiling technologiesMoffitt, J.R., Lundberg, E., Heyn, H.
Nature Reviews Genetics doi:  https://doi.org/10.1038/s41576-022-00515-3 (2022)
2024
                       Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling†Cadinu, P., †Sivanathan, K.N., Misra, A., Xu, R.J., Mangani, D., Yang, E.,Rone, J.M., Tooley, K., Kye, Y.,
					   Bod, L., Geistlinger, L., Lee, T., Mertens, R.T., Ono, N., Wang, G., Sanmarco, L., Quintana, F.J., Anderson, A.C., Kuchroo, V.K., *Moffitt, J.R., *Nowarski, R.
Cell, In Press (2024)
bioRxiv (2023)

                       Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution†Watson, B., †Paul, B., Amir-Zilberstein, L., Segerstolpe, A., Rahman, R.U., Shih, A., 
					   Deguine, J., Xavier, R.J., *Moffitt, J.R., *Mullen, A.
bioRxiv doi:  https://doi.org/10.1101/2024.02.02.578633 (2024)

                       Gut complement induced by the microbiota combats pathogens and spares commensalsWu, M., Zheng, W., Song, X., Bao, B., Wang, Y., Ramanan, D., Yang, D., Liu, R., Macbeth, J.C.,
					   Do, E.A., Andrade, W.A., Yang, T., Cho, H.S., Gazzaniga, F.S., Ilves, M., Coronado, D., Thomphson, C., 
					   Hang, S., Chiu, I.M, Moffitt, J.R., Hsiao, A., Mekalanos, J.J., Benoist, C., Kasper, D.L.
Cell, 187 897 (2024) 
bioRxiv (2023)
2023
                       Spatial and temporal profiling of the complement system uncovered novel functions of the alternative complement pathway in brain developmentZhang, Y., Watson, B., Rattan, A., Lee, T., Chawla, S., Geistlinger, G., Guan, Y., Ma, M., Caldarone, B.J., Song, W., *Moffitt, J.R., *Carroll, M.C.
bioRxiv doi:  https://doi.org/10.1101/2023.11.22.568325 (2023)

                       Understanding prefrontal cortex functions by decoding its molecular, cellular and circuit organizationBhattacherjee, A., Zhang, C., Watson,B., Djekidel, M.N., *Moffitt, J.R., *Zhang, Y.
Nature Neuroscience, 26 1880 (2023)
bioRxiv (2022)

                       Spatial enrichment of the type 1 interferon signature in the brain of a neuropsychiatric lupus murine modelAw, E., Zhang, Y., Yalcin, E., Herrmann, U., Lin, S.L., Langston, K., Castrillion, C., Ma, M., Moffitt, J.R., Carroll, M.C.
Brain, Behavior, and Immunity, 114 511 (2023) 

                       Spatial organization of the mouse retina at single cell resolutionChoi, J., Li, J., Ferdous, S., Liang, Q., Moffitt, J.R., Chen, R.
Nature Communications 14 4929 (2023) 
bioRxiv (2022)

                       Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learningLaubscher, E., Wang, X., Razin, N., Dougherty, T., Xu, R.J., Ombelets, L., Pao, E., Graf, W. Moffitt, J.R., 
					   Yue, Y., Van Valen, D.
bioRxiv doi:  https://doi.org/10.1101/2023.09.03.556122 (2023)
2022
                       The emerging landscape of spatial profiling technologiesMoffitt, J.R., Lundberg, E., Heyn, H.
Nature Reviews Genetics doi:  https://doi.org/10.1038/s41576-022-00515-3 (2022)
2021
                       Cell segmentation in imaging-based spatial transcriptomicsPetukhov, V., Xu, R.J., Soldatov, R.A., Cadinu, P., Khodosevich, K., Moffitt, J.R., Kharchenko, P.V.
Nature Biotechnology doi:  https://doi.org/10.1038/s41587-021-01044-w (2021)
2020
                       MAFG-driven astrocytes promote CNS inflammationWheeler, 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 LesionsKagan, 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 neuronsWang, G., Ang C.-E., Fan, J., Wang, A., Moffitt, J.R., Zhuang, X.
bioRxiv doi: https://doi.org/10.1101/2020.12.07.414060 (2020)
2019
                       Multiplexed Detection of RNA using MERFISH and Branched DNA AmplificationXia, C., Babcock, H., *Moffitt, J.R., *Zhuang, X.
Scientific Reports 9 7721 (2019) 
bioRxiv (2018)

