If you made any changes in Pure these will be visible here soon.

Research Output

2020

Disordered chromatin packing regulates phenotypic plasticity

Virk, R. K. A., Wu, W., Almassalha, L. M., Bauer, G. M., Li, Y., VanDerway, D., Frederick, J., Zhang, D., Eshein, A., Roy, H. K., Szleifer, I. & Backman, V., Jan 8 2020, In : Science Advances. 6, 2, eaax6232.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Dynamic Crowding Regulates Transcription

Shim, A. R., Nap, R. J., Huang, K., Almassalha, L. M., Matusda, H., Backman, V. & Szleifer, I., May 5 2020, In : Biophysical Journal. 118, 9, p. 2117-2129 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Physical and data structure of 3D genome

Huang, K., Li, Y., Shim, A. R., Virk, R. K. A., Agrawal, V., Eshein, A., Nap, R. J., Almassalha, L. M., Backman, V. & Szleifer, I., Jan 10 2020, In : Science Advances. 6, 2, eaay4055.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access
2019
Open Access

Editorial introduction to the JSTQE issue on biophotonics

Ilev, I. K., Backman, V., Georgakoudi, I., Matsuura, Y., Calhoun, W. R. & Huser, T., Jan 1 2019, In : IEEE Journal of Selected Topics in Quantum Electronics. 25, 1, 8631060.

Research output: Contribution to journalEditorial

Influence of nuclear morphology on differentiation of mesenchymal stem cells

Wang, X., Agrawal, V., Duan, C., Jiang, B., Backman, V. & Ameer, G., 2019, Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. Society for Biomaterials, 1 p. (Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium; vol. 40).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring

Spicer, G. L. C., Eid, A., Wangpraseurt, D., Swain, T. D., Winkelmann, J. A., Yi, J., Kühl, M., Marcelino, L. A. & Backman, V., Dec 1 2019, In : Scientific reports. 9, 1, 14148.

Research output: Contribution to journalArticle

Open Access

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

Gladstein, S., Almassalha, L. M., Cherkezyan, L., Chandler, J. E., Eshein, A., Eid, A., Zhang, D., Wu, W., Bauer, G. M., Stephens, A. D., Morochnik, S., Subramanian, H., Marko, J. F., Ameer, G. A., Szleifer, I. & Backman, V., Dec 1 2019, In : Nature communications. 10, 1, 1652.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation

Stephens, A. D., Liu, P. Z., Kandula, V., Chen, H., Almassalha, L. M., Herman, C., Backman, V., O'Halloran, T., Adam, S. A., Goldman, R. D., Banigan, E. J. & Marko, J. F., Aug 1 2019, In : Molecular biology of the cell. 30, 17, p. 2320-2330 11 p.

Research output: Contribution to journalArticle

Open Access
12 Scopus citations

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

Zhou, X., Gladstein, S., Almassalha, L. M., Li, Y., Eshein, A., Cherkezyan, L., Viswanathan, P., Subramanian, H., Szleifer, I. & Backman, V., Jul 1 2019, In : PloS one. 14, 7, e0219006.

Research output: Contribution to journalArticle

Open Access

Quantitative quality-control metrics for in vivo oximetry in small vessels by visible light optical coherence tomography angiography

Liu, R., Song, W., Backman, V. & Yi, J., Jan 1 2019, In : Biomedical Optics Express. 10, 2, p. 465-486 22 p.

Research output: Contribution to journalArticle

4 Scopus citations

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

Winkelmann, J. A., Eid, A., Spicer, G., Almassalha, L. M., Nguyen, T. Q. & Backman, V., Dec 1 2019, In : Light: Science and Applications. 8, 1, 7.

Research output: Contribution to journalLetter

5 Scopus citations
2018

Biophotonic detection of high order chromatin alterations in field carcinogenesis predicts risk of future hepatocellular carcinoma: A pilot study

Kalman, R., Stawarz, A., Nunes, D., Zhang, D., Dela Cruz, M. A., Mohanty, A., Subramanian, H., Backman, V. & Roy, H. K., May 2018, In : PloS one. 13, 5, e0197427.

Research output: Contribution to journalArticle

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins

Stephens, A. D., Liu, P. Z., Banigan, E. J., Almassalha, L. M., Backman, V., Adam, S. A., Goldman, R. D. & Marko, J. F., Jan 15 2018, In : Molecular biology of the cell. 29, 2, p. 220-233 14 p.

