Publications

2022

Zhang X^†, Alexander RV^†, Yuan J, Ding Y*. 2022. ” Computational Analysis of Cardiac Contractile Function.” Current Cardiology Reports, 24: 1983–1994 (2022).

Koger CR^†, Hassan SS^†, Yuan J, Ding Y*. 2022. “Virtual Reality for Interactive Medical Analysis.” Frontiers in Virtual Reality, 3: 782854.

de Lestrange-Anginieur, Ding Y*. 2022. “Modulations of face perception in response to a novel time-varying optical perturbation after aberration correction using adaptive optics.” The European Physical Journal Special Topics, 231(4): 713-722.

Baek BI, Chang SS, Chang CC, Roustaei M, Ding Y, Wang Y, Chen J, O’donnell R, Chen H, Ashby JW, Xu X, Mack JJ, Cavallero S, Roper M, Hsiai TK*. 2022. “Vascular Injury in the Zebrafish Tail Modulates Blood Flow and Peak Wall Shear Stress to Restore Embryonic Circular Network.” Frontiers in Cardiovascular Medicine, 9: 841101.

Yuan J, Ding Y, Fei S, Chen YQ. 2022. “Identification and parameter sensitivity analyses of time-delay with single-fractional-pole systems under actuator rate limit effect.” Mechanical Systems and Signal Processing, 163: 108111.

Roustaei M, Baek KI, Wang Z, Cavallero S, Satta S, Lai A, O’Donnell R, Vedula V, Ding Y, Marsden AL, Hsiai TK. 2022. “Computational Simulations of the 4-D Micro-Circulatory Network in Zebrafish Tail Amputation and Regeneration.” Journal of the Royal Society Interface, 19 (187): 20210898.

2021

Jiao Y^†, Yuan J^†, Sodimu OM, Qiang Y, Ding Y*. 2021. “Deep Neural Network-Aided Histopathological Analysis of Myocardial Injury.” Frontiers in Cardiovascular Medicine, 8: 724183.

Wang Z, Ding Y, Satta S, Roustaei M, Fei P, Hsiai TK. 2021. “A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development.” PLOS Computational Biology, 17(7): e1009175.

Wang Z, Zhu L, Zhang H, Li G, Yi C, Li Y, Yang Y, Ding Y, Zhen M, Gao S, Hsiai TK, Fei P. 2021. “Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning.” Nature Methods, 18(5): 551-556.

Chang CC^†, Chu C^†, Meyer S, Ding Y, Sun MM, Abiri P, Baek KI, Gudapati V, Ding X, Guihard P, Bostrom KI, Li S, Gordon LK, Zheng JJ, Hsiai TK. 2021. “Three-dimensional Imaging Coupled with Topological Quantification Uncovers Retinal Vascular Plexuses Undergoing Obliteration.” Theranostics, 11(3): 1162.

Before 2021

Ding Y†*, Gudapati V†, Lin R, Fei Y, Song S, Chang CC, Baek KI, Wang Z, Roustaei M, Kuang D, Kuo CCJ, Hsiai TK. 2020. “Saak Transform-Based Machine Learning for Light-Sheet Imaging of Cardiac Trabeculation.” IEEE Transactions on Biomedical Engineering, 68(1): 225-235.

Yokota T, Li J, Huang J, Xiong Z, Zhang Q, Chan T, Ding Y, Rau C, Sung K, Ren S, Kulkarni R, Hsiai TK, Xiao X, Touma M, Minamisawa S, Wang Y. 2020. “p38 Mitogen-activated protein kinase regulates chamber-specific perinatal growth in heart.“, The Journal of Clinical Investigation, 130(10): 5287-5301.

Abiri P, Yousefi A, Abiri A, Gudapati V, Ding Y, Nguyen KL, Abiri A, Markovic D, Tai YC, Hsiai TK. 2020. “A Multi-Dimensional Analysis of a Novel Approach for Wireless Stimulation.“, IEEE Transactions on Biomedical Engineering, 67(12): 3307-3316.

Chen J^†, Ding Y^†, Chen M, Gau J, Jen N, Nahal C, Tu S, Chen C, Zhou S, Chang CC, Lyu J, Xu X, Hsiai TK, Packard RRS. 2019. “Displacement analysis of myocardial mechanical deformation (DIAMOND) reveals segmental susceptibility to doxorubicin-induced injury and regeneration.“, JCI Insight, 4(8): e125362.

