headshot

Yang Liu

Associate Professor
Biomedical Optical Imaging Laboratory Lab Twitter Bioengineering Department

overview

The laboratory of Dr. Yang Liu integrates multidisciplinary approaches of engineering, chemistry, physics and biology for precision medicine. We exploit the power of light and develops a suite of imaging technologies and quantitative analysis tools including super-resolution fluorescence microscopy, single-molecule detection, quantitative phase microscopy, optical coherence microscopy, light-sheet microscopy and machine learning methods. We improve the imaging throughput and robustness, while making it simpler, cheaper and easier to use. We apply these state-of-the-art imaging tools to map molecular-scale chromatin organization and epigenomic signatures in their original spatial context on patient-derived samples such as tissue, blood, sputum and organoid. We apply them to improve personalized medicine, such as cancer detection and prevention in colon, lung, pancreas and prostate, understanding tissue microenvironment in inflammatory bowel diseases.

about

BS, Chemistry, Nankai University, 1995 - 1999

MS, Chemistry, University of Chicago, 2000 - 2001

PhD, Biomedical Engineering (biomedical optics), Northwestern University, 2002 - 2006

Ma, H., & Liu, Y. (2021). Embedded nanometer position tracking based on enhanced phasor analysis. Opt Lett, 46(16), 3825-3828.The Optical Society. doi: 10.1364/OL.433740.

Ma, H., & Liu, Y. (2021). Embedded nanometer position tracking based on enhanced phasor analysis: erratum. Optics Letters, 46(18), 4639.The Optical Society. doi: 10.1364/ol.440217.

Mela, C.A., & Liu, Y. (2021). Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images. BMC BIOINFORMATICS, 22(1), 325.Springer Science and Business Media LLC. doi: 10.1186/s12859-021-04245-x.

Xiang, Y., Sang, Z., Bitton, L., Xu, J., Liu, Y., Schneidman-Duhovny, D., & Shi, Y. (2021). Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. CELL SYSTEMS, 12(3), 220-+.Elsevier BV. doi: 10.1016/j.cels.2021.01.003.

Xu, J., & Liu, Y. (2021). Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy. Front Cell Dev Biol, 9, 653077.Frontiers Media SA. doi: 10.3389/fcell.2021.653077.

Ma, H., & Liu, Y. (2020). Super-resolution localization microscopy: Toward high throughput, high quality, and low cost. APL PHOTONICS, 5(6), 060902.AIP Publishing. doi: 10.1063/5.0011731.

Ma, H., Wang, P., Shang, D., & Liu, Y. (2020). Spatial-domain low-coherence quantitative phase microscopy to improve the cytological diagnosis of pancreatic cancer. JOURNAL OF INVESTIGATIVE MEDICINE, 68(1), 60-67.BMJ. doi: 10.1136/jim-2019-000997.

Troy, K., Liu, Y., & Hainer, S.J. (2020). PathSTORM: a road to early cancer detection. Mol Cell Oncol, 7(5), 1776086.Informa UK Limited. doi: 10.1080/23723556.2020.1776086.

Xu, J., Ma, H., & Liu, Y. (2020). Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue. Curr Protoc Cytom, 94(1), e78.Wiley. doi: 10.1002/cpcy.78.

Xu, J., Ma, H., Ma, H., Jiang, W., Mela, C.A., Duan, M., Zhao, S., Gao, C., Hahm, E.R., Lardo, S.M., Troy, K., Sun, M., Pai, R., Stolz, D.B., Zhang, L., Singh, S., Brand, R.E., Hartman, D.J., Hu, J., Hainer, S.J., & Liu, Y. (2020). Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis. NATURE COMMUNICATIONS, 11(1), 1899.Springer Science and Business Media LLC. doi: 10.1038/s41467-020-15718-7.

Liu, Y., & Xu, J. (2019). High-resolution microscopy for imaging cancer pathobiology. Curr Pathobiol Rep, 7(3), 85-96.Springer Science and Business Media LLC. doi: 10.1007/s40139-019-00201-w.

Ma, H., Xu, J., & Liu, Y. (2019). WindSTORM: Robust online image processing for high-throughput nanoscopy. SCIENCE ADVANCES, 5(4), eaaw0683.American Association for the Advancement of Science (AAAS). doi: 10.1126/sciadv.aaw0683.

Nmezi, B., Xu, J., Fu, R., Armiger, T.J., Rodriguez-Bey, G., Powell, J.S., Ma, H., Sullivan, M., Tu, Y., Chen, N.Y., Young, S.G., Stolz, D.B., Dahl, K.N., Liu, Y., & Padiath, Q.S. (2019). Concentric organization of A- and B-type lamins predicts their distinct roles in the spatial organization and stability of the nuclear lamina. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(10), 4307-4315.Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1810070116.

Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartmann, D.J., Brand, R.E., & Li, Y. (2019). Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. CANCER PREVENTION RESEARCH, 12(8), 527-538.American Association for Cancer Research (AACR). doi: 10.1158/1940-6207.CAPR-19-0024.

Xu, J., & Liu, Y. (2019). A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS JOURNAL, 286(16), 3095-3109.Wiley. doi: 10.1111/febs.14938.

Xu, J., & Liu, Y. (2019). Imaging Higher-order Chromatin Structures in Single Cells Using Stochastic Optical Reconstruction Microscopy. Bio Protoc, 9(3).Bio-Protocol, LLC. doi: 10.21769/BioProtoc.3160.

