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100. Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity.
Taylor B. Updegrove , Thomas Delerue , V. Anantharaman , Hyomoon Cho , Carissa Chan , Thomas Nipper , Hyoyoung Choo-Wosoba , Lisa Jenkins , Lixia Zhang , Yijun Su , Hari Shroff , Jiji Chen , Carole Bewley , L. Aravind , Kumaran S Ramamurthi. bioRxiv. 2024 Mar 27:. doi: 10.1101/2024.03.27.587046
99. Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine.
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98. Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis.
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97. Live-cell imaging powered by computation.
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96. Phase diversity-based wavefront sensing for fluorescence microscopy
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95. Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.
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94. Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers.
Sadhu RK, Hernandez-Padilla C, Eisenbach YE, Penič S, Zhang L, Vishwasrao HD, Behkam B, Konstantopoulos K, Shroff H, Iglič A, Peles E, Nain AS, Gov NS.Nat Commun. 2023 Sep 12;14(1):5612. doi: 10.1038/s41467-023-41273-y.PMID: 37699891
93. Three-dimensional structured illumination microscopy with enhanced axial resolution.
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92. Cell division machinery drives cell-specific gene activation during bacterial differentiation.
Chareyre S, Li X, Anjuwon-Foster BR, Clifford S, Brogan A, Su Y, Shroff H, Ramamurthi KS.bioRxiv. 2023 Aug 10:2023.08.10.552768. doi: 10.1101/2023.08.10.552768. Preprint.PMID: 37790399
91. Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches.
Reiser N, Guo M, Shroff H, Riviere PJ.ArXiv. 2023 Aug 1:arXiv:2308.00734v1. Preprint.PMID: 37791105
90. Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants.
Ngo TB, DeStefano S, Liu J, Su Y, Shroff H, Vishwasrao HD, Sadtler K.J Biomed Mater Res A. 2023 Jun;111(6):840-850. doi: 10.1002/jbm.a.37515. Epub 2023 Mar 2.PMID: 36861434
89. Practical considerations for quantitative light sheet fluorescence microscopy.
Hobson CM, Guo M, Vishwasrao HD, Wu Y, Shroff H, Chew TL.Nat Methods. 2022 Dec;19(12):1538-1549. doi: 10.1038/s41592-022-01632-x. Epub 2022 Oct 20.PMID: 36266466
88. An Exact Hypergraph Matching algorithm for posture identification in embryonic C. elegans.
Lauziere A, Christensen R, Shroff H, Balan R.PLoS One. 2022 Nov 29;17(11):e0277343. doi: 10.1371/journal.pone.0277343. eCollection 2022.PMID: 36445888
87. Incorporating the image formation process into deep learning improves network performance.
Li Y, Su Y, Guo M, Han X, Liu J, Vishwasrao HD, Li X, Christensen R, Sengupta T, Moyle MW, Rey-Suarez I, Chen J, Upadhyaya A, Usdin TB, Colón-Ramos DA, Liu H, Wu Y, Shroff H.Nat Methods. 2022 Nov;19(11):1427-1437. doi: 10.1038/s41592-022-01652-7. Epub 2022 Oct 31.PMID: 36316563
86. Multiscale fluorescence imaging of living samples.
Wu Y, Shroff H.Histochem Cell Biol. 2022 Oct;158(4):301-323. doi: 10.1007/s00418-022-02147-4. Epub 2022 Aug 29.PMID: 36036808
85. Nanotopography modulates cytoskeletal organization and dynamics during T cell activation.
Wheatley BA, Rey-Suarez I, Hourwitz MJ, Kerr S, Shroff H, Fourkas JT, Upadhyaya A.Mol Biol Cell. 2022 Sep 1;33(10):ar88. doi: 10.1091/mbc.E21-12-0601. Epub 2022 Jul 13.PMID: 35830602
84. Stereotyped behavioral maturation and rhythmic quiescence in C. elegans embryos.
Ardiel EL, Lauziere A, Xu S, Harvey BJ, Christensen RP, Nurrish S, Kaplan JM, Shroff H.Elife. 2022 Aug 5;11:e76836. doi: 10.7554/eLife.76836.PMID: 35929725
83. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein.
Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P.PNAS Nexus. 2022 May 16;1(2):pgac049. doi: 10.1093/pnasnexus/pgac049. eCollection 2022 May.PMID: 35783502
82. The HIV-1 Viral Protease Is Activated during Assembly and Budding Prior to Particle Release.
Tabler CO, Wegman SJ, Chen J, Shroff H, Alhusaini N, Tilton JC.J Virol. 2022 May 11;96(9):e0219821. doi: 10.1128/jvi.02198-21. Epub 2022 Apr 19.PMID: 35438536
81. Human deafness-associated variants alter the dynamics of key molecules in hair cell stereocilia F-actin cores.
Miyoshi T, Belyantseva IA, Kitajiri SI, Miyajima H, Nishio SY, Usami SI, Kim BJ, Choi BY, Omori K, Shroff H, Friedman TB.Hum Genet. 2022 Apr;141(3-4):363-382. doi: 10.1007/s00439-021-02304-0. Epub 2021 Jul 7.PMID: 34232383 Review.
80. Cytonemes coordinate asymmetric signaling and organization in the Drosophila muscle progenitor niche.
Patel A, Wu Y, Han X, Su Y, Maugel T, Shroff H, Roy S.Nat Commun. 2022 Mar 4;13(1):1185. doi: 10.1038/s41467-022-28587-z.PMID: 35246530
79. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein.
Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P.bioRxiv. 2022 Feb 9:2022.02.08.479556. doi: 10.1101/2022.02.08.479556. Preprint.PMID: 35169797 Updated.
78. Multiview confocal super-resolution microscopy.
Wu Y, Han X, Su Y, Glidewell M, Daniels JS, Liu J, Sengupta T, Rey-Suarez I, Fischer R, Patel A, Combs C, Sun J, Wu X, Christensen R, Smith C, Bao L, Sun Y, Duncan LH, Chen J, Pommier Y, Shi YB, Murphy E, Roy S, Upadhyaya A, Colón-Ramos D, La Riviere P, Shroff H.Nature. 2021 Dec;600(7888):279-284. doi: 10.1038/s41586-021-04110-0. Epub 2021 Nov 26.PMID: 34837071
77. Differential adhesion regulates neurite placement via a retrograde zippering mechanism.
Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler WA, Shroff H, Colón-Ramos DA.Elife. 2021 Nov 16;10:e71171. doi: 10.7554/eLife.71171.PMID: 34783657
76. Actomyosin dynamics modulate microtubule deformation and growth during T-cell activation.
Rey-Suarez I, Rogers N, Kerr S, Shroff H, Upadhyaya A.Mol Biol Cell. 2021 Aug 19;32(18):1641-1653. doi: 10.1091/mbc.E20-10-0685. Epub 2021 Apr 7.PMID: 33826369
75. Pupal behavior emerges from unstructured muscle activity in response to neuromodulation in Drosophila.
Elliott AD, Berndt A, Houpert M, Roy S, Scott RL, Chow CC, Shroff H, White BH.Elife. 2021 Jul 8;10:e68656. doi: 10.7554/eLife.68656.PMID: 34236312
74. Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes.
Chen J, Sasaki H, Lai H, Su Y, Liu J, Wu Y, Zhovmer A, Combs CA, Rey-Suarez I, Chang HY, Huang CC, Li X, Guo M, Nizambad S, Upadhyaya A, Lee SJ, Lucas LAG, Shroff H.Nat Methods. 2021 Jun;18(6):678-687. doi: 10.1038/s41592-021-01155-x. Epub 2021 May 31.PMID: 34059829
73. Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10.