Shigeta A^†, Huang V^†, Zuo J, Basada R, Nakashima Y, Lu Y, Ding Y, Pellegrini M, Kulkarni RP, Hsiai TK, Deb A, Zhou B, Nakano H, Nakano A. 2019. “Endocardially-derived macrophages are essential for valvular remodeling.” Developmental Cell, 48(5): 617-630.

Hsu JJ, Vedula V, Baek KI, Chen C, Chen J, Chou MI, Lam J, Subhedar S, Wang J, Ding Y, Chang CC, Lee J, Demer LL, Tintut Y, Marsden AL, Hsiai TK. 2019. “Contractile and Hemodynamic Forces Coordinate Notch1b-Mediated Outflow Tract Valve Formation.” JCI Insight, 4(10): e124460.

Fei P^†, Nie J^†, Lee J^†, Ding Y^†, Li S, Yu Z, Zhang H, Yu T, Hagiwara M, Segura T, Ho CM, Zhu D, Hsiai TK. 2019. “Sub-voxel light-sheet microscopy for high-resolution, high-throughput volumetric imaging of large biomedical specimens.” Advanced Photonics, 1(1): 016002.

Zhou K, Ding Y, Vuletic I, Tian Y, Li J, Liu J, Huang Y, Sun H, Ren Q. 2018 “In vivo long-term investigation of tumor bearing mKate2 by an in-house fluorescence molecular imaging system.” BioMedical Engineering OnLine, 17(1): 187.

Ding Y, Bailey Z, Messerschmidt V, Bryant R, Lee J, Hsiai TK. 2018. “Light-sheet fluorescence microscopy for the study of the murine heart.” Journal of Visualized Experiments, 139: e57769.

Messerschmidt V^†, Bailey Z^†, Baek KI, Ding Y, Hsu JJ, Bryant R, Li R, Hsiai TK, Lee J. 2018. “Light-sheet Fluorescence Microscopy to Capture 4-Dimensional Images of the Effects of Modulating Shear Stress on the Developing Zebrafish Heart.” Journal of Visualized Experiments, 138: e57763.

Ding Y, Lee J, Packard RRS, Hsu JJ, Baek KI, Hsiai TK. 2018. “Light-Sheet Imaging to Elucidate Cardiovascular Injury and Repair.” Current Cardiology Reports, 20(5): 1-8.

Ding Y, Ma J, Langenbacher A, Baek KI, Lee J, Chang CC, Hsu JJ, Kulkarni RP, Belperio J, Shi W, Ranjbarvaziri S, Ardehali R, Tintut Y, Demer LL, Chen JN, Fei P, Packard RRS, Hsiai TK. 2018 “Multi-scale light-sheet for rapid imaging of cardiopulmonary system.” JCI Insight, 3(16): e121396.

Baek KI†, Ding Y†, Chang CC†, Packard RRS, Hsu JJ, Fei P, Hsiai TK. 2018. “Application of Light-Sheet Fluorescence Microscopy to Elucidate Zebrafish Model of Cardiovascular Injury and Regeneration.” Progress in Biophysics and Molecular Biology, 138: 105-115.

Abiri A^†, Ding Y^†, Vedula V, Abiri P, Packard RRS, Marsden A, Hsiai TK. 2018. “Deformable Image Registration in 4-Dimensional Cardiac Imaging for Interactive Virtual Reality.” Annals of Biomedical Engineering, 46(12): 2177-2188.

Lee J^†, Vedula V^†, Chen J, Hsu JJ, Ding Y, Baek KI^†, Chang CC, Kang H, Fei P, Chuong CM, Li R, Packard RRS, Marsden AL, Hsiai TK. 2018. “4-D Hemodynamic Forces Regulate Trabeculation and Consequent Cardiac Function during Development.” JCI Insight, 3(13): e96672.

Hsu JJ, Lu J, Umar S, Lee JT, Kulkarni RP, Ding Y, Chang CC, Hsiai TK, Hokugo A, Gkouveris I, Tetradis S, Nishimura I, Demer LL, Tintut Y. 2018. “Effects of teriparatide on morphology of aortic calcification in aged hyperlipidemic mice” American Journal of Physiology-Heart and Circulatory Physiology, 314(6): H1203-1213.

