Publications

Ji Sun Choi, Yue Zhuo, Brian T. Cunningham, and Brendan A. Harley. Non-invasive optical imaging on photonic crystalsurface of stem cell differentiation in biomaterials, pages 195--207. Elsevier Inc., 2017. [ bib | PDF ]

Yue Zhuo and Brian T. Cunningham. Label-Free Biosensor Imaging on Photonic Crystal Surfaces (Chpater 2), pages 31--55. 2016. [ bib | PDF ]

Yue Zhuo, Xiao-Long Wu, Justin P. Haldar, Thibault Marin, Wen-mei W. Hwu, Zhi-Pei Liang, and Bradley P. Sutton. Using GPUs to Accelerate Advanced MRI Reconstruction with Field Inhomogeneity Compensation. Elsevier Science, 2011. [ bib | DOI | PDF ]

Chao Ma, Paul Kyu Han, Yue Zhuo, Yanis Djebra, Thibault Marin, and Georges El Fakhri. Joint spectral quantification of MR spectroscopic imaging using linear tangent space alignment (LTSA)-based manifold learning. Magnetic Resonance in Medicine, 2022. [ bib | DOI ]

Paul H. Dannenberg, Jie Wang, Yue Zhuo, Sangyeon Cho, Kwon-Hyeon Kim, and Seok-Hyun Yun. Droplet microfluidic generation of a million optical microparticle barcodes. Optics Express, 2021. [ bib | DOI ]

Thibault Marin, Yue Zhuo, Rita Maria Lahoud, Fei Tian, Xiaoyue Ma, Fangxu Xing, Maryam Moteabbed, Xiaofeng Liu, Kira Grogg, Nadya Shusharina, Jonghye Woo, Chao Ma, Yen-Lin Chen, and Georges El Fakhri. Deep learning-based GTV contouring modeling inter- and intra- observer variability in sarcomas. Radiotherapy and Oncology, 2021. [ bib | DOI | PDF ]

Paul K. Han, Thibault Marin, Yanis Djebra, Vanessa Landes, Yue Zhuo, Georges El Fakhri, and Chao Ma. Free-breathing 3D Cardiac T1 Mapping with Transmit B1 Correction at 3T. Magnetic Resonance in Medicine, 2021. [ bib | DOI | PDF ]

Shui-Jing Tang, Paul H. Dannenberg, Andreas C. Liapis, Nicola Martino, Yue Zhuo, Yun-Feng Xiao, and Seok-Hyun Yun. Laser particles with omnidirectional emission for cell tracking. Light, Science & Applications, 10(1):23, 2021. [ bib | DOI | PDF ]

Yue Zhuo, Huan Hu, Yifei Wang, Thibault Marin, and Meng Lu. Photonic crystal slab biosensors fabricated with helium ion lithography (HIL). Sensors and Actuators A: Physical, 297:111493, 2019. [ bib | DOI | PDF ]

Arturo Canales-Benavides, Yue Zhuo, Andrea M. Amitrano, Minsoo Kim, Raul I. Hernandez-Aranda, P. Scott Carney, and Martin Schnell. Accessible quantitative phase imaging in confocal microscopy with sinusoidal-phase synthetic optical holography. Applied Optics, 58(5):A55--A64, 2019. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM). Light: Science & Applications, 7(1):9, 2018. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Quantitative imaging of cell membrane-associated effective mass density using Photonic Crystal Enhanced Microscopy (PCEM). Progress in Quantum Electronics, 50:1--18, 2016. [ bib | DOI | PDF ]

Brian T. Cunningham, Meng Zhang, Yue Zhuo, Lydia Kwon, and Caitlin Race. Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review. IEEE Sensors Journal, 16(10):3349--3366, 2016. [ bib | DOI | PDF ]

Yue Zhuo and Brian T. Cunningham. Label-Free Biosensor Imaging on Photonic Crystal Surfaces. Sensors (Basel, Switzerland), 15(9):21613--21635, 2015. [ bib | DOI | PDF ]

Yue Zhuo, Tongcheng Qian, Yiqian Wu, Jihye Seong, Ya Gong, Hongwei Ma, Yingxiao Wang, and Shaoying Lu. Subcellular and Dynamic Coordination between Src Activity and Cell Protrusion in Microenvironment. Scientific Reports, 5:12963, 2015. [ bib | DOI | PDF ]

Yue Zhuo, Huan Hu, Weili Chen, Meng Lu, Limei Tian, Hojeong Yu, Kenneth D. Long, Edmond Chow, William P. King, Srikanth Singamaneni, and Brian T. Cunningham. Single nanoparticle detection using photonic crystal enhanced microscopy. The Analyst, 139(5):1007--1015, 2014. [ bib | DOI | PDF ]