Campanello L, Traver MK, Shroff H, Schaefer BC, Losert W.PLoS Comput Biol. 2021 May 20;17(5):e1007986. doi: 10.1371/journal.pcbi.1007986. eCollection 2021 May.PMID: 34014917
72. A polymer index-matched to water enables diverse applications in fluorescence microscopy.
Han X, Su Y, White H, O'Neill KM, Morgan NY, Christensen R, Potarazu D, Vishwasrao HD, Xu S, Sun Y, Huang SY, Moyle MW, Dai Q, Pommier Y, Giniger E, Albrecht DR, Probst R, Shroff H.Lab Chip. 2021 Apr 20;21(8):1549-1562. doi: 10.1039/d0lc01233e.PMID: 33629685
71. Structural and developmental principles of neuropil assembly in C. elegans.
Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA.Nature. 2021 Mar;591(7848):99-104. doi: 10.1038/s41586-020-03169-5. Epub 2021 Feb 24.PMID: 33627875
70. Nanoscale Pattern Extraction from Relative Positions of Sparse 3D Localizations.
Curd AP, Leng J, Hughes RE, Cleasby AJ, Rogers B, Trinh CH, Baird MA, Takagi Y, Tiede C, Sieben C, Manley S, Schlichthaerle T, Jungmann R, Ries J, Shroff H, Peckham M.Nano Lett. 2021 Feb 10;21(3):1213-1220. doi: 10.1021/acs.nanolett.0c03332. Epub 2020 Nov 30.PMID: 33253583
69. Semi-automated single-molecule microscopy screening of fast-dissociating specific antibodies directly from hybridoma cultures.
Miyoshi T, Zhang Q, Miyake T, Watanabe S, Ohnishi H, Chen J, Vishwasrao HD, Chakraborty O, Belyantseva IA, Perrin BJ, Shroff H, Friedman TB, Omori K, Watanabe N.Cell Rep. 2021 Feb 2;34(5):108708. doi: 10.1016/j.celrep.2021.108708.PMID: 33535030
68. Zebrafish Posterior Lateral Line primordium migration requires interactions between a superficial sheath of motile cells and the skin.
Dalle Nogare DE, Natesh N, Vishwasrao HD, Shroff H, Chitnis AB.Elife. 2020 Nov 25;9:e58251. doi: 10.7554/eLife.58251.PMID: 33237853
67. Rapid image deconvolution and multiview fusion for optical microscopy.
Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, Shroff H.Nat Biotechnol. 2020 Nov;38(11):1337-1346. doi: 10.1038/s41587-020-0560-x. Epub 2020 Jun 29.PMID: 32601431
66. Spatio-angular fluorescence microscopy III. Constrained angular diffusion, polarized excitation, and high-NA imaging.
Chandler T, Shroff H, Oldenbourg R, La Rivière P.J Opt Soc Am A Opt Image Sci Vis. 2020 Sep 1;37(9):1465-1479. doi: 10.1364/JOSAA.389217.PMID: 32902437
65. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters.
Trcek T, Douglas TE, Grosch M, Yin Y, Eagle WVI, Gavis ER, Shroff H, Rothenberg E, Lehmann R.Mol Cell. 2020 Jun 4;78(5):941-950.e12. doi: 10.1016/j.molcel.2020.05.008. Epub 2020 May 27.PMID: 32464092
64. WASP family proteins regulate the mobility of the B cell receptor during signaling activation.
Rey-Suarez I, Wheatley BA, Koo P, Bhanja A, Shu Z, Mochrie S, Song W, Shroff H, Upadhyaya A.Nat Commun. 2020 Jan 23;11(1):439. doi: 10.1038/s41467-020-14335-8.PMID: 31974357
63. Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association.