Research output: Contribution to journalArticle

44 Scopus citations

Correction: Biophotonic detection of high order chromatin alterations in field carcinogenesis predicts risk of future hepatocellular carcinoma: A pilot study(PLoS ONE (2018)13: 5 (e0197427) DOI : 10.1371/journal.pone.0197427)

Kalman, R. S., Stawarz, A., Nunes, D., Zhang, D., Dela Cruz, M. A., Mohanty, A., Subramanian, H., Backman, V. & Roy, H. K., Jul 2018, In : PloS one. 13, 7, e0201500.

Research output: Contribution to journalComment/debate

1 Scopus citations

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

Gladstein, S., Damania, D., Almassalha, L. M., Smith, L. T., Gupta, V., Subramanian, H., Rex, D. K., Roy, H. K. & Backman, V., May 2018, In : Cancer medicine. 7, 5, p. 2109-2120 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

Early increase in blood supply (EIBS) is associated with tumor risk in the Azoxymethane model of colon cancer

Ruderman, S., Eshein, A., Valuckaite, V., Dougherty, U., Almoghrabi, A., Gomes, A., Singh, A., Pabla, B., Roy, H. K., Hart, J., Bissonnette, M., Konda, V. & Backman, V., Aug 13 2018, In : BMC cancer. 18, 1, 814.

Research output: Contribution to journalArticle

2 Scopus citations

Fully automated fiber-based optical spectroscopy system for use in a clinical setting

Eshein, A., Radosevich, A. J., Gould, B., Wu, W., Konda, V., Yang, L. W., Koons, A., Feder, S., Valuckaite, V., Roy, H. K., Backman, V. & Nguyen, T. Q., Jul 1 2018, In : Journal of Biomedical Optics. 23, 7, 075003.

Research output: Contribution to journalArticle

1 Scopus citations

In vivo broadband visible light optical coherence tomography probe enables inverse spectroscopic analysis

Winkelmann, J. A., Eid, A., Nguyen, T. Q., Thang, B. U. I., Ji, Y. I. & Backman, V., Feb 1 2018, In : Optics Letters. 43, 3, p. 619-622 4 p.

Research output: Contribution to journalArticle

2 Scopus citations

Label free localization of nanoparticles in live cancer cells using spectroscopic microscopy

Spicer, G. L. C., Almassalha, L., Martinez, I. A., Ellis, R., Chandler, J. E., Gladstein, S., Zhang, D., Nguyen, T. Q., Feder, S., Subramanian, H., De La Rica, R., Thompson, S. A. & Backman, V., Oct 28 2018, In : Nanoscale. 10, 40, p. 19125-19130 6 p.

Research output: Contribution to journalArticle

1 Scopus citations

Measuring nanoscale chromatin heterogeneity with partial wave spectroscopic microscopy

Gladstein, S., Stawarz, A., Almassalha, L. M., Cherkezyan, L., Chandler, J. E., Zhou, X., Subramanian, H. & Backman, V., 2018, Methods in Molecular Biology. Humana Press Inc., p. 337-360 24 p. (Methods in Molecular Biology; vol. 1745).

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations

Nanoscale imaging of chromatin with Labeled and Label- Free super-resolution microscopy and partial-wave spectroscopy

Eshein, A., Li, Y., Zhou, X., Spicer, G., Nguyen, T. Q., Almassalha, L. M., Chandler, J. E., Gladstein, S., Dong, B., Sun, C., Zhang, H. F. & Backman, V., Jan 1 2018, Microscopy Histopathology and Analytics, MICROSCOPY 2018. OSA - The Optical Society, (Optics InfoBase Conference Papers; vol. Part F89-MICROSCOPY 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Physiological integration of coral colonies is correlated with bleaching resistance

Swain, T. D., Bold, E. C., Osborn, P. C., Baird, A. H., Westneat, M. W., Backman, V. & Marcelino, L. A., Jan 11 2018, In : Marine Ecology Progress Series. 586, p. 1-10 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

Relating coral skeletal structures at different length scales to growth, light availability to symbiodinium, and thermal bleaching

Swain, T. D., Lax, S., Lake, N., Grooms, H., Backman, V. & Marcelino, L. A., Nov 27 2018, In : Frontiers in Marine Science. 5, NOV, 450.

Research output: Contribution to journalArticle

6 Scopus citations

Single capillary oximetry and tissue ultrastructural sensing by dual-band dual-scan inverse spectroscopic optical coherence tomography

Liu, R., Winkelmann, J. A., Spicer, G., Zhu, Y., Eid, A., Ameer, G. A., Backman, V. & Yi, J., Dec 1 2018, In : Light: Science and Applications. 7, 1, 57.