Gao, Y., Tan, J., Jin, J., Ma, H., Chen, X., Leger, B., Xu, J., Spagnol, S.T., Dahl, K.N., Levine, A.S., Liu, Y., & Lan, L. (2018). SIRT6 facilitates directional telomere movement upon oxidative damage. SCIENTIFIC REPORTS, 8(1), 5407.Springer Science and Business Media LLC. doi: 10.1038/s41598-018-23602-0.

Teng, Y., Yadav, T., Duan, M., Tan, J., Xiang, Y., Gao, B., Xu, J., Liang, Z., Liu, Y., Nakajima, S., Shi, Y., Levine, A.S., Zou, L., & Lan, L. (2018). ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB. NATURE COMMUNICATIONS, 9(1), 4115.Springer Science and Business Media LLC. doi: 10.1038/s41467-018-06586-3.

Uttam, S., & Liu, Y. (2018). Fourier phase based depth-resolved nanoscale nuclear architecture mapping for cancer detection. METHODS, 136, 134-151.Elsevier BV. doi: 10.1016/j.ymeth.2017.10.011.

Xu, J., Ma, H., Jin, J., Uttam, S., Fu, R., Huang, Y., & Liu, Y. (2018). Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells. CELL REPORTS, 24(4), 873-882.Elsevier BV. doi: 10.1016/j.celrep.2018.06.085.

Gao, Y., Li, C., Wei, L., Teng, Y., Nakajima, S., Chen, X., Xu, J., Legar, B., Ma, H., Spagnol, S.T., Wan, Y., Dahl, K.N., Liu, Y., Levine, A.S., & Lan, L. (2017). SSRP1 Cooperates with PARP and XRCC1 to Facilitate Single-Strand DNA Break Repair by Chromatin Priming. CANCER RESEARCH, 77(10), 2674-2685.American Association for Cancer Research (AACR). doi: 10.1158/0008-5472.CAN-16-3128.

Ma, H., Fu, R., Xu, J., & Liu, Y. (2017). A simple and cost-effective setup for super-resolution localization microscopy. SCIENTIFIC REPORTS, 7(1), 1542.Springer Science and Business Media LLC. doi: 10.1038/s41598-017-01606-6.

Ma, H., Xu, J., Jin, J., Huang, Y., & Liu, Y. (2017). A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy. BIOPHYSICAL JOURNAL, 112(10), 2196-2208.Elsevier BV. doi: 10.1016/j.bpj.2017.04.025.

Xu, J., Ma, H., & Liu, Y. (2017). Stochastic Optical Reconstruction Microscopy (STORM). Curr Protoc Cytom, 81(1), 12.46.1-12.46.27.Wiley. doi: 10.1002/cpcy.23.

Pham, H.V., Pantanowitz, L., & Liu, Y. (2016). Quantitative phase imaging to improve the diagnostic accuracy of urine cytology. CANCER CYTOPATHOLOGY, 124(9), 641-650.Wiley. doi: 10.1002/cncy.21734.

Del Portillo, A., Lagana, S.M., Yao, Y., Uehara, T., Jhala, N., Ganguly, T., Nagy, P., Gutierrez, J., Luna, A., Abrams, J., Liu, Y., Brand, R., Sepulveda, J.L., Falk, G.W., & Sepulveda, A.R. (2015). Evaluation of Mutational Testing of Preneoplastic Barrett's Mucosa by Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Endoscopic Samples for Detection of Concurrent Dysplasia and Adenocarcinoma in Barrett's Esophagus. JOURNAL OF MOLECULAR DIAGNOSTICS, 17(4), 412-419.Elsevier BV. doi: 10.1016/j.jmoldx.2015.02.006.

Glassford, W.J., Johnson, W.C., Dall, N.R., Smith, S.J., Liu, Y., Boll, W., Noll, M., & Rebeiz, M. (2015). Co-option of an Ancestral Hox-Regulated Network Underlies a Recently Evolved Morphological Novelty. DEVELOPMENTAL CELL, 34(5), 520-531.Elsevier BV. doi: 10.1016/j.devcel.2015.08.005.

Ma, H., Xu, J., Jin, J., Gao, Y., Lan, L., & Liu, Y. (2015). Fast and Precise 3D Fluorophore Localization based on Gradient Fitting. SCIENTIFIC REPORTS, 5(1), 14335.Springer Science and Business Media LLC. doi: 10.1038/srep14335.

Sun, L., Tan, R., Xu, J., LaFace, J., Gao, Y., Xiao, Y., Attar, M., Neumann, C., Li, G.M., Su, B., Liu, Y., Nakajima, S., Levine, A.S., & Lan, L. (2015). Targeted DNA damage at individual telomeres disrupts their integrity and triggers cell death. NUCLEIC ACIDS RESEARCH, 43(13), 6334-6347.Oxford University Press (OUP). doi: 10.1093/nar/gkv598.

Uttam, S., & Liu, Y. (2015). Fourier phase in Fourier-domain optical coherence tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, 32(12), 2286-2306.The Optical Society. doi: 10.1364/JOSAA.32.002286.

Uttam, S., Pham, H.V., LaFace, J., Leibowitz, B., Yu, J., Brand, R.E., Hartman, D.J., & Liu, Y. (2015). Early Prediction of Cancer Progression by Depth-Resolved Nanoscale Mapping of Nuclear Architecture from Unstained Tissue Specimens. CANCER RESEARCH, 75(22), 4718-4727.American Association for Cancer Research (AACR). doi: 10.1158/0008-5472.CAN-15-1274.