Huan Hu, Yue Zhuo, Muhammed E. Oruc, Brian T. Cunningham, and William P. King. Nanofluidic channels of arbitrary shapes fabricated by tip-based nanofabrication. Nanotechnology, 25(45):455301, 2014. [ bib | DOI | PDF ]

Weili Chen, Kenneth D. Long, Meng Lu, Vikram Chaudhery, Hojeong Yu, Ji Sun Choi, James Polans, Yue Zhuo, Brendan A. C. Harley, and Brian T. Cunningham. Photonic crystal enhanced microscopy for imaging of live cell adhesion. The Analyst, 138(20):5886--5894, 2013. [ bib | DOI | PDF ]

Jie Sun, Shaoying Lu, Mingxing Ouyang, Li-Jung Lin, Yue Zhuo, Bo Liu, Shu Chien, Benjamin G. Neel, and Yingxiao Wang. Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2. Nature Communications, 4:2037, 2013. [ bib | DOI | PDF ]

Xiaoling Liao, Shaoying Lu, Yiqian Wu, Wenfeng Xu, Yue Zhuo, Qin Peng, Bo Li, Ling Zhang, and Yingxiao Wang. The effect of differentiation induction on FAK and Src activity in live HMSCs visualized by FRET. PloS one, 8(8):e72233, 2013. [ bib | DOI | PDF ]

Xiaoling Liao, Shaoying Lu, Yue Zhuo, Christina Winter, Wenfeng Xu, and Yingxiao Wang. Visualization of Src and FAK Activity during the Differentiation Process from HMSCs to Osteoblasts (Src and FAK Activity during Differentiation). PloS one, 7(8):e42709, 2012. [ bib | DOI | PDF ]

Jihye Seong, Mingxing Ouyang, Taejin Kim, Jie Sun, Po-Chao Wen, Shaoying Lu, Yue Zhuo, Nicholas M. Llewellyn, David D. Schlaepfer, Jun-Lin Guan, Shu Chien, and Yingxiao Wang. Detection of focal adhesion kinase activation at membrane microdomains by fluorescence resonance energy transfer. Nature Communications, 2:406, 2011. [ bib | DOI | PDF ]

Xiaoling Liao, Shaoying Lu, Yue Zhuo, Christina Winter, Wenfeng Xu, Bo Li, and Yingxiao Wang. Bone Physiology, Biomaterial and the Effect of Mechanical/Physical Microenvironment on MSC Osteogenesis: A Tribute to Shu Chiens 80th Birthday. Cellular and Molecular Bioengineering, 4(4):579--590, 2011. [ bib | DOI | PDF ]

Tianjian Lu, Thibault Marin, Yue Zhuo, Yi-Fan Chen, and Chao Ma. Nonuniform Fast Fourier Transform on TPUs. In IEEE International Symposium on Biomedical Imaging, 2021. [ bib | PDF ]

Thibault Marin, Paul K. Han, Yue Zhuo, Yanis Djebra, Fang Liu, Georges El Fakhri, and Chao Ma. Three-dimensional cardiac T1 mapping using subspace and sparsity constrained direct estimation. In Proc. ISMRM, 2021. [ bib | PDF ]

Thibault Marin, Yanis Djebra, Paul K. Han, Vanessa Landes, Yue Zhuo, Kuan-Hao Su, Georges El Fakhri, and Chao Ma. Comparison of deformable registration techniques for real-time MR-based motion correction in PET/MR. In Proc. ISMRM, 2021. [ bib | PDF ]

Tianjian Lu, Thibault Marin, Yue Zhuo, Yi-Fan Chen, and Chao Ma. Accelerating MRI Reconstruction on TPUs. In IEEE High Performance Extreme Computing Conference, pages 1--9. Ieee, 2020. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Stem Cell Adhesion Imaging with Photonic Resonator Outcoupler Microscopy (PROM). In Biomedical Engineering Society Annual Meeting, 2018. [ bib | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Photonic Resonator Outcoupler Microscopy (PROM) for Quantitative Monitoring of Stem Cell Focal Adhesion Area. In Frontiers in Optics, page JTu3A.119. Optical Society of America, 2018. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Label-free Imaging of Stem Cell Adhesion and Dynamic Tracking of Boundary Evolution Using Photonic Crystal Enhanced Microscopy (PCEM). In Proceedings of Microscopy & Microanalysis, volume 23, pages 1142--1143, 2017. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Quantitative Label-free Imaging of Live-cell Adhesion Using Photonic Crystal Enhanced Microscopy (PCEM). In Conference on Lasers and Electro-Optics (CLEO), 2017. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Cell Adhesion Phenotype Library with Photonic Crystal Enhanced Microscopy. In Optics in the Life Sciences Congress, page BoS2A7, 2017. [ bib | DOI | PDF ]

