Hongqiang Ma

Education

• B.S. in Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China, 2009
• Ph.D. in Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China, 2014

Academic Positions

• Research Assistant Professor, Department of Bioengineering, University of Illinois Urbana-Champaign, January 2024 - present
• Research Assistant Professor, Departments of Medicine, University of Pittsburgh, November 2017 - December 2023

Other Professional Employment

• Research Assistant Professor, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, January 2025 - present

Research Interests

• Predictive label-free imaging approaches for characterizing morphodynamics in three-dimensional samples
• Information-rich 3D super-resolution spatial biology

Research Topics

• Bioimaging at Multi-Scale

Chapters in Books

• Hongqiang Ma and Yang Liu, "Super-Resolution Imaging through Single-Molecule Localization," in Biomedical Optical Imaging: From Nanoscopy to Tomography, edited by Jun Xia and Regine Choe (AIP Publishing, Melville, New York, 2021), Chapter 4, pp. 4-1–4-26.

Selected Articles in Journals

• Chen, M., Ma, H., Sun, X. et al. Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment. npj Imaging 3, 26 (2025). 
• Ma H, Nguyen P, Liu Y. A Versatile Drift-Free Super-Resolution Imaging Method via Oblique Bright-Field Correlation. Adv. Sci.2025, 12, 2412127.
• Ma H, Chen M, Xu J, Yang Y, Zhao Y, Liu Y. An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization. Science Advances, 2024; 10: eadq5009.
• Xu J, Sun X, Chen Z, Ma H, Liu Y. Super-resolution imaging of T lymphocyte activation reveals chromatin decondensation and disrupted nuclear envelope. Communications Biology, 2024; 7: 717.
• Ma H, Chen M, Nguyen P, Liu Y. Towards drift-free high-throughput nanoscopy through adaptive intersection maximization. Science Advances, 2024; 10: eadm7765.
• Skoko JJ, Cao J, Gaboriau D, Attar M, Asan A, Hong L, Paulsen CE, Ma H, Liu Y, Wu H, Harkness T, Furdui CM, Manevich Y, Morrison CG, Brown ET, Normolle D, Spies M, Spies MA, Carroll K, Neumann CA. Redox regulation of RAD51 Cys319 and homologous recombination by peroxiredoxin 1. Redox Biol. 2022 Oct;56:102443. 
• Xu J, Sun X, Kim K, Brand RM, Hartman D, Ma H, Brand RE, Bai M, Liu Y. Ultrastructural visualization of chromatin in cancer pathogenesis using a simple small-molecule fluorescent probe. Sci Adv. 2022 Mar 4;8(9):eabm8293.
• Ma H, Liu Y. Robust emitter localization with enhanced harmonic analysis. Opt Lett. 2021 Dec 1;46(23):5798-5801
• Ma H, Jiang W, Xu J, Liu Y. Enhanced super-resolution microscopy by extreme value based emitter recovery. Sci Rep. 2021 Oct 14;11(1):20417. 
• Ma H, Liu Y. Embedded nanometer position tracking based on enhanced phasor analysis. Opt Lett. 2021 Aug 15;46(16):3825-3828. 
• [Ma H#, Xu J#], Ma HB, Jiang W, Mela CA, Duan M, Zhao S, Gao C, Hahm ER, Lardo SM, Troy K, Sun M, Pai R, Stolz DB, Zhang L, Singh S, Brand RE, Hartman DJ, Hu J, Hainer SJ, Liu Y. Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis. Nat Commun. 2020 Apr 20;11(1):1899.
• Ma. H, Liu. Y, Super-resolution localization microscopy: Toward high throughput, high quality, and low cost. APL Photonics, 5 (2020).
• Xu. J, Ma H.,Liu Y., Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue. Current Protocols in Cytometry, 94, e78 (2020).
• Ma H, Xu J, Liu Y. WindSTORM: Robust online image processing for high-throughput nanoscopy. Sci Adv. 2019 Apr;5(4):eaaw0683.
• Nmezi B, Xu J, Fu R, Armiger TJ, Rodriguez-Bey G, Powell JS, Ma H, Sullivan M, Tu Y, Chen NY, Young SG, Stolz DB, Dahl KN, Liu Y, Padiath QS. Concentric organization of A- and B-type lamins predicts their distinct roles in the spatial organization and stability of the nuclear lamina. Proc Natl Acad Sci U S A. 2019 Mar 5;116(10):4307-4315. 
• Xu J, Ma H, Jin J, Uttam S, Fu R, Huang Y, Liu Y. Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells. Cell Rep. 2018 Jul 24;24(4):873-882. 
• Gao Y, Tan J, Jin J, Ma H, Chen X, Leger B, Xu J, Spagnol ST, Dahl KN, Levine AS, Liu Y, Lan L. SIRT6 facilitates directional telomere movement upon oxidative damage. Sci Rep. 2018 Mar 29;8(1):5407. 
• Ma H, Xu J, Jin J, Huang Y, Liu Y. A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy. Biophys J. 2017 May 23;112(10):2196-2208. 
• Gao Y, Li C, Wei L, Teng Y, Nakajima S, Chen X, Xu J, Leger B, Ma H, Spagnol ST, Wan Y, Dahl KN, Liu Y, Levine AS, Lan L. SSRP1 Cooperates with PARP and XRCC1 to Facilitate Single-Strand DNA Break Repair by Chromatin Priming. Cancer Res. 2017 May 15;77(10):2674-2685.
• Xu. J, Ma. H, Liu. Y, Stochastic Optical Reconstruction Microscopy (STORM). Current Protocols in Cytometry, 81, 12.46.1-12.46.27 (2017).
• Ma H, Fu R, Xu J, Liu Y. A simple and cost-effective setup for super-resolution localization microscopy. Sci Rep. 2017 May 8;7(1):1542. 
• Ma H, Xu J, Jin J, Gao Y, Lan L, Liu Y. Fast and Precise 3D Fluorophore Localization based on Gradient Fitting. Sci Rep. 2015 Sep 22;5:14335. 
• Ma H, Kawai H, Toda E, Zeng S, Huang ZL. Localization-based super-resolution microscopy with an sCMOS camera part III: camera embedded data processing significantly reduces the challenges of massive data handling. Opt Lett. 2013 Jun 1;38(11):1769-71. 
• Ma H, Long F, Zeng S, Huang ZL. Fast and precise algorithm based on maximum radial symmetry for single molecule localization. Opt Lett. 2012 Jul 1;37(13):2481-3. 
• Huang ZL, Zhu H, Long F, Ma H, Qin L, Liu Y, Ding J, Zhang Z, Luo Q, Zeng S. Localization-based super-resolution microscopy with an sCMOS camera. Opt Express. 2011 Sep 26;19(20):19156-68. 