Bhagwat AR, Le Sage V, Nturibi E, Kulej K, Jones J, Guo M, Tae Kim E, Garcia BA, Weitzman MD, Shroff H, Lakdawala SS.Nat Commun. 2020 Jan 7;11(1):23. doi: 10.1038/s41467-019-13838-3.PMID: 31911620
62. A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface.
Peluso EA, Updegrove TB, Chen J, Shroff H, Ramamurthi KS.Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21789-21799. doi: 10.1073/pnas.1907397116. Epub 2019 Oct 9.PMID: 31597735
61. Spatio-angular fluorescence microscopy II. Paraxial 4f imaging.
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59. Transforming the development and dissemination of cutting-edge microscopy and computation.
Colón-Ramos DA, La Riviere P, Shroff H, Oldenbourg R.Nat Methods. 2019 Aug;16(8):667-669. doi: 10.1038/s41592-019-0475-y.PMID: 31363203
58. Author Correction: Anchoring cortical granules in the cortex ensures trafficking to the plasma membrane for post-fertilization exocytosis.
Vogt EJ, Tokuhiro K, Guo M, Dale R, Yang G, Shin SW, Movilla MJ, Shroff H, Dean J.Nat Commun. 2019 Jun 27;10(1):2926. doi: 10.1038/s41467-019-10935-1.PMID: 31249315
57. Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution.
Duncan LH, Moyle MW, Shao L, Sengupta T, Ikegami R, Kumar A, Guo M, Christensen R, Santella A, Bao Z, Shroff H, Mohler W, Colón-Ramos DA.J Vis Exp. 2019 Jun 6;(148):10.3791/59533. doi: 10.3791/59533.PMID: 31233035
56. Anchoring cortical granules in the cortex ensures trafficking to the plasma membrane for post-fertilization exocytosis.
Vogt EJ, Tokuhiro K, Guo M, Dale R, Yang G, Shin SW, Movilla MJ, Shroff H, Dean J.Nat Commun. 2019 May 22;10(1):2271. doi: 10.1038/s41467-019-10171-7.PMID: 31118423
55. Author Correction: Faster, sharper, and deeper: structured illumination microscopy for biological imaging.
Wu Y, Shroff H.Nat Methods. 2019 Feb;16(2):205. doi: 10.1038/s41592-018-0296-4.PMID: 30594947
54. Faster, sharper, and deeper: structured illumination microscopy for biological imaging.
Wu Y, Shroff H.Nat Methods. 2018 Dec;15(12):1011-1019. doi: 10.1038/s41592-018-0211-z. Epub 2018 Nov 26.PMID: 30478322 Review.
53. A Genetically Encoded Biosensor Strategy for Quantifying Non-muscle Myosin II Phosphorylation Dynamics in Living Cells and Organisms.
Markwardt ML, Snell NE, Guo M, Wu Y, Christensen R, Liu H, Shroff H, Rizzo MA.Cell Rep. 2018 Jul 24;24(4):1060-1070.e4. doi: 10.1016/j.celrep.2018.06.088.PMID: 30044973
52. A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo.
Xu M, Wu Y, Shroff H, Wu M, Mani M.PLoS One. 2018 Jul 10;13(7):e0199151. doi: 10.1371/journal.pone.0199151. eCollection 2018.PMID: 29990323
51. Single-shot super-resolution total internal reflection fluorescence microscopy.
Guo M, Chandris P, Giannini JP, Trexler AJ, Fischer R, Chen J, Vishwasrao HD, Rey-Suarez I, Wu Y, Wu X, Waterman CM, Patterson GH, Upadhyaya A, Taraska JW, Shroff H.Nat Methods. 2018 Jun;15(6):425-428. doi: 10.1038/s41592-018-0004-4. Epub 2018 May 7.PMID: 29735999
50. Single-fluorophore orientation determination with multiview polarized illumination: modeling and microscope design.
Chandler T, Mehta S, Shroff H, Oldenbourg R, La Rivière PJ.Opt Express. 2017 Dec 11;25(25):31309-31325. doi: 10.1364/OE.25.031309.PMID: 29245807
49. Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy.