Research output: Contribution to journalArticle

11 Scopus citations

Single Nucleotide Polymorphism Facilitated Down-Regulation of the Cohesin Stromal Antigen-1: Implications for Colorectal Cancer Racial Disparities

Datta, S., Sherva, R. M., De La Cruz, M., Long, M. T., Roy, P., Backman, V., Chowdhury, S. & Roy, H. K., Mar 2018, In : Neoplasia (United States). 20, 3, p. 289-294 6 p.

Research output: Contribution to journalArticle

1 Scopus citations

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

Eshein, A., Li, Y., Dong, B., Almassalha, L. M., Chandler, J. E., Nguyen, T. Q., Hujsak, K. A., Dravid, V. P., Sun, C., Zhang, H. F. & Backman, V., Dec 1 2018, In : Optics Letters. 43, 23, p. 5817-5820 4 p.

Research output: Contribution to journalArticle

2017

A Laboratory Manual in Biophotonics

Backman, V., Wax, A. & Zhang, H., 2017, CRC Press. 344 p.

Research output: Book/ReportBook

ASPirin Intervention for the REDuction of colorectal cancer risk (ASPIRED): A study protocol for a randomized controlled trial

Drew, D. A., Chin, S. M., Gilpin, K. K., Parziale, M., Pond, E., Schuck, M. M., Stewart, K., Flagg, M., Rawlings, C. A., Backman, V., Carolan, P. J., Chung, D. C., Colizzo, F. P., Freedman, M., Gala, M., Garber, J. J., Huttenhower, C., Kedrin, D., Khalili, H., Kwon, D. S. & 8 others, Markowitz, S. D., Milne, G. L., Nishioka, N. S., Richter, J. M., Roy, H. K., Staller, K., Wang, M. & Chan, A. T., Feb 1 2017, In : Trials. 18, 1, 50.

Research output: Contribution to journalArticle

20 Scopus citations

Bleaching response of coral species in the context of assemblage response

Swain, T. D., DuBois, E., Goldberg, S. J., Backman, V. & Marcelino, L. A., Jun 1 2017, In : Coral Reefs. 36, 2, p. 395-400 6 p.

Research output: Contribution to journalArticle

4 Scopus citations

Colocalization of cellular nanostructure using confocal fluorescence and partial wave spectroscopy

Chandler, J. E., Stypula-Cyrus, Y., Almassalha, L., Bauer, G., Bowen, L., Subramanian, H., Szleifer, I. & Backman, V., Mar 1 2017, In : Journal of Biophotonics. 10, 3, p. 377-384 8 p.

Research output: Contribution to journalArticle

9 Scopus citations
28 Scopus citations

Convergence of nanoimaging, physics and biology: Can engineering lead to a cancer cure?

Backman, V., Jan 1 2017, CLEO: Applications and Technology, CLEO_AT 2017. OSA - The Optical Society, Vol. Part F43-CLEO_AT 2017.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Macrogenomic engineering via modulation of the scaling of chromatin packing density

Almassalha, L. M., Bauer, G. M., Wu, W., Cherkezyan, L., Zhang, D., Kendra, A., Gladstein, S., Chandler, J. E., Vanderway, D., Seagle, B. L. L., Ugolkov, A., Billadeau, D. D., O'Halloran, T. V., Mazar, A. P., Roy, H. K., Szleifer, I., Shahabi, S. & Backman, V., Nov 1 2017, In : Nature Biomedical Engineering. 1, 11, p. 902-913 12 p.

Research output: Contribution to journalArticle

16 Scopus citations

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

Li, Y., Zhang, D., Capoglu, I., Hujsak, K. A., Damania, D., Cherkezyan, L., Roth, E., Bleher, R., Wu, J. S., Subramanian, H., Dravid, V. P. & Backman, V., Jun 1 2017, In : Microscopy and Microanalysis. 23, 3, p. 661-667 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Metabolic reprogramming of the premalignant colonic mucosa is an early event in carcinogenesis

Dela Cruz, M., Ledbetter, S., Chowdhury, S., Tiwari, A. K., Momi, N., Wali, R. K., Bliss, C., Huang, C., Lichtenstein, D., Bhattacharya, S., Varma-Wilson, A., Backman, V. & Roy, H. K., 2017, In : Oncotarget. 8, 13, p. 20543-20557 15 p.

Research output: Contribution to journalArticle

17 Scopus citations

Nanoscale chromatin structure characterization for optical applications: a transmission electron microscopy study

Li, Y., Cherkezyan, L., Zhang, D., Almassalha, L., Roth, E., Chandler, J., Bleher, R., Subramanian, H., Dravid, V. P. & Backman, V., May 1 2017, Proc. SPIE - Biophysics, Biology and Biophotonics II: the Crossroads. Wax, A. & Backman, V. (eds.). Vol. 10075.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Parallel Three-Dimensional Tracking of Quantum Rods Using Polarization-Sensitive Spectroscopic Photon Localization Microscopy

Dong, B., Soetikno, B. T., Chen, X., Backman, V., Sun, C. & Zhang, H. F., Jul 19 2017, In : ACS Photonics. 4, 7, p. 1747-1752 6 p.