Pending Articles

• H. Ma, C. Zhang, S. Zheng, S. Chen, Y. Liu. Automated Cyclic Super-Resolution Microscopy for Nanoscale Protein Mapping.

Patents

• H. Ma, Y. Liu, inventors; University of Pittsburgh, assignee. Hyper-throughput, multiplex, single molecule imaging platform. PCT patent WO2024158609. 2024
• H. Ma, Liu Y, inventors; University of Pittsburgh, assignee. Drift-free high-throughput localization microscopy. PCT patent WO2024097628. 2024
• H. Ma, Y. Liu, inventors; University of Pittsburgh, assignee. Automated nanoscopy system having integrated artifact minimization modules, including embedded nanometer position tracking based on phasor analysis. United States patent US12567268B2. 2024
• H. Ma, Y. Liu, inventors; University of Pittsburgh, assignee. Systems and methods for robust background correction and/or emitter localization for super-resolution localization microscopy. United States patent US12044625B2. 2024
• H. Ma, Y. Liu, inventors; University of Pittsburgh, assignee. System and method for estimating and compensating for sample drift during data acquisition in fluorescence microscopy. United States patent US11067510B2. 2021.

Service on Department Committees

• 2024-present, BIOE PhD qualifying exam,  Committee member

Service to Federal and State Government

• 2026, Reviewer and panelist, NIH/MCST: Small Business for Instrumentation, Environmental, and Occupational Safety
• 2025, Reviewer and panelist, National Institute of General Medical Sciences (NIH/NIGMS)
• 2024, Reviewer and panelist, National Institute of Allergy and Infectious Diseases (NIH/NIAID)

Recent Courses Taught

• BIOE 483 - Biomed Computed Imaging System