Zhu G, Lynn GM, Jacobson O, Chen K, Liu Y, Zhang H, Ma Y, Zhang F, Tian R, Ni Q, Cheng S, Wang Z, Lu N, Yung BC, Wang Z, Lang L, Fu X, Jin A, Weiss ID, Vishwasrao H, Niu G, Shroff H, Klinman DM, Seder RA, Chen X.Nat Commun. 2017 Dec 5;8(1):1954. doi: 10.1038/s41467-017-02191-y.PMID: 29203865
48. Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapy.
Zhu G, Mei L, Vishwasrao HD, Jacobson O, Wang Z, Liu Y, Yung BC, Fu X, Jin A, Niu G, Wang Q, Zhang F, Shroff H, Chen X.Nat Commun. 2017 Nov 14;8(1):1482. doi: 10.1038/s41467-017-01386-7.PMID: 29133898
47. Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy.
Wu Y, Kumar A, Smith C, Ardiel E, Chandris P, Christensen R, Rey-Suarez I, Guo M, Vishwasrao HD, Chen J, Tang J, Upadhyaya A, La Riviere PJ, Shroff H.Nat Commun. 2017 Nov 13;8(1):1452. doi: 10.1038/s41467-017-01250-8.PMID: 29129912
46. Anticipating, measuring, and minimizing MEMS mirror scan error to improve laser scanning microscopy's speed and accuracy.
Giannini JP, York AG, Shroff H.PLoS One. 2017 Oct 3;12(10):e0185849. doi: 10.1371/journal.pone.0185849. eCollection 2017.PMID: 28973013
45. Real-time visualization of chromatin modification in isolated nuclei.
Sardo L, Lin A, Khakhina S, Beckman L, Ricon L, Elbezanti W, Jaison T, Vishwasrao H, Shroff H, Janetopoulos C, Klase ZA.J Cell Sci. 2017 Sep 1;130(17):2926-2940. doi: 10.1242/jcs.205823. Epub 2017 Jul 25.PMID: 28743737
44. Adaptive optics improves multiphoton super-resolution imaging.
Zheng W, Wu Y, Winter P, Fischer R, Nogare DD, Hong A, McCormick C, Christensen R, Dempsey WP, Arnold DB, Zimmerberg J, Chitnis A, Sellers J, Waterman C, Shroff H.Nat Methods. 2017 Sep;14(9):869-872. doi: 10.1038/nmeth.4337. Epub 2017 Jun 19.PMID: 28628128
43. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.
Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R.Mol Cell. 2017 Aug 17;67(4):566-578.e10. doi: 10.1016/j.molcel.2017.07.013. Epub 2017 Aug 10.PMID: 28803781
42. mRNA quantification using single-molecule FISH in Drosophila embryos.
Trcek T, Lionnet T, Shroff H, Lehmann R.Nat Protoc. 2017 Jul;12(7):1326-1348. doi: 10.1038/nprot.2017.030. Epub 2016 Jun 8.PMID: 28594816
41. Assessing phototoxicity in live fluorescence imaging.
Laissue PP, Alghamdi RA, Tomancak P, Reynaud EG, Shroff H.Nat Methods. 2017 Jun 29;14(7):657-661. doi: 10.1038/nmeth.4344.PMID: 28661494
40. Visualizing Calcium Flux in Freely Moving Nematode Embryos.
Ardiel EL, Kumar A, Marbach J, Christensen R, Gupta R, Duncan W, Daniels JS, Stuurman N, Colón-Ramos D, Shroff H.Biophys J. 2017 May 9;112(9):1975-1983. doi: 10.1016/j.bpj.2017.02.035.PMID: 28494967
39. Fluorescence Microscopy: A Concise Guide to Current Imaging Methods.
Combs CA, Shroff H.Curr Protoc Neurosci. 2017 Apr 10;79:2.1.1-2.1.25. doi: 10.1002/cpns.29.PMID: 28398640
38. Immunogenic cancer cell death selectively induced by near infrared photoimmunotherapy initiates host tumor immunity.
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37. Correction: Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm.