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Photonic Crystal Enhanced Microscopy (PCEM) for Multimode Dynamic Quantitative Imaging of Cell Adhesion. In International Engineering in Medicine and Biology Conference (EMBC), 2016. [ bib | PDF ]

Ji Sun Choi, Yelena Ilin, Yue Zhuo, Mary Kraft, Brian Cunningham, and Brendan Harley. In vitro control of hematopoietic stem cell fate decisions and analysis in a bone marrow-inspired synthetic niche. In NIH-NIDDK Effects of Aging on Hematopoiesis Workshop, 2016. [ bib ]

Ji Sun Choi, Yelena Ilin, Yue Zhuo, Brian Cunningham, Mary Kraft, and Brendan Harley. Tracing of individual hematopoietic stem cell specification events using Raman Spectroscopy and photonic crystal enhanced microscopy. In Frontiers in Bioengineering and Biotechnology, volume 4, 2016. [ bib | DOI | PDF ]

Ji Sun Choi, Yelena Ilin, Yue Zhuo, Brian Cunningham, Mary Kraft, and Brendan Harley. Label-Free Analysis of Single Hematopoietic Stem and Progenitor Cells. In Tissue Engineering Part A, volume 21, pages S237--S238, 2015. [ bib ]

Yue Zhuo, Ji Sun Choi, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Surface Attachment Profiling of Stem Cell Differentiation Using Photonic Crystal Enhanced Microscopy (PCEM). In The American Society of Mechanical Engineers -- NanoEngineering for Medicine and Biology (ASME-NEMB), 2015. [ bib | PDF ]

Yue Zhuo, Ji Sun Choi, Hojeong Yu, Brendan A. Harley, and Brian T. Cunningham. Dynamic label-free imaging of live-cell adhesion using photonic crystal enhanced microscopy (PCEM). In Conference on Lasers and Electro-Optics (CLEO), 2015 Conference on Lasers and Electro-Optics (CLEO), pages 1--2, 2015. [ bib | PDF ]

Brian T. Cunningham, Weili Chen, Kenneth D. Long, Yue Zhuo, Ji Sun Choi, and Brendan A. Harley. Photonic crystal enhanced microscopy. In 2015 Conference on Lasers and Electro-Optics (CLEO), pages 1--2, 2015. [ bib | DOI | PDF ]

Brian T. Cunningham, Meng Zhang, Yue Zhuo, Lydia Kwon, and Caitlin Race. Review of Recent Advances in Biosensing with Photonic Crystal Surfaces. In Special Issue on Selected Papers From The IEEE Sensors 2014 Conference, 2015. [ bib | DOI | PDF ]

Ji Sun Choi, Yelena Ilin, Yue Zhuo, Brian Cunningham, Mary Kraft, and Brendan Harley. Single-Cell Approaches to Assess Hematopoietic Stem Cell Responses to Matrix Cues. In Biomedical Engineering Society Annual Meeting, 2014. [ bib ]

Yue Zhuo, Huan Hu, Weili Chen, Meng Lu, Limei Tian, Hojeong Yu, Kenneth D. Long, Edmond Chow, William P. King, Srikanth Singamaneni, and Brian T. Cunningham. Detection of single nanoparticles using photonic crystal enhanced microscopy. In 2014 Conference on Lasers and Electro-Optics (CLEO) -- Laser Science to Photonic Applications, pages 1--2, 2014. [ bib | DOI | PDF ]

Yue Zhuo, Limei Tian, Weili Chen, Hojeong Yu, Srikanth Singamaneni, and Brian T. Cunningham. Protein-protein binding detection with nanoparticle photonic crystal enhanced microscopy (NP-PCEM). In 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 2069--2072. IEEE, 2014. [ bib | DOI | PDF ]

Yue Zhuo, Tongcheng Qian, Shaoying Lu, and Yingxiao Wang. Src Activity Dynamic Detection In The Initiation Of Tension-released Cell Migration. In BMES, 2012. [ bib | PDF ]

