University of Pittsburgh

Biomedical Optical Imaging Laboratory

Journal Publications

Recent Publications


The amyloid precursor protein modulates the position and length of the axon initial segment

The amyloid precursor protein modulates the position and length of the axon initial segment


Ma F, Akolkar H, Xu J, Liu Y, Popova D, Xie J, Youssef M, Benosman Y, Hart R, Herrup K

Journal of Neuroscience, 43(10), 1830-1844, 2023
Changes in nuclear pore numbers control nuclear import and stress response of mouse hearts

Changes in nuclear pore numbers control nuclear import and stress response of mouse hearts


Han L, Mich-Basso JD, Li Y, Ammanamanchi N, Xu J, Bargaje AP, Liu H, Wu L, Jeong J-H, Franks J, Stolz DB, Wu Y, Rajasundaram D, Liu Y, Kühn B

Developmental Cell, 57(20), 2397-2411, 2022

Press Release

Redox Regulation of RAD51 Cys319 and Homologous Recombination by Peroxiredoxin 1

Redox Regulation of RAD51 Cys319 and Homologous Recombination by Peroxiredoxin 1


Skoko JJ, Cao J, Gaboriau D, Attar M, Asan A, Hong L, Paulsen CE, Ma H, Liu Y, Wu H, Furdui CM, Manevich Y, Morrison CG, Brown ET, Normolle DP, Carroll K, Neumann C

Redox Biology, 55, 102443, 2022
Robust emitter localization with enhanced harmonic analysis

Robust emitter localization with enhanced harmonic analysis


Ma H, Liu Y

Optics Letters, 46(23), 5798-5801, 2021
Enhanced super-resolution microscopy by extreme value based emitter recovery

Enhanced super-resolution microscopy by extreme value based emitter recovery


Ma H, Jiang W, Xu J, Liu Y

Scientific Reports, 11, 20417, 2021
Embedded nanometer position tracking based on enhanced phasor analysis

Embedded nanometer position tracking based on enhanced phasor analysis


Ma H, Liu Y

Optics Letters, 46, 3825-3828, 2021
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images

Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images


Mela CA, Liu Y

BMC Bioinformatics, 22, 325, 2021
Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy


Xu J, Liu Y

Frontiers in Cell and Developmental Biology, 9, 653077, 2021
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies

Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies


Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y

Cell Systems, 12, 220–234, 2021
Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue

Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue


Xu J, Ma H, Liu Y

Current Protocols in Cytometry, 94(1), e78, 2020
Super-resolution localization microscopy: Toward high throughput, high quality, and low cost

Super-resolution localization microscopy: Toward high throughput, high quality, and low cost


Ma H, Liu Y

APL Photonics, 5, 060902, 2020
Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease

Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease


Uttam S, Hashash JG, LaFace J, Binion D, Regueiro M, Hartman DJ, Brand RE, Liu Y

Cancer Prevention Resesarch, 12(8), 527-538, 2019

Cover Article

A guide to visualizing the spatial epigenome with super‐resolution microscopy

A guide to visualizing the spatial epigenome with super‐resolution microscopy


Xu J, Liu Y

The FEBS Journal, 286(16): 3095-3109, 2019

Cover Article

Top Downloaded Papers

Imaging Higher-order Chromatin Structures in Single Cells Using Stochastic Optical Reconstruction Microscopy

Imaging Higher-order Chromatin Structures in Single Cells Using Stochastic Optical Reconstruction Microscopy


Xu J, Liu Y

Bio-protocol, 9(3): e3160, 2019
ROS-Induced R Loops Trigger a Transcription-Coupled but BRCA1/2-Independent Homologous Recombination Pathway through CSB

ROS-Induced R Loops Trigger a Transcription-Coupled but BRCA1/2-Independent Homologous Recombination Pathway through CSB


Teng Y, Yadav T, Duan M, Tan J, Xiang Y, Gao B, Xu J, Liang Z, Liu Y, Nakajima S, Shi Y, Levine AS, Zou L, and Lan L

Nature Communications, 9: 4115, 2019
Fourier phase based depth-resolved nanoscale nuclear architecture mapping for cancer detection

Fourier phase based depth-resolved nanoscale nuclear architecture mapping for cancer detection


Uttam S, Liu Y

Methods, 136: 134-151, 2018
SIRT6 facilitates directional telomere movement upon oxidative damage

SIRT6 facilitates directional telomere movement upon oxidative damage


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

Scientific Reports, 8: 5401, 2018
A simple marker-assisted three-dimensional nanometer drift correction method for super-resolution microscopy

A simple marker-assisted three-dimensional nanometer drift correction method for super-resolution microscopy


Ma H, Xu J, Jin J, Huang Y, Liu Y

Biophysical Journal, 112: 2196-2208, 2017
A simple and cost-effective setup for super-resolution localization microscopy