Hartman, D.J., Krasinskas, A.M., Uttam, S., Staton, K., Bista, R., Rizvi, S., Slivka, A., Brand, R., & Liu, Y. (2014). Assessment of Nuclear Nanomorphology Marker to Improve the Detection of Malignancy From Bile Duct Biopsy Specimens. AMERICAN JOURNAL OF CLINICAL PATHOLOGY, 141(6), 884-891.Oxford University Press (OUP). doi: 10.1309/AJCPXQD0NSJNK0CX.

Liu, Y., Uttam, S., Alexandrov, S., & Bista, R.K. (2014). Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer. BMC BIOPHYSICS, 7(1), 1.Springer Science and Business Media LLC. doi: 10.1186/2046-1682-7-1.

Fasanella, K.E., Bista, R.K., Staton, K., Rizvi, S., Uttam, S., Zhao, C., Sepulveda, A., Brand, R.E., McGrath, K., & Liu, Y. (2013). Nuclear Nano-architecture Markers of Gastric Cardia and Upper Squamous Esophagus Detect Esophageal Cancer "Field Effect". JOURNAL OF CANCER, 4(8), 626-634.Ivyspring International Publisher. doi: 10.7150/jca.6990.

Uttam, S., Alexandrov, S.A., Bista, R.K., & Liu, Y. (2013). Tomographic imaging via spectral encoding of spatial frequency. OPTICS EXPRESS, 21(6), 7488-7504.The Optical Society. doi: 10.1364/OE.21.007488.

Uttam, S., Bista, R.K., Staton, K., Alexandrov, S., Choi, S., Bakkenist, C.J., Hartman, D.J., Brand, R.E., & Liu, Y. (2013). Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation: erratum (vol 4, pg 596, 2013). BIOMEDICAL OPTICS EXPRESS, 4(11), 2491.The Optical Society. doi: 10.1364/BOE.4.002491.

Uttam, S., Bista, R.K., Staton, K., Alexandrov, S., Choi, S., Bakkenist, C.J., Hartman, D.J., Brand, R.E., & Liu, Y. (2013). Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation. BIOMEDICAL OPTICS EXPRESS, 4(4), 596-613.The Optical Society. doi: 10.1364/BOE.4.000596.

Wu, D., He, D., Qiu, J., Lin, R., & Liu, Y. (2013). Comparing social tags with subject headings on annotating books: A study comparing the information science domain in English and Chinese. JOURNAL OF INFORMATION SCIENCE, 39(2), 169-187.SAGE Publications. doi: 10.1177/0165551512451808.

Alexandrov, S.A., Uttam, S., Bista, R.K., Staton, K., & Liu, Y. (2012). Spectral encoding of spatial frequency approach for characterization of nanoscale structures. APPLIED PHYSICS LETTERS, 101(3), 33702.AIP Publishing. doi: 10.1063/1.4737209.

Alexandrov, S.A., Uttam, S., Bista, R.K., Zhao, C., & Liu, Y. (2012). Real-time quantitative visualization of 3D structural information. OPTICS EXPRESS, 20(8), 9203-9214.The Optical Society. doi: 10.1364/OE.20.009203.

Bista, R.K., Uttam, S., Hartman, D.J., Qiu, W., Yu, J., Zhang, L., Brand, R.E., & Liu, Y. (2012). Investigation of nuclear nano-morphology marker as a biomarker for cancer risk assessment using a mouse model. JOURNAL OF BIOMEDICAL OPTICS, 17(6), 066014.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.JBO.17.6.066014.

Bista, R.K., Wang, P., Bhargava, R., Uttam, S., Hartman, D.J., Brand, R.E., & Liu, Y. (2012). Nuclear nano-morphology markers of histologically normal cells detect the "field effect" of breast cancer. BREAST CANCER RESEARCH AND TREATMENT, 135(1), 115-124.Springer Science and Business Media LLC. doi: 10.1007/s10549-012-2125-2.

Chen, Y., Liang, C.P., Liu, Y., Fischer, A.H., Parwani, A.V., & Pantanowitz, L. (2012). Review of advanced imaging techniques. J Pathol Inform, 3(1), 22.Medknow. doi: 10.4103/2153-3539.96751.

Alexandrov, S.A., Uttam, S., Bista, R.K., & Liu, Y. (2011). Spectral contrast imaging microscopy. OPTICS LETTERS, 36(17), 3323-3325.The Optical Society. doi: 10.1364/OL.36.003323.

Bista, R.K., Brentnall, T.A., Bronner, M.P., Langmead, C.J., Brand, R.E., & Liu, Y. (2011). Using Optical Markers of Nondysplastic Rectal Epithelial Cells to Identify Patients with Ulcerative Colitis-associated Neoplasia. INFLAMMATORY BOWEL DISEASES, 17(12), 2427-2435.Oxford University Press (OUP). doi: 10.1002/ibd.21639.

Bista, R.K., Uttam, S., Wang, P., Staton, K., Choi, S., Bakkenist, C.J., Hartman, D.J., Brand, R.E., & Liu, Y. (2011). Quantification of nanoscale nuclear refractive index changes during the cell cycle. JOURNAL OF BIOMEDICAL OPTICS, 16(7), 070503.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.3597723.

Fang, C., Brokl, D., Brand, R.E., & Liu, Y. (2011). Depth-selective fiber-optic probe for characterization of superficial tissue at a constant physical depth. BIOMEDICAL OPTICS EXPRESS, 2(4), 838-849.The Optical Society. doi: 10.1364/BOE.2.000838.

Rizvi, S., Davison, J.M., Bista, R.K., Wang, P., Holinga, J., Staton, K.D., Hartman, D.I., Brand, R., Fasanella, K.E., Liu, Y., & McGrath, K. (2011). Nuclear Refractive Index Properties of Non-Dysplastic Metaplastic Cells to Detect the Presence of Esophageal High-Grade Dysplasia and Adenocarcinoma From Barrett's Esophagus. GASTROENTEROLOGY, 140, (p. S217).

