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Items: 21

1.

Physical and data structure of 3D genome.

Huang K, Li Y, Shim AR, Virk RKA, Agrawal V, Eshein A, Nap RJ, Almassalha LM, Backman V, Szleifer I.

Sci Adv. 2020 Jan 10;6(2):eaay4055. doi: 10.1126/sciadv.aay4055. eCollection 2020 Jan.

2.

Disordered chromatin packing regulates phenotypic plasticity.

Virk RKA, Wu W, Almassalha LM, Bauer GM, Li Y, VanDerway D, Frederick J, Zhang D, Eshein A, Roy HK, Szleifer I, Backman V.

Sci Adv. 2020 Jan 8;6(2):eaax6232. doi: 10.1126/sciadv.aax6232. eCollection 2020 Jan.

3.

Dynamic Crowding Regulates Transcription.

Shim AR, Nap RJ, Huang K, Almassalha LM, Matusda H, Backman V, Szleifer I.

Biophys J. 2019 Nov 15. pii: S0006-3495(19)30930-0. doi: 10.1016/j.bpj.2019.11.007. [Epub ahead of print]

PMID:
31818468
4.

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation.

Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF.

Mol Biol Cell. 2019 Aug 1;30(17):2320-2330. doi: 10.1091/mbc.E19-05-0286.

5.

Preservation of cellular nano-architecture by the process of chemical fixation for nanopathology.

Zhou X, Gladstein S, Almassalha LM, Li Y, Eshein A, Cherkezyan L, Viswanathan P, Subramanian H, Szleifer I, Backman V.

PLoS One. 2019 Jul 22;14(7):e0219006. doi: 10.1371/journal.pone.0219006. eCollection 2019.

6.

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation.

Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF.

Mol Biol Cell. 2019 Jun 19:mbcE19050286T. doi: 10.1091/mbc.E19-05-0286-T. [Epub ahead of print]

PMID:
31216230
7.

Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm.

Gladstein S, Almassalha LM, Cherkezyan L, Chandler JE, Eshein A, Eid A, Zhang D, Wu W, Bauer GM, Stephens AD, Morochnik S, Subramanian H, Marko JF, Ameer GA, Szleifer I, Backman V.

Nat Commun. 2019 Apr 10;10(1):1652. doi: 10.1038/s41467-019-09717-6.

8.

Spectral contrast optical coherence tomography angiography enables single-scan vessel imaging.

Winkelmann JA, Eid A, Spicer G, Almassalha LM, Nguyen TQ, Backman V.

Light Sci Appl. 2019 Jan 16;8:7. doi: 10.1038/s41377-018-0117-7. eCollection 2019.

9.

Sub-10-nm imaging of nucleic acids using spectroscopic intrinsic-contrast photon-localization optical nanoscopy (SICLON).

Eshein A, Li Y, Dong B, Almassalha LM, Chandler JE, Nguyen TQ, Hujsak KA, Dravid VP, Sun C, Zhang HF, Backman V.

Opt Lett. 2018 Dec 1;43(23):5817-5820. doi: 10.1364/OL.43.005817.

10.

Correlating colorectal cancer risk with field carcinogenesis progression using partial wave spectroscopic microscopy.

Gladstein S, Damania D, Almassalha LM, Smith LT, Gupta V, Subramanian H, Rex DK, Roy HK, Backman V.

Cancer Med. 2018 May;7(5):2109-2120. doi: 10.1002/cam4.1357. Epub 2018 Mar 23.

11.

Measuring Nanoscale Chromatin Heterogeneity with Partial Wave Spectroscopic Microscopy.

Gladstein S, Stawarz A, Almassalha LM, Cherkezyan L, Chandler JE, Zhou X, Subramanian H, Backman V.

Methods Mol Biol. 2018;1745:337-360. doi: 10.1007/978-1-4939-7680-5_19.

12.

Macrogenomic engineering via modulation of the scaling of chromatin packing density.

Almassalha LM, Bauer GM, Wu W, Cherkezyan L, Zhang D, Kendra A, Gladstein S, Chandler JE, VanDerway D, Seagle BL, Ugolkov A, Billadeau DD, O'Halloran TV, Mazar AP, Roy HK, Szleifer I, Shahabi S, Backman V.

Nat Biomed Eng. 2017 Nov;1(11):902-913. doi: 10.1038/s41551-017-0153-2. Epub 2017 Nov 6.

13.

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins.

Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF.

Mol Biol Cell. 2018 Jan 15;29(2):220-233. doi: 10.1091/mbc.E17-06-0410. Epub 2017 Nov 15.

14.

The transformation of the nuclear nanoarchitecture in human field carcinogenesis.

Bauer GM, Stypula-Cyrus Y, Subramanian H, Cherkezyan L, Viswanathan P, Zhang D, Iyengar R, Bagalkar S, Derbas J, Graff T, Gladstein S, Almassalha LM, Chandler JE, Roy HK, Backman V.

Future Sci OA. 2017 May 5;3(3):FSO206. doi: 10.4155/fsoa-2017-0027. eCollection 2017 Aug. Review.

15.

The effects of chemical fixation on the cellular nanostructure.

Li Y, Almassalha LM, Chandler JE, Zhou X, Stypula-Cyrus YE, Hujsak KA, Roth EW, Bleher R, Subramanian H, Szleifer I, Dravid VP, Backman V.

Exp Cell Res. 2017 Sep 15;358(2):253-259. doi: 10.1016/j.yexcr.2017.06.022. Epub 2017 Jun 30.

16.

Stochastic fluorescence switching of nucleic acids under visible light illumination.

Dong B, Almassalha LM, Soetikno BT, Chandler JE, Nguyen TQ, Urban BE, Sun C, Zhang HF, Backman V.

Opt Express. 2017 Apr 3;25(7):7929-7944. doi: 10.1364/OE.25.007929.

17.

The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.

Almassalha LM, Tiwari A, Ruhoff PT, Stypula-Cyrus Y, Cherkezyan L, Matsuda H, Dela Cruz MA, Chandler JE, White C, Maneval C, Subramanian H, Szleifer I, Roy HK, Backman V.

Sci Rep. 2017 Jan 24;7:41061. doi: 10.1038/srep41061.

18.

Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy.

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Cherkezyan L, Stypula-Cyrus Y, Weinberg S, Zhang D, Thusgaard Ruhoff P, Roy HK, Subramanian H, Chandel NS, Szleifer I, Backman V.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6372-E6381. Epub 2016 Oct 4.

19.

The Greater Genomic Landscape: The Heterogeneous Evolution of Cancer.

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Szleifer I, Roy HK, Backman V.

Cancer Res. 2016 Oct 1;76(19):5605-5609. Epub 2016 Aug 22.

20.

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast.

Dong B, Almassalha LM, Stypula-Cyrus Y, Urban BE, Chandler JE, Nguyen TQ, Sun C, Zhang HF, Backman V.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9716-21. doi: 10.1073/pnas.1602202113. Epub 2016 Aug 17.

21.

Clostridium difficile ribotype does not predict severe infection.

Walk ST, Micic D, Jain R, Lo ES, Trivedi I, Liu EW, Almassalha LM, Ewing SA, Ring C, Galecki AT, Rogers MA, Washer L, Newton DW, Malani PN, Young VB, Aronoff DM.

Clin Infect Dis. 2012 Dec;55(12):1661-8. doi: 10.1093/cid/cis786. Epub 2012 Sep 12.

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