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Items: 37

1.

Multiplexed detection of RNA using MERFISH and branched DNA amplification.

Xia C, Babcock HP, Moffitt JR, Zhuang X.

Sci Rep. 2019 May 22;9(1):7721. doi: 10.1038/s41598-019-43943-8.

2.

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.

Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X.

Science. 2018 Nov 16;362(6416). pii: eaau5324. doi: 10.1126/science.aau5324. Epub 2018 Nov 1.

3.

Author Correction: Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy.

Wang G, Moffitt JR, Zhuang X.

Sci Rep. 2018 Apr 19;8(1):6487. doi: 10.1038/s41598-018-24844-8.

4.

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy.

Wang G, Moffitt JR, Zhuang X.

Sci Rep. 2018 Mar 19;8(1):4847. doi: 10.1038/s41598-018-22297-7. Erratum in: Sci Rep. 2018 Apr 19;8(1):6487.

5.

High-throughput, image-based screening of pooled genetic-variant libraries.

Emanuel G, Moffitt JR, Zhuang X.

Nat Methods. 2017 Dec;14(12):1159-1162. doi: 10.1038/nmeth.4495. Epub 2017 Oct 30.

6.

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing.

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

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14456-14461. Epub 2016 Nov 22.

7.

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.

Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X.

Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):11046-51. doi: 10.1073/pnas.1612826113. Epub 2016 Sep 13.

8.

Spatial organization of chromatin domains and compartments in single chromosomes.

Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X.

Science. 2016 Aug 5;353(6299):598-602. doi: 10.1126/science.aaf8084. Epub 2016 Jul 21.

9.

RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).

Moffitt JR, Zhuang X.

Methods Enzymol. 2016;572:1-49. doi: 10.1016/bs.mie.2016.03.020. Epub 2016 Apr 27.

10.

Spatial organization shapes the turnover of a bacterial transcriptome.

Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X.

Elife. 2016 May 20;5. pii: e13065. doi: 10.7554/eLife.13065.

11.

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X.

Nature. 2016 Jan 21;529(7586):418-22. doi: 10.1038/nature16496. Epub 2016 Jan 13.

12.

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X.

Science. 2015 Apr 24;348(6233):aaa6090. doi: 10.1126/science.aaa6090. Epub 2015 Apr 9.

13.

Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging.

Wang S, Moffitt JR, Dempsey GT, Xie XS, Zhuang X.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8452-7. doi: 10.1073/pnas.1406593111. Epub 2014 May 27.

14.

Simultaneous dual-color 3D STED microscopy.

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

Opt Express. 2014 Mar 24;22(6):7028-39. doi: 10.1364/OE.22.007028.

PMID:
24664051
15.

Fast compressed sensing analysis for super-resolution imaging using L1-homotopy.

Babcock HP, Moffitt JR, Cao Y, Zhuang X.

Opt Express. 2013 Nov 18;21(23):28583-96. doi: 10.1364/OE.21.028583.

16.

Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations.

Moffitt JR, Bustamante C.

FEBS J. 2014 Jan;281(2):498-517. doi: 10.1111/febs.12545. Epub 2013 Oct 25. Review.

17.

Statistical analysis of molecular signal recording.

Glaser JI, Zamft BM, Marblestone AH, Moffitt JR, Tyo K, Boyden ES, Church G, Kording KP.

PLoS Comput Biol. 2013;9(7):e1003145. doi: 10.1371/journal.pcbi.1003145. Epub 2013 Jul 18.

18.

Robust circadian oscillations in growing cyanobacteria require transcriptional feedback.

Teng SW, Mukherji S, Moffitt JR, de Buyl S, O'Shea EK.

Science. 2013 May 10;340(6133):737-40. doi: 10.1126/science.1230996.

19.

High degree of coordination and division of labor among subunits in a homomeric ring ATPase.

Chistol G, Liu S, Hetherington CL, Moffitt JR, Grimes S, Jardine PJ, Bustamante C.

Cell. 2012 Nov 21;151(5):1017-28. doi: 10.1016/j.cell.2012.10.031.