Research output: Contribution to journalArticle

10 Scopus citations

Reflection statistics of weakly disordered optical medium when its mean refractive index is different from an outside medium

Pradhan, P., John Park, D., Capoglu, I., Subramanian, H., Damania, D., Cherkezyan, L., Taflove, A. & Backman, V., Jun 15 2017, In : Optics Communications. 393, p. 185-190 6 p.

Research output: Contribution to journalArticle

Review of interferometric spectroscopy of scattered light for the quantification of subdiffractional structure of biomaterials

Cherkezyan, L., Zhang, D., Subramanian, H., Capoglu, I., Taflove, A. & Backman, V., Mar 1 2017, In : Journal of Biomedical Optics. 22, 3, 030901.

Research output: Contribution to journalReview article

9 Scopus citations

Spectral biomarkers for chemoprevention of colonic neoplasia: A placebo-controlled double-blinded trial with aspirin

Roy, H. K., Turzhitsky, V., Wali, R., Radosevich, A. J., Jovanovic, B., Della'Zanna, G., Umar, A., Rubin, D. T., Goldberg, M. J., Bianchi, L., De La Cruz, M., Bogojevic, A., Helenowski, I. B., Rodriguez, L., Chatterton, R., Skripkauskas, S., Page, K., Weber, C. R., Huang, X., Richmond, E. & 2 others, Bergan, R. C. & Backman, V., Feb 1 2017, In : Gut. 66, 2, p. 285-292 8 p.

Research output: Contribution to journalArticle

15 Scopus citations

Stochastic fluorescence switching of nucleic acids under visible light illumination

Dong, B., Almassalha, L. M., Soetikno, B. T., Chandler, J. E., Nguyen, T. Q., Urban, B. E., Sun, C., Zhang, H. F. & Backman, V., Apr 3 2017, In : Optics Express. 25, 7, p. 7929-7944 16 p.

Research output: Contribution to journalArticle

4 Scopus citations

The effects of chemical fixation on the cellular nanostructure

Li, Y., Almassalha, L. M., Chandler, J. E., Zhou, X., Stypula-Cyrus, Y. E., Hujsak, K. A., Roth, E. W., Bleher, R., Subramanian, H., Szleifer, I., Dravid, V. P. & Backman, V., Sep 15 2017, In : Experimental Cell Research. 358, 2, p. 253-259 7 p.

Research output: Contribution to journalArticle

17 Scopus citations

The global relationship between chromatin physical topology, fractal structure, and gene expression

Almassalha, L. M., Tiwari, A., Ruhoff, P. T., Stypula-Cyrus, Y., Cherkezyan, L., Matsuda, H., Dela Cruz, M. A., Chandler, J. E., White, C., Maneval, C., Subramanian, H., Szleifer, I., Roy, H. K. & Backman, V., Jan 24 2017, In : Scientific reports. 7, 41061.

Research output: Contribution to journalArticle

32 Scopus citations
12 Scopus citations

The transformation of the nuclear nanoarchitecture in human field carcinogenesis

Bauer, G. M., Stypula-Cyrus, Y., Subramanian, H., Cherkezyan, L., Viswanathan, P., Zhang, D., Iyengar, R., Bagalkar, S., Derbas, J., Graff, T., Gladstein, S., Almassalha, L. M., Chandler, J. E., Roy, H. K. & Backman, V., Jan 1 2017, In : Future Science OA. 3, 3, FSO206.

Research output: Contribution to journalReview article

Open Access
4 Scopus citations
2016

Automated Cell Selection Using Support Vector Machine for Application to Spectral Nanocytology

Miao, Q., Derbas, J., Eid, A., Subramanian, H. & Backman, V., 2016, In : BioMed Research International. 2016, 6090912.

Research output: Contribution to journalArticle

3 Scopus citations

Coral bleaching response index: a new tool to standardize and compare susceptibility to thermal bleaching

Swain, T. D., Vega-Perkins, J. B., Oestreich, W. K., Triebold, C., DuBois, E., Henss, J., Baird, A., Siple, M., Backman, V. & Marcelino, L., Jul 1 2016, In : Global change biology. 22, 7, p. 2475-2488 14 p.

Research output: Contribution to journalArticle

27 Scopus citations