Sereti KI^†, Nguyen N^†, Kamran P^†, Zhao P, Ranjbarvaziri S, Park S, Engel J, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Mikkola HKA, Sahoo D, Iruela-Arispe ML, Ardehali R. 2018. “Analysis of cardiomyocyte clonal expansion during mouse heart development and injury.” Nature Communications, 9(1): 754.

Ding Y^†, Abiri A^†, Li S, Abiri P, Lee J, Chang CC, Baek KI, Sideris E, Li Y, Bui A, Segura T, Nguyen TP, Packard RRS, Fei P, Hsiai TK. 2017. “Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics.” JCI Insight, 2(22): e97180.

Baek KI, Packard RRS, Hsu J, Saffari A, Ma Z, Luu AP, Pietersen A, Yen H, Ding Y, Ren B, Sioutas C, Li R, Hsiai TK. 2017. “Ultrafine Particle Exposure Reveals the Importance of FOXO1/Notch Activation Complex for Vascular Regeneration.” Antioxidants & Redox Signaling, 28(13): 1209-1223.

Ding Y^†, Lee J^†, Ma J^†, Sung K, Yokota T, Singh N, Dooraghi M, Abiri P, Wang Y, Kulkarni RP, Nakano A, Nguyen TP, Fei P, Hsiai TK. 2017. “Light-sheet fluorescence imaging to localize cardiac lineage and protein distribution.” Scientific Reports, 7: 42209.

Vuletic I, Zhou K, Li H, Bai H, Meng X, Zhu S, Ding Y, Li J, Sun H, Ren Q. 2017. “Validation of Bevacizumab therapy effect on colon cancer subtypes by using whole body imaging in mice.” Molecular Imaging and Biology, 19(6): 847-856.

Lee J^†, Chou TC^†, Kang D, Kang H, Chen J, Baek KI^†, Wang W, Ding Y, Di Carlo D, Tai YC, Hsiai TK. 2017. “A Rapid Capillary-Pressure Driven Micro-Channel to Demonstrate Newtonian Fluid Behavior of Zebrafish Blood at High Shear Rates.” Scientific Reports, 7: 1980.

Abiri P, Abiri A, Packard RRS, Ding Y, Yousefi A, Ma J, Bersohn M, Nguyen KL, Markovic D, Moloudi S, Hsiai TK. 2017. “Inductively powered wireless pacing via a miniature pacemaker and remote stimulation control system.” Scientific Reports, 7: 6180.

Packard RRS, Baek KI, Beebe T, Jen N, Ding Y, Fei P, Kang B, Chen PH, Gau J, Chen M, Tang J, Shih YH, Ding Y, Li D, Xu X, Hsiai TK. 2017. “Automated Segmentation of Light-Sheet Fluorescent Imaging to Characterize Experimental Doxorubicin-Induced Cardiac Injury and Repair.” Scientific Reports, 7: 8603.

Sideris E, Griffin D, Ding Y, Li S, Weaver W, Di Carlo D, Hsiai TK, Segura T. 2016. “Particle hydrogels based on hyaluronic acid building blocks.” ACS Biomaterials Science & Engineering, 2(11): 2034-2041.

Sung K, Ding Y, Ma J, Chen H, Huang V, Cheng M, Yang CF, Kim JT, Eguchi D, Di Carlo D, Hsiai TK, Nakano A, Kulkarni RP. 2016. “Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping.” Scientific Reports, 6: 30736.

Ma J, Luo Y, Packard RRS, Ma T, Ding Y, Abiri P, Tai YC, Zhou Q, Shung KK, Li R, Hsiai TK. 2016. “Ultrasonic transducer-guided electrochemical impedance spectroscopy to assess lipid-laden plaques.” Sensors and Actuators B: Chemical, 235: 154-161.

Fei P^†, Lee J^†, Packard RRS^†, Sereti KI, Xu H, Ma J, Ding Y, Kang H, Chen H, Sung K, Kulkarni RP, Ardehali R, Kuo CCJ, Xu X, Ho CM, Hsiai TK. 2016. “Cardiac Light-Sheet Fluorescent Microscopy for Multi-Scale and Rapid Imaging of Architecture and Function.” Scientific Reports, 6: 22489.