A simple and cost-effective setup for super-resolution localization microscopy


Ma H, Fu R. Xu J, Liu Y

Scientific Reports, 7(1): 1542, 2017
SSRP1 cooperates with PARP and XRCC1, facilitating single strand break repair through chromatin priming

SSRP1 cooperates with PARP and XRCC1, facilitating single strand break repair through chromatin priming


Gao Y, Li C, Wei L, Teng Y, Nakajima S, Chen X, Xu J, Legar B, Ma H, Spagnol ST, Wan Y, Dahl KN, Liu Y, Levine A, Lan L

Cancer Research, 77: 2674-2685, 2017
Stochastic optical reconstruction microscopy (STORM)

Stochastic optical reconstruction microscopy (STORM)


Xu J, Ma H, Liu Y

Current Protocols in Cytometry, 81: 12.46.1–12.46.27, 2017
Quantitative phase imaging to improve the diagnostic accuracy of urine cytology

Quantitative phase imaging to improve the diagnostic accuracy of urine cytology


Pham HV, Pantanowitz L, Liu Y

Cancer Cytopathology, 124:641-650, 2016
Fourier phase in Fourier-domain optical coherence tomography

Fourier phase in Fourier-domain optical coherence tomography


Uttam S, Liu Y

Journal of the Optical Society of America A, 32(12):2286-2306, 2015
Fast and precise 3D fluorophore localization based on gradient fitting

Fast and precise 3D fluorophore localization based on gradient fitting


Ma H, Xu J, Jin J, Gao Y, Lan L, Liu Y

Scientific Reports, 5: 14335, 2015

Source code of gradient fitting

Targeted DNA damage at individual telomeres disrupts their integrity and triggers cell death

Targeted DNA damage at individual telomeres disrupts their integrity and triggers cell death


Sun L, Tan R, Xu J, LaFace J, Gao Y, Xiao, Y, Attar, M, Neumann C, Li G-M; Su B, Liu Y, Levine A, Nakajima S, Lan L

Nucleic Acids Research, 43: 6334-6347, 2015
Evaluation of Mutational Testing of Pre-neoplastic Barrett’s Mucosa by Next Generation Sequencing of FFPE Endoscopic Samples for Detection of Concurrent Dysplasia and Adenocarcinoma in Barrett’s Esophagus

Evaluation of Mutational Testing of Pre-neoplastic Barrett’s Mucosa by Next Generation Sequencing of FFPE Endoscopic Samples for Detection of Concurrent Dysplasia and Adenocarcinoma in Barrett’s Esophagus


Del Portillo A, Lagana SM, Yao Y, Uehara T, Jhala N, Ganguly T, Nagy P, Gutierrez J, Luna A, Abrams J, Liu Y, Brand R, Sepulveda JL, Falk GW, Sepulveda AR