Uttam, S., Bista, R.K., Hartman, D.J., Brand, R.E., & Liu, Y. (2011). Correction of stain variations in nuclear refractive index of clinical histology specimens. JOURNAL OF BIOMEDICAL OPTICS, 16(11), 116013.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.3650306.

Mahmoud, B.H., Ruvolo, E., Hexsel, C.L., Liu, Y., Owen, M.R., Kollias, N., Lim, H.W., & Hamzavi, I.H. (2010). Impact of Long-Wavelength UVA and Visible Light on Melanocompetent Skin. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 130(8), 2092-2097.Elsevier BV. doi: 10.1038/jid.2010.95.

Wang, P., Bista, R., Bhargava, R., Brand, R.E., & Liu, Y. (2010). Spatial-domain low-coherence quantitative phase microscopy for cancer diagnosis. OPTICS LETTERS, 35(17), 2840-2842.The Optical Society. doi: 10.1364/ol.35.002840.

Wang, P., Bista, R.K., Khalbuss, W.E., Qiu, W., Uttam, S., Staton, K., Zhang, L., Brentnall, T.A., Brand, R.E., & Liu, Y. (2010). Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy. JOURNAL OF BIOMEDICAL OPTICS, 15(6), 066028.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.3523618.

Wang, P., Bista, R.K., Qiu, W., Khalbuss, W.E., Zhang, L., Brand, R.E., & Liu, Y. (2010). An insight into statistical refractive index properties of cell internal structure via low-coherence statistical amplitude microscopy. OPTICS EXPRESS, 18(21), 21950-21958.The Optical Society. doi: 10.1364/OE.18.021950.

Backman, V., Subramanian, H., Pradhan, P., Liu, Y., Capoglu, I., Rogers, J.D., Roy, H.K., & Taflove, A. (2009). Detecting alterations in cell ultrastructure with optical imaging. Annu Int Conf IEEE Eng Med Biol Soc, 2009, 6325-6326.IEEE. doi: 10.1109/IEMBS.2009.5333173.

Subramanian, H., Pradhan, P., Liu, Y., Capoglu, I.R., Rogers, J.D., Roy, H.K., Brand, R.E., & Backman, V. (2009). Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis. OPTICS LETTERS, 34(4), 518-520.The Optical Society. doi: 10.1364/OL.34.000518.

Roy, H.K., Turzhitsky, V., Kim, Y.L., Goldberg, M.J., Muldoon, J.P., Liu, Y., Brand, R.E., Hall, C., Hasabou, N., Jameel, M., & Backman, V. (2008). Spectral slope from the endoscopically-normal mucosa predicts concurrent colonic neoplasia: A pilot Ex-Vivo clinical study. DISEASES OF THE COLON & RECTUM, 51(9), 1381-1386.Ovid Technologies (Wolters Kluwer Health). doi: 10.1007/s10350-008-9384-3.

Subramanian, H., Pradhan, P., Liu, Y., Capoglu, I.R., Li, X., Rogers, J.D., Heifetz, A., Kunte, D., Roy, H.K., Taflove, A., & Backman, V. (2008). Optical methodology for detecting histologically unapparent nanoscale consequences of genetic alterations in biological cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(51), 20118-20123.Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.0804723105.

Turzhitsky, V., Liu, Y., Hasabou, N., Goldberg, M., Roy, H.K., Backman, V., & Brand, R. (2008). Investigating population risk factors of pancreatic cancer by evaluation of optical markers in the duodenal mucosa. DISEASE MARKERS, 25(6), 313-321.Hindawi Limited. doi: 10.1155/2008/958214.

Turzhitsky, V.M., Gomes, A.J., Kim, Y.L., Liu, Y., Kromine, A., Rogers, J.D., Jameel, M., Roy, H.K., & Backman, V. (2008). Measuring mucosal blood supply in vivo with a polarization-gating probe. APPLIED OPTICS, 47(32), 6046-6057.The Optical Society. doi: 10.1364/AO.47.006046.

Allen, J., Liu, Y., Kim, Y.L., Turzhitsky, V.M., Backman, V., & Ameer, G.A. (2007). Spectroscopic translation of cell-material interactions. BIOMATERIALS, 28(2), 162-174.Elsevier BV. doi: 10.1016/j.biomaterials.2006.07.002.

Figueiredo, R.J., Backman, V., Liu, Y., & Paladugula, J. (2007). Architecture and performance of a grid-enabled lookup-based biomedical optimization application: Light scattering spectroscopy. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 11(2), 170-178.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/TITB.2006.876032.

Liu, Y., Brand, R.E., Turzhitsky, V., Kim, Y.L., Roy, H.K., Hasabou, N., Sturgis, C., Shah, D., Hall, C., & Backman, V. (2007). Optical markers in duodenal mucosa predict the presence of pancreatic cancer. CLINICAL CANCER RESEARCH, 13(15), 4392-4399.American Association for Cancer Research (AACR). doi: 10.1158/1078-0432.CCR-06-1648.

Roy, H.K., Wali, R.K., Kim, Y., Liu, Y., Hart, J., Kunte, D.P., Koetsier, J.L., Goldberg, M.J., & Backman, V. (2007). Inducible nitric oxide synthase (iNOS) mediates the early increase of blood supply (EIBS) in colon carcinogenesis. FEBS LETTERS, 581(20), 3857-3862.Wiley. doi: 10.1016/j.febslet.2007.07.012.