20.

The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities.

Moffitt JR, Lee JB, Cluzel P.

Lab Chip. 2012 Apr 21;12(8):1487-94. doi: 10.1039/c2lc00009a. Epub 2012 Mar 7.

21.

Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase.

Cheng W, Arunajadai SG, Moffitt JR, Tinoco I Jr, Bustamante C.

Science. 2011 Sep 23;333(6050):1746-9. doi: 10.1126/science.1206023.

22.

Time-gating improves the spatial resolution of STED microscopy.

Moffitt JR, Osseforth C, Michaelis J.

Opt Express. 2011 Feb 28;19(5):4242-54. doi: 10.1364/OE.19.004242.

PMID:
21369254
23.

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations.

Moffitt JR, Chemla YR, Bustamante C.

Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15739-44. doi: 10.1073/pnas.1006997107. Epub 2010 Aug 20.

24.

Methods in statistical kinetics.

Moffitt JR, Chemla YR, Bustamante C.

Methods Enzymol. 2010;475:221-57. doi: 10.1016/S0076-6879(10)75010-2.

PMID:
20627160
25.

DNA based molecular motors.

Michaelis J, Muschielok A, Andrecka J, K├╝gel W, Moffitt JR.

Phys Life Rev. 2009 Dec;6(4):250-66. doi: 10.1016/j.plrev.2009.09.001. Epub 2009 Oct 3.

PMID:
20416848
26.

High-resolution dual-trap optical tweezers with differential detection: an introduction.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.top60. doi: 10.1101/pdb.top60.

PMID:
20147062
27.

High-resolution dual-trap optical tweezers with differential detection: alignment of instrument components.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip76. doi: 10.1101/pdb.ip76.

PMID:
20147041
28.

High-resolution dual-trap optical tweezers with differential detection: minimizing the influence of measurement noise.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip75. doi: 10.1101/pdb.ip75.

PMID:
20147040
29.

High-resolution dual-trap optical tweezers with differential detection: data collection and instrument calibration.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip74. doi: 10.1101/pdb.ip74.

PMID:
20147039
30.

High-resolution dual-trap optical tweezers with differential detection: instrument design.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip73. doi: 10.1101/pdb.ip73.

PMID:
20147038
31.

High-resolution dual-trap optical tweezers with differential detection: managing environmental noise.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip72. doi: 10.1101/pdb.ip72.

PMID:
20147037
32.

Substrate interactions and promiscuity in a viral DNA packaging motor.

Aathavan K, Politzer AT, Kaplan A, Moffitt JR, Chemla YR, Grimes S, Jardine PJ, Anderson DL, Bustamante C.

Nature. 2009 Oct 1;461(7264):669-73. doi: 10.1038/nature08443.

33.

Intersubunit coordination in a homomeric ring ATPase.

Moffitt JR, Chemla YR, Aathavan K, Grimes S, Jardine PJ, Anderson DL, Bustamante C.

Nature. 2009 Jan 22;457(7228):446-50. doi: 10.1038/nature07637. Epub 2009 Jan 7.

34.

Exact solutions for kinetic models of macromolecular dynamics.

Chemla YR, Moffitt JR, Bustamante C.

J Phys Chem B. 2008 May 15;112(19):6025-44. doi: 10.1021/jp076153r. Epub 2008 Mar 29.

PMID:
18373360
35.

Recent advances in optical tweezers.

Moffitt JR, Chemla YR, Smith SB, Bustamante C.

Annu Rev Biochem. 2008;77:205-28. doi: 10.1146/annurev.biochem.77.043007.090225. Review.

PMID:
18307407
36.

Differential detection of dual traps improves the spatial resolution of optical tweezers.

Moffitt JR, Chemla YR, Izhaky D, Bustamante C.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9006-11. Epub 2006 Jun 2.

37.

Self-erasing perturbations of Abelian sandpiles.

Moffitt JR, Macdonald P, Lindner JF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004;70(1 Pt 2):016203. Epub 2004 Jul 12.

PMID:
15324148

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