Lakdawala SS, Wu Y, Wawrzusin P, Kabat J, Broadbent AJ, Lamirande EW, Fodor E, Altan-Bonnet N, Shroff H, Subbarao K.PLoS Pathog. 2016 Dec 27;12(12):e1006121. doi: 10.1371/journal.ppat.1006121. eCollection 2016 Dec.PMID: 28027316
36. Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy.
Wu Y, Chandris P, Winter PW, Kim EY, Jaumouillé V, Kumar A, Guo M, Leung JM, Smith C, Rey-Suarez I, Liu H, Waterman CM, Ramamurthi KS, La Riviere PJ, Shroff H.Optica. 2016 Aug 20;3(8):897-910. doi: 10.1364/OPTICA.3.000897. Epub 2016 Aug 11.PMID: 27761486
35. Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM).
Kumar A, Christensen R, Guo M, Chandris P, Duncan W, Wu Y, Santella A, Moyle M, Winter PW, Colón-Ramos D, Bao Z, Shroff H.Biol Bull. 2016 Aug;231(1):26-39. doi: 10.1086/689589.PMID: 27638693
34. Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium.
Dundon SE, Chang SS, Kumar A, Occhipinti P, Shroff H, Roper M, Gladfelter AS.Mol Biol Cell. 2016 Jul 1;27(13):2000-7. doi: 10.1091/mbc.E16-02-0129. Epub 2016 May 18.PMID: 27193301
33. Untwisting the Caenorhabditis elegans embryo.
Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H.Elife. 2015 Dec 3;4:e10070. doi: 10.7554/eLife.10070.PMID: 26633880
32. Construction of an instant structured illumination microscope.
Curd A, Cleasby A, Makowska K, York A, Shroff H, Peckham M.Methods. 2015 Oct 15;88:37-47. doi: 10.1016/j.ymeth.2015.07.012. Epub 2015 Jul 22.PMID: 26210400
31. Drosophila germ granules are structured and contain homotypic mRNA clusters.
Trcek T, Grosch M, York A, Shroff H, Lionnet T, Lehmann R.Nat Commun. 2015 Aug 5;6:7962. doi: 10.1038/ncomms8962.PMID: 26242323
30. WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.
Santella A, Catena R, Kovacevic I, Shah P, Yu Z, Marquina-Solis J, Kumar A, Wu Y, Schaff J, Colón-Ramos D, Shroff H, Mohler WA, Bao Z.BMC Bioinformatics. 2015 Jun 9;16(1):189. doi: 10.1186/s12859-015-0627-8.PMID: 26051157
29. Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy.
Winter PW, Chandris P, Fischer RS, Wu Y, Waterman CM, Shroff H.Opt Express. 2015 Feb 23;23(4):5327-34. doi: 10.1364/OE.23.005327.PMID: 25836564
28. Three-dimensional photoactivated localization microscopy with genetically expressed probes.
Temprine K, York AG, Shroff H.Methods Mol Biol. 2015;1251:231-61. doi: 10.1007/978-1-4939-2080-8_13.PMID: 25391803
27. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging.
Kumar A, Wu Y, Christensen R, Chandris P, Gandler W, McCreedy E, Bokinsky A, Colón-Ramos DA, Bao Z, McAuliffe M, Rondeau G, Shroff H.Nat Protoc. 2014 Nov;9(11):2555-73. doi: 10.1038/nprot.2014.172. Epub 2014 Oct 9.PMID: 25299154
26. Two-photon instant structured illumination microscopy improves the depth penetration of super-resolution imaging in thick scattering samples.