Subramanian, H., Pradhan, P., Kim, Y.L., & Backman, V. (2007). Penetration depth of low-coherence enhanced backscattered light in subdiffusion regime. PHYSICAL REVIEW E, 75(4), 041914.American Physical Society (APS). doi: 10.1103/PhysRevE.75.041914.

Gong, J.M., Liu, B., Kim, Y.L., Liu, Y., Li, X., & Backman, V. (2006). Optimal spectral reshaping for resolution improvement in optical coherence tomography. OPTICS EXPRESS, 14(13), 5909-5915.The Optical Society. doi: 10.1364/OE.14.005909.

Kim, Y.L., Pradhan, P., Kim, M.H., & Backman, V. (2006). Circular polarization memory effect in low-coherence enhanced backscattering of light. OPTICS LETTERS, 31(18), 2744-2746.The Optical Society. doi: 10.1364/OL.31.002744.

Kim, Y.L., Pradhan, P., Subramanian, H., Liu, Y., Kim, M.H., & Backman, V. (2006). Origin of low-coherence enhanced backscattering. OPTICS LETTERS, 31(10), 1459-1461.The Optical Society. doi: 10.1364/OL.31.001459.

Kim, Y.L., Turzhitsky, V.M., Liu, Y., Roy, H.K., Wali, R.K., Subramanian, H., Pradhan, P., & Backman, V. (2006). Low-coherence enhanced backscattering: review of principles and applications for colon cancer screening. JOURNAL OF BIOMEDICAL OPTICS, 11(4), 041125.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.2236292.

Roy, H.K., Kim, Y.L., Liu, Y., Wali, R.K., Goldberg, M.J., Turzhitsky, V., Horwitz, J., & Backman, V. (2006). Risk stratification of colon carcinogenesis through enhanced backscattering spectroscopy analysis of the uninvolved colonic mucosa. CLINICAL CANCER RESEARCH, 12(3), 961-968.American Association for Cancer Research (AACR). doi: 10.1158/1078-0432.CCR-05-1605.

Roy, H.K., Kunte, D.P., Koetsier, J.L., Hart, J., Kim, Y.L., Liu, Y., Bissonnette, M., Goldberg, M., Backman, V., & Wali, R.K. (2006). Chemoprevention of colon carcinogenesis by polyethylene glycol: suppression of epithelial proliferation via modulation of SNAIL/beta-catenin signaling. MOLECULAR CANCER THERAPEUTICS, 5(8), 2060-2069.American Association for Cancer Research (AACR). doi: 10.1158/1535-7163.MCT-06-0054.

Subramanian, H., Pradhan, P., Kim, Y.L., Liu, Y., Li, X., & Backman, V. (2006). Modeling low-coherence enhanced backscattering using Monte Carlo simulation. APPLIED OPTICS, 45(24), 6292-6300.The Optical Society. doi: 10.1364/AO.45.006292.

Xia, X., Liu, Y., Backman, V., & Ameer, G.A. (2006). Engineering sub-100 nm multi-layer nanoshells. NANOTECHNOLOGY, 17(21), 5435-5440.IOP Publishing. doi: 10.1088/0957-4484/17/21/025.

Chen, K., Liu, Y., Ameer, G., & Backman, V. (2005). Optimal design of structured nanospheres for ultrasharp light-scattering resonances as molecular imaging multilabels. JOURNAL OF BIOMEDICAL OPTICS, 10(2), 024005.SPIE-Intl Soc Optical Eng. doi: 10.1117/1.1899684.

Kim, Y.L., Liu, Y., Turzhitsky, V.M., Wali, R.K., Roy, H.K., & Backman, V. (2005). Depth-resolved low-coherence enhanced backscattering. OPTICS LETTERS, 30(7), 741-743.The Optical Society. doi: 10.1364/OL.30.000741.

Kim, Y.L., Liu, Y., Wali, R.K., Roy, H.K., & Backman, V. (2005). Low-coherent backscattering spectroscopy for tissue characterization. APPLIED OPTICS, 44(3), 366-377.The Optical Society. doi: 10.1364/AO.44.000366.

Liu, Y., Kim, Y.L., & Backman, V. (2005). Development of a bioengineered tissue model and its application in the investigation of the depth selectivity of polarization gating. APPLIED OPTICS, 44(12), 2288-2299.The Optical Society. doi: 10.1364/AO.44.002288.

Liu, Y., Kim, Y.L., Li, X., & Backman, V. (2005). Investigation of depth selectivity of polarization gating for tissue characterization. OPTICS EXPRESS, 13(2), 601-611.The Optical Society. doi: 10.1364/OPEX.13.000601.

Liu, Y., Li, X., Kim, Y.L., & Backman, V. (2005). Elastic backscattering spectroscopic microscopy. OPTICS LETTERS, 30(18), 2445-2447.The Optical Society. doi: 10.1364/OL.30.002445.

Roy, H.K., Kim, Y.L., Wali, R.K., Liu, Y., Koetsier, J., Kunte, D.P., Goldberg, M.J., & Backman, V. (2005). Spectral markers in preneoplastic intestinal mucosa: An accurate predictor of tumor risk in the MIN mouse. CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION, 14(7), 1639-1645.American Association for Cancer Research (AACR). doi: 10.1158/1055-9965.EPI-04-0837.

Wali, R.K., Roy, H.K., Kim, Y.L., Liu, Y., Koetsier, J.L., Kunte, D.P., Goldberg, M.J., Turzhitsky, V., & Backman, V. (2005). Increased microvascular blood content is an early event in colon carcinogenesis. GUT, 54(5), 654-660.BMJ. doi: 10.1136/gut.2004.056010.