Jie Sun, Shaoying Lu, Mingxing Ouyang, Li-Jung Lin, Yue Zhuo, Bo Liu, Richard Chan, Shu Chien, Benjamin G. Neel, and Yingxiao Wang. Circuit algorithm of tunable intramolecular interactions embedded within Shp2 revealed by FRET. In ACS National Meeting Book of Abstracts, volume 243, 2012. [ bib ]

Xiao-Long Wu, Yue Zhuo, Jiading Gai, Fan Lam, Maojing Fu, Justin P. Haldar, Wen-Mei Hwu, Zhi-Pei Liang, and Bradley P. Sutton. Advanced MRI reconstruction toolbox with accelerating on GPU. In John D. Owens, I-Jong Lin, Yu-Jin Zhang, and Giordano B. Beretta, editors, Parallel Processing for Imaging Applications, volume 7872, pages 241--250. Spie, 2011. [ bib | DOI | PDF ]

Xiao-Long Wu, Jiading Gai, Fan Lam, Maojing Fu, Justin P. Haldar, Yue Zhuo, Zhi-pei Liang, Wen-Mei Hwu, and Bradley P. Sutton. Impatient MRI: Illinois Massively Parallel Acceleration Toolkit for Image reconstruction with ENhanced Throughput in MRI. In 2011 The International Society for Magnetic Resonance in Medicine (ISMRM), 2011. [ bib | PDF ]

Xiao-Long Wu, Jiading Gai, Fan Lam, Maojing Fu, Justin P. Haldar, Yue Zhuo, Zhi-Pei Liang, Wen-Mei Hwu, and Bradley P. Sutton. Impatient MRI: Illinois Massively Parallel Acceleration Toolkit for image reconstruction with enhanced throughput in MRI. In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 69--72. IEEE, 2011. [ bib | DOI | PDF ]

Yue Zhuo, Xiao-Long Wu, Justin P. Haldar, Wen-mei W. Hwu, Zhi-Pei Liang, and Bradley P. Sutton. Accelerating iterative field-compensated MR image reconstruction on GPUs. In 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 820--823, 2010. [ bib | DOI | PDF ]

Yue Zhuo, Xiao-Long Wu, Justin P. Haldar, Wen-mei W. Hwu, Zhi-Pei Liang, and Bradley P. Sutton. Multi-GPU Implementation for Iterative MR Image Reconstruction with Field Correction. In ISMRM, 2010. [ bib | PDF ]

Yue Zhuo and Bradley P. Sutton. Susceptibility-induced BOLD Sensitivity Variation in Breath Hold Task. In ISMRM, 2010. [ bib | PDF ]

Yue Zhuo and Bradley P. Sutton. fMRI calibration using effective BOLD signals estimated from susceptibility-induced echo-time-shift. In OHBM, 2010. [ bib | PDF ]

Yue Zhuo, Xiao-Long Wu, Justin P. Haldar, Wen-mei W. Hwu, Zhi-Pei Liang, and Bradley P. Sutton. Sparse regularization in MRI iterative reconstruction using GPUs. In 2010 3rd International Conference on Biomedical Engineering and Informatics, volume 2, pages 578--582, 2010. [ bib | DOI | PDF ]

Yue Zhuo and Bradley P. Sutton. Iterative image reconstruction model including susceptibility gradients combined with Z-shimming gradients in fMRI. IEEE Engineering in Medicine and Biology Society, 2009:5721--5724, 2009. [ bib | DOI | PDF ]

Yue Zhuo and Bradley P. Sutton. Effect on BOLD sensitivity due to susceptibility-induced echo time shift in spiral-in based functional MRI. IEEE Engineering in Medicine and Biology Society, 2009:4449--4452, 2009. [ bib | DOI | PDF ]

Bradley P. Sutton and Yue Zhuo. Susceptibility, echo time shifts, and T2* considerations for functional magnetic resonance imaging. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 710--713, 2009. [ bib | DOI | PDF ]

Yue Zhuo and Bradley P. Sutton. Iterative, Field-inhomogeneity Compensated Image Reconstruction for MRI with Z-shim Gradient. In 2008 Conference: Biomedical Engineering Society (BMES), 2008. [ bib | PDF ]

Brian T. Cunningham, Yue Zhuo, Brendan A. Harley, Ji Sun Choi, Thibault Marin, and Yi Lu. Photonic Resonator Absorption Microscopy (PRAM) for Digital Resolution Biomolecular Diagnostics, 2019. [ bib | DOI | PDF ]

Brian T. Cunningham, Yue Zhuo, Brendan A. Harley, Ji Sun Choi, and Thibault Marin. Photonic Resonator Outcoupler Microscopy (PROM), 2019. [ bib | DOI | PDF ]