Winter PW, York AG, Nogare DD, Ingaramo M, Christensen R, Chitnis A, Patterson GH, Shroff H.Optica. 2014 Sep 20;1(3):181-191. doi: 10.1364/OPTICA.1.000181.PMID: 25485291
25. Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA.
Eswaramoorthy P, Winter PW, Wawrzusin P, York AG, Shroff H, Ramamurthi KS.PLoS Genet. 2014 Aug 7;10(8):e1004526. doi: 10.1371/journal.pgen.1004526. eCollection 2014 Aug.PMID: 25101664
24. Faster fluorescence microscopy: advances in high speed biological imaging.
Winter PW, Shroff H.Curr Opin Chem Biol. 2014 Jun;20:46-53. doi: 10.1016/j.cbpa.2014.04.008. Epub 2014 May 9.PMID: 24815857 Review.
23. Two-photon excitation improves multifocal structured illumination microscopy in thick scattering tissue.
Ingaramo M, York AG, Wawrzusin P, Milberg O, Hong A, Weigert R, Shroff H, Patterson GH.Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5254-9. doi: 10.1073/pnas.1314447111. Epub 2014 Mar 24.PMID: 24706872
22. Richardson-Lucy deconvolution as a general tool for combining images with complementary strengths.
Ingaramo M, York AG, Hoogendoorn E, Postma M, Shroff H, Patterson GH.Chemphyschem. 2014 Mar 17;15(4):794-800. doi: 10.1002/cphc.201300831. Epub 2014 Jan 16.PMID: 24436314
21. Influenza a virus assembly intermediates fuse in the cytoplasm.
Lakdawala SS, Wu Y, Wawrzusin P, Kabat J, Broadbent AJ, Lamirande EW, Fodor E, Altan-Bonnet N, Shroff H, Subbarao K.PLoS Pathog. 2014 Mar 6;10(3):e1003971. doi: 10.1371/journal.ppat.1003971. eCollection 2014 Mar.PMID: 24603687
20. Advanced optical imaging techniques for neurodevelopment.
Wu Y, Christensen R, Colón-Ramos D, Shroff H.Curr Opin Neurobiol. 2013 Dec;23(6):1090-7. doi: 10.1016/j.conb.2013.06.008. Epub 2013 Jul 5.PMID: 23831260 Review.
19. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy.
Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colón-Ramos DA, McAuliffe M, Shroff H.Nat Biotechnol. 2013 Nov;31(11):1032-8. doi: 10.1038/nbt.2713. Epub 2013 Oct 13.PMID: 24108093
18. Instant super-resolution imaging in live cells and embryos via analog image processing.
York AG, Chandris P, Nogare DD, Head J, Wawrzusin P, Fischer RS, Chitnis A, Shroff H.Nat Methods. 2013 Nov;10(11):1122-6. doi: 10.1038/nmeth.2687. Epub 2013 Oct 6.PMID: 24097271
17. Tools for the quantitative analysis of sedimentation boundaries detected by fluorescence optical analytical ultracentrifugation.
Zhao H, Casillas E Jr, Shroff H, Patterson GH, Schuck P.PLoS One. 2013 Oct 18;8(10):e77245. doi: 10.1371/journal.pone.0077245. eCollection 2013.PMID: 24204779
16. Photoactivated Localization Microscopy (PALM) of adhesion complexes.
Shroff H, White H, Betzig E.Curr Protoc Cell Biol. 2013 Mar;Chapter 4:Unit4.21. doi: 10.1002/0471143030.cb0421s58.PMID: 23456603
15. Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy.
York AG, Parekh SH, Dalle Nogare D, Fischer RS, Temprine K, Mione M, Chitnis AB, Combs CA, Shroff H.Nat Methods. 2012 May 13;9(7):749-54. doi: 10.1038/nmeth.2025.PMID: 22581372
14. Microscopy in 3D: a biologist's toolbox.
Fischer RS, Wu Y, Kanchanawong P, Shroff H, Waterman CM.Trends Cell Biol. 2011 Dec;21(12):682-91. doi: 10.1016/j.tcb.2011.09.008. Epub 2011 Oct 31.PMID: 22047760 Review.
13. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans.
Wu Y, Ghitani A, Christensen R, Santella A, Du Z, Rondeau G, Bao Z, Colón-Ramos D, Shroff H.Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17708-13. doi: 10.1073/pnas.1108494108. Epub 2011 Oct 17.PMID: 22006307
12. Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes.
York AG, Ghitani A, Vaziri A, Davidson MW, Shroff H.Nat Methods. 2011 Apr;8(4):327-33. doi: 10.1038/nmeth.1571. Epub 2011 Feb 13.PMID: 21317909
11. Single-molecule discrimination of discrete perisynaptic and distributed sites of actin filament assembly within dendritic spines.
Frost NA, Shroff H, Kong H, Betzig E, Blanpied TA.Neuron. 2010 Jul 15;67(1):86-99. doi: 10.1016/j.neuron.2010.05.026.PMID: 20624594
10. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.
Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, Betzig E, Liphardt J.PLoS Biol. 2009 Jun 16;7(6):e1000137. doi: 10.1371/journal.pbio.1000137. Epub 2009 Jun 23.PMID: 19547746
9. Multilayer three-dimensional super resolution imaging of thick biological samples.
Vaziri A, Tang J, Shroff H, Shank CV.Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20221-6. doi: 10.1073/pnas.0810636105. Epub 2008 Dec 16.PMID: 19088193
8. Advances in the speed and resolution of light microscopy.
Ji N, Shroff H, Zhong H, Betzig E.Curr Opin Neurobiol. 2008 Dec;18(6):605-16. doi: 10.1016/j.conb.2009.03.009. Epub 2009 Apr 15.PMID: 19375302 Review.
7. Photoactivated localization microscopy (PALM) of adhesion complexes.
Shroff H, White H, Betzig E.Curr Protoc Cell Biol. 2008 Dec;Chapter 4:Unit 4.21. doi: 10.1002/0471143030.cb0421s41.PMID: 19085989
6. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics.
Shroff H, Galbraith CG, Galbraith JA, Betzig E.Nat Methods. 2008 May;5(5):417-23. doi: 10.1038/nmeth.1202. Epub 2008 Apr 13.PMID: 18408726
5. Optical measurement of mechanical forces inside short DNA loops.
Shroff H, Sivak D, Siegel JJ, McEvoy AL, Siu M, Spakowitz A, Geissler PL, Liphardt J.Biophys J. 2008 Mar 15;94(6):2179-86. doi: 10.1529/biophysj.107.114413. Epub 2007 Dec 7.PMID: 18065484
4. High-density mapping of single-molecule trajectories with photoactivated localization microscopy.
Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF, Betzig E, Lippincott-Schwartz J.Nat Methods. 2008 Feb;5(2):155-7. doi: 10.1038/nmeth.1176. Epub 2008 Jan 13.PMID: 18193054
3. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes.
Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, Olenych S, Davidson MW, Betzig E.Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20308-13. doi: 10.1073/pnas.0710517105. Epub 2007 Dec 12.PMID: 18077327
2. Optical trapping and integration of semiconductor nanowire assemblies in water.
Pauzauskie PJ, Radenovic A, Trepagnier E, Shroff H, Yang P, Liphardt J.Nat Mater. 2006 Feb;5(2):97-101. doi: 10.1038/nmat1563. Epub 2006 Jan 22.PMID: 16429143
1. Biocompatible force sensor with optical readout and dimensions of 6 nm3.
Shroff H, Reinhard BM, Siu M, Agarwal H, Spakowitz A, Liphardt J.Nano Lett. 2005 Jul;5(7):1509-14. doi: 10.1021/nl050875h.PMID: 16178266