Kim, Y., Liu, Y., & Backman, V. (2004). Coherent backscattering spectroscopy: a new technique for tissue diagnosis. Conf Proc IEEE Eng Med Biol Soc, 2004, 5285-5288.IEEE. doi: 10.1109/IEMBS.2004.1404476.

Kim, Y.L., Liu, Y., Turzhitsky, V.M., Roy, H.K., Wali, R.K., & Backman, V. (2004). Coherent backscattering spectroscopy. OPTICS LETTERS, 29(16), 1906-1908.The Optical Society. doi: 10.1364/OL.29.001906.

Roy, H.K., Iversen, P., Hart, J., Liu, Y., Koetsier, J.L., Kim, Y., Kunte, D.P., Madugula, M., Backman, V., & Wali, R.K. (2004). Down-regulation of SNAIL suppresses MIN mouse tumorigenesis: Modulation of apoptosis proliferation, and fractal dimension. MOLECULAR CANCER THERAPEUTICS, 3(9), 1159-1165.

Roy, H.K., Liu, Y., Wali, R.K., Kim, Y.L., Kromine, A.K., Goldberg, M.J., & Backman, V. (2004). Four-dimensional elastic light-scattering fingerprints as preneoplastic markers in the rat model of colon carcinogenesis. GASTROENTEROLOGY, 126(4), 1071-1081.Elsevier BV. doi: 10.1053/j.gastro.2004.01.009.

Kim, Y.L., Liu, Y., Wali, R.K., Roy, H.K., Goldberg, M.J., Kromin, A.K., Chen, K., & Backman, V. (2003). Simultaneous measurement of angular and spectral properties of light scattering for characterization of tissue microarchitecture and its alteration in early precancer. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS, 9(2), 243-256.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/JSTQE.2003.814183.

Zhu, X.Q., Cao, L., Liu, Y., Yang, Y., Lu, J.Y., Wang, J.S., & Cheng, J.P. (2003). Thermodynamics and kinetics of the hydride-transfer cycles for 1-aryl-1,4-dihydronicotinamide and its 1,2-dihydroisomer. Chemistry, 9(16), 3937-3945.Wiley. doi: 10.1002/chem.200304714.

Zhu, X., Liu, Y., Zhao, B., & Cheng, J. (2001). An old but simple and efficient method to elucidate the oxidation mechanism of NAD(P)H model by cations 2-methyl-5-nitroisoquinolium, tropylium, and xanthylium in aqueous solution. Journal of Organic Chemistry, 66(2), 370-375.

Zhu, X., Zou, H., Yuan, P., Liu, Y., Cao, L., & Cheng, J. (2000). A detailed investigation into the oxidation mechanism of Hantzsch by ethyl a-cyanocinnamates and benzylidenemalononitriles. Journal of the Chemical Society, Perkin Transactions 2, 9, 1857-1861.

Zhu, X.Q., Zou, H.L., Yuan, P.W., Liu, Y., Cao, L., & Cheng, J.P. (2000). A detailed investigation into the oxidation mechanism of Hantzsch 1,4-dihydropyridines by ethyl alpha-cyanocinnamates and benzylidenemalononitriles. JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, (9), 1857-1861.Royal Society of Chemistry (RSC). doi: 10.1039/b003404p.

Liu, Y., Ma, H., & Xu, J. (2020). Visualizing cancer pathogenesis at the nanoscale. In Biophotonics Congress: Biomedical Optics 2020 (Translational, Microscopy, OCT, OTS, BRAIN), Part F177-Microscopy-2020.OSA. doi: 10.1364/microscopy.2020.mw1a.1.

Ma, H., Xu, J., & Liu, Y. (2019). Robust online image processing for high-throughput super-resolution localization microscopy. In Advances in Microscopic Imaging II, Part F142-ECBO 2019.SPIE. doi: 10.1117/12.2526541.

Uttam, S., & Liu, Y. (2019). Three-dimensional nanoscale nuclear architecture mapping for improved cancer risk stratification. In Advances in Microscopic Imaging II, 11076.SPIE. doi: 10.1117/12.2526469.

Skoko, J., Asan, A., Woodcock, C., Cao, J., Gaboriau, D., Paulsen, C., Attar, M., Wingert, B., Woodcock, S., Schulte, J., Ma, H., Camacho, C., Liu, Y., Morrison, C., Carroll, K., Freeman, B., & Neumann, C. (2018). Loss of PRDX1 increases RAD51 Cys319 oxidation and decreases homologous recombination. In FREE RADICAL BIOLOGY AND MEDICINE, 128, (pp. S73-S74).Elsevier BV. doi: 10.1016/j.freeradbiomed.2018.10.159.

Skoko, J.J., Asan, A., Woodcock, C.S.C., Cao, J., Gaboriau, D., Paulsen, C.E., Attar, M., Wingert, B.M., Woodcock, S.R., Schulte, J., Ma, H., Camacho, C.J., Liu, Y., Morrison, C.G., Carroll, K., Freeman, B.A., & Neumann, C.A. (2017). Redox Regulation of RAD51 and Homologous Recombination by Peroxiredoxin 1 and Electrophilic Nitrofatty Acids. In FREE RADICAL BIOLOGY AND MEDICINE, 112, (pp. 100-101).Elsevier BV. doi: 10.1016/j.freeradbiomed.2017.10.151.

Ma, H., Xu, J., Jin, J., Gao, Y., Lan, L., & Liu, Y. (2016). Fast and precise 3D fluorophore localization by gradient fitting. In Single Molecule Spectroscopy and Superresolution Imaging IX, 9714.SPIE. doi: 10.1117/12.2211731.