The Journal of Molecular Diagnostics, 25: 1-7, 2015

Early Publications


2010-2014


  1. Hartman DJ, Krasinskas AM, Bista RK, Uttam S, Staton KD, Rizvi R, Slivka A, Brand RE, Liu Y. Assessment of nuclear nano-morphology marker to improve the detection of malignancy from bile duct biopsies, American Journal of Clinical Pathology, 141:884-891, 2014.
  2. Liu Y, Uttam S, Alexandrov S, Bista R. Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer, BMC Biophysics, 7: 1, 2014.
  3. Fasanella KE, Bista RK, Staton K, Rizvi S, Uttam S, Zhao C, Sepulveda A, Brand RE, McGrath K, and Liu Y. Nuclear Nano-architecture Markers of Gastric Cardia and Upper Squamous Esophagus Detect Esophageal Cancer “Field Effect”, Journal of Cancer, 4(8):626-634, 2013.
  4. Uttam S, Bista RK, Staton K, Alexandrov S, Choi S, Bakkenist CJ, Hartman DJ, Brand RE, and Liu Y. Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation, Biomedical Optics Express, 4(4): 596-613, 2013.
  5. Uttam S, Alexandrov S, Bista RK, Liu Y. Tomographic imaging via spectral encoding of spatial frequency, Optics Express, 21(6): 7488-7504, 2013.
  6. Alexandrov S, Uttam S, Bista RK, Liu Y. Spectral encoding of spatial frequency approach for characterization of nanoscale structures, Applied Physics Letters, 101(4): 033702, 2012.
  7. Bista RK, Wang P, Bhargava R, Uttam S, Hartman DJ, Brand RE, Liu Y. Nuclear nano-morphology markers of histologically normal cells detect the "field effect" of breast cancer., Breast Cancer Research and Treatment 135(1): 115-124, 2012.
  8. Chen Y, Liang C-P, Liu Y, Fischer AH, Parwani AV, Pantanowitz L. Review of Advanced Imaging Techniques, Journal of Pathology Informatics, 3:22, 2012.
  9. Bista RK, Uttam S, Hartman DJ, Qiu W, Yu J, Zhang L, Brand RE and Liu Y. Investigation of nuclear nano-morphology marker as a biomarker for cancer risk assessment using a mouse model, Journal of Biomedical Optics, 17(6): 066014, 2012.
  10. Alexandrov S, Uttam S, Bista RK, Zhao C, Liu Y. Real-time quantitative visualization of 3D structural information, Optics Express, 20(8): 9203-9214, 2012.
  11. Uttam S, Bista RK, Hartman DJ, Brand RE and Liu Y. Correction of stain variations in nuclear refractive index of clinical histology specimens, Journal of Biomedical Optics, 16(11): 116013, 2011.
  12. Alexandrov S, Uttam S, Bista RK, Liu Y. Spectral contrast imaging microscopy, Optics Letters, 36(11): 3323-3325, 2011.
  13. Bista RK, Uttam S, Wang P, Staton K, Choi S, Bakkenist CJ, Hartman DJ, Brand RE and Liu Y. Quantification of Nanoscale Nuclear Refractive Index Changes during the Cell Cycle, Journal of Biomedical Optics (Letters), 16(7): 070503, 2011.
  14. Fang C, Brokl D, Brand RE, Liu Y. A depth-selective fiber-optic probe for characterization of superficial tissue with a constant physical depth, Biomedical Optics Express, 2(4): 838-849, 2011.
  15. Bista, RK, Brentnall, TA, Bronner, MA, Langmead, CJ, Brand, RE, Liu Y. Using optical markers of nondysplastic rectal epithelial cells to identify patients with ulcerative colitis-associated neoplasia, Inflammatory Bowel Disease, 17(12): 2427-2435, 2011.
  16. Wang P, Bista R, Khalbuss WE, Qiu W, Staton K, Zhang L, Brentnall TA, Brand RE, Liu Y. Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy, Journal of Biomedical Optics, 15:066028, 2010
  17. Wang P, Bista RK, Qiu W, Khalbuss WE, Zhang L, Brand RE, Liu Y. An insight into statistical refractive index properties of cell internal structure via low-coherence statistical amplitude microscopy, Optics Express, 18(21): 21950-21958, 2010.
  18. Wang P, Bista R, Bhargava R, Brand RE, Liu Y. Spatial-domain low-coherence quantitative phase microscopy for cancer diagnosis,, Optics Letters, 35 (17): 2840-2842, 2010.

Prior to 2009 (Selected Publications)


  1. Mahmoud BH, Ruvolo E, Hexsel CL, Liu Y, Owen MR, Kollias N, Lim HW, Hamzavi IH. Impact of long wavelength UVA and visible light on melanocompetent skin, Journal of Investigative Dermatolology, 130: 2092-2097, 2010.
  2. Subramanian H, Pradhan P, Liu Y, Capoglu I, Li X, Rogers J, Heiftez A, Kunte D, Roy HR, Taflove A, Backman V. Optical methodology for detecting histologically unapparent nanoscale consequences of genetic alterations in biological cells, Proceedings of the National Academy of Sciences, 105(51):20124-20129, 2008.
  3. Liu Y, Brand RE, Turzhitsky V, Kim YL, Roy HK, Hasabou N, Sturgis C, Shah D, Hall C, Backman V. Optical markers in duodenal mucosa predict the presence of pancreatic cancer, Clinical Cancer Research, 13(15 Pt 1):4392-9, 2007.
  4. Liu Y, Li X, Kim YL, Backman V. Elastic backscattering spectroscopic microscopy, Optics Letters. 30(18):2445-7, 2005.
  5. Roy HK, Liu Y, Wali RK, Kim YL, Kromin A, Goldberg MJ, Backman V. Four-dimensional elastic light-scattering fingerprints as preneoplastic markers in the rat model of colon carcinogenesis, Gastroenterology, 126:1071-81, 2004.
  6. Liu Y, Kim YL, Li X, Backman V. Investigation of depth selectivity of polarization gating for tissue characterization, Optics Express, 13(2):526-33, 2005.
  7. Liu Y, Kim YL, Backman V. Development of a bioengineered tissue model and its application in the investigation of the depth selectivity of polarization gating, Applied Optics, 44(12): 2288-99, 2005.
  8. Allen J, Liu Y, Kim YL, Turzhitsky VM, Backman V, Ameer GA. Spectroscopic translation of cell-material interactions, Biomaterials, 28:162-74, 2007.
  9. Kim YL, Liu Y, Turzhitsky VM, Wali RK, Roy HK, and Backman V. Depth-resolved low-coherent backscattering in tissue, Optics Letters 30(7):741-743, 2005.
  10. Kim YL, Liu Y, Turzhitsky V, Roy HK, Wali RK and Backman V. Coherent backscattering spectroscopy, Optics Letters, 29(16):1906-1908, 2004.
  11. Kim YL, Liu Y, Wali RK, Roy HK, Goldberg MJ, Kromin A, Chen K and Backman V. 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, 2003.