                 Prior Publications
              
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 MicroscopyWang, G., Moffitt, J.R., Zhuang, X.
Scientific Reports 8, 4847 (2018).
2017
                       High-Throughput, Image-Based Screening of Genetic Variant LibrariesEmanuel, G., *Moffitt, J.R., *Zhuang, X.
Nature Methods 14, 1159-1162 (2017)
2016
                       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 ChromosomesWang, 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 TranscriptomeMoffitt, 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 StatesBoettiger, 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)
2015
                       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)
2014
                       Characterization and Development of Photoactivatable Fluorescent Proteins for Single-Molecule-Based Superresolution ImagingWang S., Moffitt, J.R., Dempsey, G.T., Xie, X.S., Zhuang, X.
PNAS 111, 8452-8457 (2014)

                       Simultaneous Dual-Color 3D STED MicroscopyOsseforth, C., Moffitt, J.R., Schermelleh, L., Michaelis J.
Optics Express 22, 7028-7039 (2014)

                       Extracting Signal from Noise: Kinetic Mechanisms from a Michaelis-Menten-Like Expression for Enzymatic Fluctuations*Moffitt, J.R. and *Bustamante, C.
FEBS Journal 281, 498-517 (2014)
2013
                       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 RegulationTeng, S., †Mukherji, S., †Moffitt, J.R., †de Buyl, S., and O’Shea, E. K.
Science 340, 737-740 (2013)

                       Statistical Analysis of Molecular Signal RecordingGlaser, 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)
2012
                       High Degree of Coordination and Division of Labor among Subunits in a Homomeric Ring ATPaseChistol, G., Liu, S., Hetherington, C.L., Moffitt, J.R., Grimes, S., Jardine, P.J., and Bustamante, C.
Cell 151, 1017 (2012)

                       The Single-Cell Chemostat: an Agarose-Based, Microfluidic Device for High-Throughput, Single-Cell Studies of Bacteria and Bacterial Communities†Moffitt, J.R., †Lee, J.B., and Cluzel, P.
Lab on a Chip 12, 1487 (2012)

                       Lessons from Viral Packaging MotorsHetherington, C. L., Chistol, G., Moffitt, J.R., and Bustamante, C.
in Comprehensive Biophysics, Ed. Goldman, Y., 4, 420 (2012)
2011
                       Single-Base Pair Unwinding and Asynchronous RNA Release by the Hepatitis C Virus NS3 HelicaseCheng, 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)
2010
                       Mechanistic Constraints from the Substrate Concentration Dependence of Enzymatic FluctuationsMoffitt, J.R., Chemla, Y.R., and Bustamante, C.
PNAS 107, 15739 (2010)

                       Methods in Statistical KineticsMoffitt, J.R., Chemla, Y.R., and Bustamante, C.
Methods in Enzymology 475, 221 (2010)

                       Mechanochemistry of a Viral DNA Packaging MotorYu, J., Moffitt, J.R., Hetherington, C.L., Bustamante, C., and Oster, G.
Journal of Molecular Biology 400, 186 (2010)
2009
                       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 MotorsMichaelis, J., Muschielok, A., Andrecka, J., Kügel, W., and Moffitt, J.R.
Physics of Life 6, 250 (2009)
Viral Packaging: One Step at a TimeBustamante, 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 TranscriptionBustamante, C., and Moffitt, J.R.
in RNA polymerases as a molecular motors, Eds. Strict, T. and Buc, H., RSC (2009)
2008
                       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 TweezersMoffitt, 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 DetectionBustamante, C., Chemla, Y.R., and Moffitt, J.R.
in Single-Molecule Techniques: A Laboratory Manual, Eds. Selvin, P.J. and Ha, T., CSHL (2008)
2006
                       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)
2004
                       Self-Erasing Perturbations of Abelian SandpilesMoffitt, J.R., Macdonald, P., Lindner, J.F.
Physical Review E 70, 016203 (2004)
2003
                       System Level Implementation of Beam Position Monitors with Local Data Processing Capability for the Cornell Electron Storage RingPalmer, 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 2024
Jeffrey Moffitt