Uttam, S., & Liu, Y. (2016). Theory of Fourier phase within the framework of Fourier-domain optical coherence tomography. In Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XX, 9697.SPIE. doi: 10.1117/12.2214821.

Uttam, S., Pham, H.V., LaFace, J., Hartman, D.J., & Liu, Y. (2016). Depth-resolved nanoscale nuclear architecture mapping for early prediction of cancer progression. In Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XX, 9697.SPIE. doi: 10.1117/12.2214688.

Del Portillo, A., Yuan, Y., Uehara, T., Jhala, N., Ganguly, T., Lagana, S., Gutierrez-Pajares, J.L., Sepulveda, J.L., Liu, Y., Brand, R., Falk, G.W., & Sepulveda, A.R. (2014). Next-Generation Sequencing Mutational Analysis of Intestinal Metaplasia and Neoplastic Lesions in Barrett's Esophagus from Endoscopic Samples. In LABORATORY INVESTIGATION, 94, (p. 171A).

Del Portillo, A., Yuan, Y., Uehara, T., Jhala, N., Ganguly, T., Lagana, S., Quierrez-Pajares, J.L., Sepulveda, J.L., Liu, Y., Brand, R., Falk, G.W., & Sepulveda, A.R. (2014). Next-Generation Sequencing Mutational Analysis of Intestinal Metaplasia and Neoplastic Lesions in Barrett's Esophagus from Endoscopic Samples. In MODERN PATHOLOGY, 27, (p. 171A).

Li, Z., Bhargava, R., Staton, K., Wang, H., Uttam, S., Brand, R.E., Soran, A., Ahrendt, G.M., & Liu, Y. (2014). Nuclear Nano-Morphology Markers Predict Breast Cancer Risk in Patients with Atypical Breast Epithelial Hyperplasia. In MODERN PATHOLOGY, 27, (p. 64A).

Li, Z., Bhargava, R., Staton, K., Wang, H., Uttam, S., Brand, R.E., Soran, A., Ahrendt, G.M., & Liu, Y. (2014). Nuclear Nano-Morphology Markers Predict Breast Cancer Risk in Patients with Atypical Breast Epithelial Hyperplasia. In LABORATORY INVESTIGATION, 94, (p. 64A).

Hashash, J.G., Bista, R.K., Staton, K.D., Hartman, D.J., Alnabhan, S., Baidoo, L., Regueiro, M., Schwartz, M., Binion, D.G., Brand, R., & Liu, Y. (2013). Nuclear Nano-Morphology Markers From Rectal Tissue Predict Colonic Dysplasia/Neoplasia in Ulcerative Colitis Patients. In GASTROENTEROLOGY, 144(5), (pp. S175-S176).

Alexandrov, S.A., Uttam, S., Bista, R.K., & Liu, Y. (2012). Spectral encoding of spatial frequency approach for quantitative visualization and characterization of 3D structures. In Biomedical Optics and 3-D Imaging.OSA. doi: 10.1364/biomed.2012.btu3a.57.

Hashash, J.G., Bista, R.K., Hartman, D.J., Regueiro, M., Schwartz, M., Staton, K.D., Baidoo, L., Binion, D.G., Brand, R., & Liu, Y. (2012). Nuclear Nano-Morphology Markers From Rectal Tissue for the Surveillance of Colorectal Cancer in Patients With Ulcerative Colitis. In GASTROENTEROLOGY, 142(5), (pp. S538-S539).

Liu, Y., Alexandrov, S., Uttam, S., & Bista, R.K. (2012). Probing Cell Nanoscale Structural Properties Using Intrinsic Contrast of Light Scattering. In BIOPHYSICAL JOURNAL, 102(3), (p. 4A).Elsevier BV. doi: 10.1016/j.bpj.2011.11.039.

Brokl, D.A., Lo, D.Y., Khalbuss, W.E., Wang, P., Bista, R.K., Uttam, S., Liu, Y., & Brand, R. (2011). Spatial-Domain Low-Coherence Quantitative Phase Microscopy to Improve the Cytological Diagnosis of Pancreatic Cancer. In GASTROENTEROLOGY, 140(5), (p. S53).

Hashash, J.G., Bista, R.K., Hartman, D.J., Qiu, W., Wang, P., Zhang, L., Brand, R., & Liu, Y. (2011). Nuclear Refractive Index Detects the Field Effect of Carcinogenesis. In GASTROENTEROLOGY, 140(5), (p. S339).

Krasinskas, A.M., Bista, R.K., Rizvi, S., Hartman, D.J., Sanders, M., Gelrud, A., Slivka, A., Brand, R., & Liu, Y. (2011). Assessment of Nuclear Refractive Index to Improve the Diagnostic Accuracy of Cholangiocarcinoma of Bile Duct Biopsies. In GASTROENTEROLOGY, 140(5), (p. S68).

Wang, P., Bista, R., Bhargava, R., Brand, R.E., & Liu, Y. (2011). Spatial-domain low-coherence quantitative phase microscopy for cancer diagnosis. In Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XV, 7889.SPIE. doi: 10.1117/12.873620.

Wang, P., Bista, R.K., Khalbuss, W.E., Qiu, W., Staton, K.D., Zhang, L., Brentnall, T.A., Brand, R.E., & Liu, Y. (2011). Nanoscale nuclear architecture for cancer diagnosis by spatial-domain low-coherence quantitative phase microscopy. Poster session presented at the meeting of SPIE BiOS.Baltimore, MD.