Jiang X, Ding Y, Wang W, Huang Z, Wang Z, de Lestrange Anginieur E, Yu Y, Li J, Pu M, Ren Q, Li C. 2016. “Developing a contact probe for rodent fundus imaging in a confocal scanning laser ophthalmoscope.” Chinese Optics Letters, 14(3): 031701.

Ding Y, Zhang M, Lang J, Leng J, Ren Q, Yang J, Li C. 2015. “In vivo study of endometriosis in mice by photoacoustic microscopy.” Journal of Biophotonics, 8(1-2): 94-101.

Wang G, Zhang B, Ding Y, He Y, Chen J, Lu Y, Jiang X, Shi J, Bai J, Ren Q, Li C. 2015. “A fluorescence molecular tomography system for multi-modality imaging.” Journal of X-ray Science and Technology, 23: 147-156.

Vuletic I^†, Liu J^†, Wu H, Ding Y, Lei Y, Sun H, Li C, Zhu D, Ren Q, Li J. 2015. “Establishment of an mKate2-expressing cell line for non-invasive real-time breast cancer in vivo imaging.” Molecular Imaging and Biology, 17(6): 811-818.

Vuletic I, Ren A, Li J, Ding Y, Li J. 2015. “Whole-body imaging of bacteria expressing mKate2 fluorescence. ” Journal of Medical and Bioengineering, 4(5): 381-385.

Tian J, Ding Y, Yang K, Ren Q. 2015. “Performance Testing and Clinical Trials of RAY-SCAN 64 PET/CT.” China Medical Devices, 30(2): 11-15.

Li S, Meng X, Zhou K, Xie Z, Ding Y, Yang K, Ren Q. 2015. “Overview of Advances in Molecular Imaging (Part1).” China Medical Devices, 30(2): 1-6.

Yu J, Yang C, Li J, Ding Y, Zhang L, Yousaf MZ, Lin J, Pang R, Wei L, Xu L, Sheng F, Li C, Li G, Zhao L, Hou Y. 2014. “Multifunctional Fe5C2 nanoparticles: a targeted theranostic platform for magnetic resonance imaging and photoacoustic tomography-guided photothermal therapy.” Advanced Materials, 26(24): 4114-4120.

Xie H, Jin D, Yu J, Peng T, Ding Y, Zhou C, Xi P. 2014 “Schlieren confocal microscopy for phase-relief imaging.” Optics Letters, 39(5): 1238-1241.

Lu Y, Yang K, Zhou K, Pang B, Wang G, Ding Y, Zhang Q, Han H, Tian J, Li C, Ren Q. 2014. “An integrated quad-modality molecular imaging system for small animal.” Journal of Nuclear Medicine, 55(8): 1375-1379.

Ding Y^†, Zhang Y^†, Peng T, Lu Y, Jin D, Ren Q, Liu Y, Han J, Xi P. 2013. “Observation of mesenteric microcirculatory disturbance in rat by laser oblique scanning optical microscopy.” Scientific Reports, 3: 1762.

Liu Y, Ding Y, Alonas E, Zhao W, Santangelo PJ, Jin D, Piper JA, Teng J, Ren Q, Xi P. 2012. “Achieving λ/10 Resolution CW STED Nanoscopy with a Ti:Sapphire Laser from a Two-photon Fluorescence Microscope.” PLoS ONE, 7(6): e40003.

Peng T, Xie H, Ding Y, Wang W, Li Z, Jin D, Tang Y, Ren Q, Xi P. 2012. “CRAFT: multimodality confocal skin imaging for early cancer diagnosis.” Journal of Biophotonics, 5(5-6): 469-476.

Ding Y, Xie H, Peng T, Lu Y, Jin D, Teng J, Ren Q, Xi P. 2012. “Laser Oblique Scanning Optical Microscopy (LOSOM) for Phase Relief Imaging.” Optics Express, 20(13): 14100-14108.

Ding Y, Xi P, Ren Q. 2011. “Hacking the optical diffraction limit: Review on recent developments of fluorescence nanoscopy.” Science Bulletin, 56(18): 1857-1876.