Lo, D., Liu, Y., Khalbuss, W., Wang, P., & Brand, R. (2009). Using Novel Optical Technology to Improve the Cytological Diagnosis of Pancreatic Cancer. In AMERICAN JOURNAL OF GASTROENTEROLOGY, 104, (pp. S77-S78).Ovid Technologies (Wolters Kluwer Health). doi: 10.14309/00000434-200910003-00199.

Backman, V., Subramanian, H., Pradhan, P., Liu, Y., Capoglu, I., & Rogers, J. (2008). Detecting alterations in cell nanoarchitecture with optical imaging: Implications for cancer detection. In Optics InfoBase Conference Papers.

Subramanian, H., Brand, R., Deep, P.P.N., Parikh, V., Hasabou, N., Polidoro, D., Sturgis, C., & Backman, V. (2007). Pilot study determining the feasibility of diagnosing pancreatic cancer using single cell partial wave spectroscopy of the duodenal mucosa. In PANCREAS, 35(4), (pp. 429-430).Ovid Technologies (Wolters Kluwer Health). doi: 10.1097/01.mpa.0000297793.78884.bb.

Backman, V., Liu, Y., Pradhan, P., Kim, Y.L., Li, X., Taflove, A., Roy, H.K., & Brand, R. (2006). Single cell partial wave spectroscopy: Understanding alterations of intracellular nanoarchitecture in cancer. In Optics InfoBase Conference Papers.

Backman, V., Liu, Y., Pradhan, P., Kim, Y.L., Li, X., Taflove, A., Roy, H.K., & Brand, R. (2006). SINGLE CELL PARTIAL WAVE SPECTROSCOPY: UNDERSTANDING ALTERATIONS OF INTRACELLULAR NANOARCHITECTURE IN CANCER. In Frontiers in Optics.OSA. doi: 10.1364/fio.2006.ftuq2.

Brand, R., Liu, Y., Sturgis, C., Hasabou, N., Regner, M., Yoon, H., & Backman, V. (2006). Feasibility of using biophotonics to assist in cytologic diagnosis of pancreatic cancer. In PANCREAS, 33(4), (p. 449).Ovid Technologies (Wolters Kluwer Health). doi: 10.1097/00006676-200611000-00048.

Kim, Y.L., Liu, Y., Turzhitsky, V.M., Wali, R.K., Roy, H.K., & Backman, V. (2006). Risk stratification of colon cancer using low-coherence enhanced backscattering spectroscopy. In Optics InfoBase Conference Papers.

Kim, Y.L., Pradhan, P., Subramanian, H., Liu, Y., Kim, M.H., & Backman, V. (2006). Minimal scattering events in enhanced backscattering (EBS) of light: Origin of low-coherence EBS in discrete tissue models. In Optics InfoBase Conference Papers.

Kim, Y.L., Pradhan, P., Subramanian, H., Liu, Y., Kim, M.H., & Backman, V. (2006). Probing minimal scattering events in coherent backscattering of light using low-coherence induced dephasing. In Optics InfoBase Conference Papers.

Liu, Y., Pradhan, P., Li, X., Kim, Y.L., Wali, R.K., Roy, H.K., & Backman, V. (2006). Partial-wave spectroscopy to detect the initial stage of colon carcinogenesis. In Optics InfoBase Conference Papers.

Subramanian, H., Pradhan, P., Kim, Y.L., Liu, Y., & Backman, V. (2006). Monte carlo model of low-coherence enhanced backscattering (LEBS) from anisotropic disordered media. In Optics InfoBase Conference Papers.

Kim, Y.L., Liu, Y., Turzhitsky, V., Wali, R.K., Roy, H.K., & Backman, V. (2005). Low-coherence enhanced backscattering (LEBS) for colon cancer screening. In Optics InfoBase Conference Papers.

Horwitz, J., Cohen, E., Goldberg, M.J., Pema, M., Chang, S.Y., Kim, Y., Liu, Y., Master, S., Elton, E., Roy, H.K., & Backman, V. (2004). Micro-architectural alterations in endoscopically-normal mucosa provides accurate risk stratification for colorectal neoplasia. In AMERICAN JOURNAL OF GASTROENTEROLOGY, 99(10), (p. S326).Ovid Technologies (Wolters Kluwer Health). doi: 10.14309/00000434-200410001-00987.

Yang, J., Liu, Y., Backman, V., Webb, A.R., Pickerill, S.J., & Ameer, G.A. (2004). Novel optical technique for the characterization of materials. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 227, (p. U126).

Chen, Y., Kim, Y.L., Kromin, A., Liu, Y., Wessels, B., Ulmer, M., & Backman, V. (2003). Determination of nano-sphere sizes using UV light scattering spectroscopy beyond the diffraction limit. In LASERS IN SURGERY AND MEDICINE, (p. 14).

Kim, Y.L., Liu, K., Wali, R.K., Roy, H.K., Goldberg, M.J., Kromine, A.K., Chen, K., & Backman, V. (2003). Detection of the initial stages of colorectal carcinogenesis using polarization light scattering spectroscopy with multivariate statistical analysis. In LASERS IN SURGERY AND MEDICINE, (p. 13).

Liu, Y., Kim, Y.L., Wali, R.K., Roy, H.K., Goldberg, M.J., Kromine, A.K., Chen, K., & Backman, V. (2003). Characterization of increased mucosal blood flow as an early marker of colon carcinogenesis using polarization light scattering spectroscopy. In LASERS IN SURGERY AND MEDICINE, (p. 14).

Research interests

biomedical optics
cancer detection
fourier optics
light scattering
optical microscopy
super-resolution imaging