Publications

Journal Papers

[Google Scholar]

[23] Tajima S*, Kim YS*, Fukuda M, Jo YJ, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K+, Kato HE+.

"Structural basis for ion selectivity in potassium-selective channelrhodopsins"

Cell 186, 1–20 (2023)

[22] Hsueh B*, Chen R*, Jo YJ, Tang D, Raffiee M, Kim YS, Inoue M, Randles S, Ramakrishnan C, Patel S, Kim DK, Liu TX, Kim SH, Tan L, Mortazavi L, Cordero A, Shi J, Zhao M, Ho TT, Crow A, Yoo ACW, Raja C, Evans K, Bernstein D, Zeineh M, Goubran M, Deisseroth K. 

"Cardiogenic control of affective behavioural state" 

Nature 615, 292–299 (2023)

[21] Sylwestrak EL*+, Jo YJ*, Vesuna S*, Wang X, Holcomb B, Tien RH, Kim DK, Fenno L, Ramakrishnan C, Allen WE, Chen R, Shenoy KV, Sussillo D, Deisseroth K+.

"Cell-type-specific population dynamics of diverse reward computations"

Cell 185, 3568–3587 (2022) [Cover Article]

[20] Jo YJ*, Cho H*, Park WS*, Kim G, Ryu DH, Kim YS, Lee M, Park S, Lee MJ, Joo H, Jo HH, Lee S, Lee S, Min HS+, Heo WD+, Park YK+. 

"Label-free multiplexed microtomography of endogenous subcellular dynamics using generalizable deep learning" 

Nature Cell Biology  23, 1329–1337 (2021)

[19] Kim G, Ahn D, Kang M, Park J, Ryu DH, Jo YJ, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY+, Park YK+. 

"Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network" 

Light: Science & Applications 11, 190 (2022)

[18] Kim JM+, Jo YJ, Jung JW, Park K+.

"A mechanogenetic role for the actomyosin complex in branching morphogenesis of epithelial organs"

Development 148 (6), dev190785 (2021) [Cover Article]

[17] Lee M*, Lee YH*, Song J*, Kim G, Jo YJ, Min HS, Kim CH+, Park YK+. 

"Deep-learning-based three-dimensional label-free tracking and analysis of immunological synapses of CAR-T cells" 

eLife 9, e49023 (2020)

[16] Chang T*, Ryu DH*, Jo YJ, Choi G, Min HS, Park YK. 

"Calibration-free quantitative phase imaging using data-driven aberration modeling" 

Optics Express  28 (23), 34835–34847 (2020)

[15] Park S*, Ahn JW*, Jo YJ*, Kang HY, Kim HJ, Cheon Y, Kim JW, Park YK, Lee S+, Park K+. 

"Label-Free Tomographic Imaging of Lipid Droplets in Foam Cells for Machine-Learning-Assisted Therapeutic Evaluation of Targeted Nanodrugs"

ACS Nano 14 (2), 1856–1865 (2020) [Supplementary Cover Article]

[14] Yu D, Lee H, Hong J, Jung H, Jo YJ, Oh BH, Park BO+, Heo WD+.

"Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins"

Nature Methods 16, 1095–1100 (2019)

[13] Kim J*, Lee S*, Jung K*, Oh WC, Kim N, Son S, Jo YJ, Kwon HB+, Heo WD+.

"Intensiometric biosensors visualize the activity of multiple small GTPases in vivo"

Nature Communications 10, 211 (2019)

[12] Ryu DH, Jo YJ, Yoo J, Chang T, Ahn D, Kim YS, Kim G, Min HS, Park YK.

"Deep learning-based optical field screening for robust optical diffraction tomography" 

Scientific Reports 9, 15239 (2019)

[11] Lee J, Kim H, Cho H, Jo YJ, Song Y, Ahn D, Lee K, Park YK, Ye SJ.

"Deep-Learning-Based Label-Free Segmentation of Cell Nuclei in Time-Lapse Refractive Index Tomograms" 

IEEE Access 7, 83449–83460 (2019)

[10] Choi G*, Ryu DH*, Jo YJ, Kim YS, Park WS, Min HS, Park YK.

"Cycle-consistent deep learning approach to coherent noise reduction in optical diffraction tomography"

Optics Express 27 (4), 4927–4943 (2019)

[9] Kim G*, Jo YJ*, Cho H, Min HS, Park YK.

"Learning-based screening of hematologic disorders using quantitative phase imaging of individual red blood cells"

Biosensors and Bioelectronics 123, 69–76 (2019)

[8] Jo YJ*, Cho H*, Lee SY, Choi G, Kim G, Min HS, Park YK.

"Quantitative Phase Imaging and Artificial Intelligence: A Review" [Review]

IEEE Journal of Selected Topics in Quantum Electronics 25 (1), 6800914 (2018)

[7] Yoon J, Jo YJ, Kim YS, Yu Y, Park J, Lee S, Park WS, Park YK.

"Label-free Identification of Lymphocyte Subtypes Using Three-Dimensional Quantitative Phase Imaging and Machine Learning" [Protocol]

Journal of Visualized Experiments 141, e58305 (2018)

[6] Jo YJ*, Park S*, Jung JH, Yoon J, Joo H, Kim M, Kang SJ, Choi MC, Lee SY+, Park YK+.

"Holographic deep learning for rapid optical screening of anthrax spores"

Science Advances 3 (8), e1700606 (2017)

[5] Yoon J*, Jo YJ*, Kim M, Kim K, Lee SY, Kang SJ, Park YK.

"Identification of non-activated lymphocytes using three-dimensional refractive index tomography and machine learning"

Scientific Reports 7, 6654 (2017)

[4] Yu H, Lee P, Jo YJ, Lee KR, Tuchin VV, Jeong Y, Park YK.

"Collaborative effects of wavefront shaping and optical clearing agent in optical coherence tomography"

Journal of Biomedical Optics 21 (12), 121510 (2016)

[3] Jo YJ, Jung JH, Kim M, Park H, Kang SJ, Park YK.

"Label-free identification of individual bacteria using Fourier transform light scattering"

Optics Express 23 (12), 15792–15805 (2015) 

[2] Jo YJ, Jung JH, Lee JW, Shin D, Park H, Nam KT, Park JH, Park YK.

"Angle-resolved light scattering of individual rod-shaped bacteria based on Fourier transform light scattering"

Scientific Reports 4, 5090 (2014)

[1] Lee KR, Kim K, Jung JH, Heo JH, Cho S, Lee SY, Chang G, Jo YJ, Park H, Park YK.

"Quantitative phase imaging techniques for the study of cell pathophysiology: from principles to applications" [Review]

Sensors 13 (4), 4170–4191 (2013)

Conference Presentations

[35] Jo YJ, Wang PY, Inoue M, Drinnenberg A, Li C, Byrne EFX, 
Shenoy TC, Shi J, Kim J, Patron KA, Kim DK, Pyo KE, Andini N, Ramakrishnan C, Quirin S, Fan LZ, Kim YS, Kato HE, Deisseroth K. "KALI family channelrhodopsins: from structure-guided engineering to in vivo applications" Sculpted Light in the Brain 2024, Paris, France, 19-Jun-2024 [Selected Talk]

[34] Jo YJ*, Liu TX*, O'Shea DJ*, Shi J, Shenoy TC, Patron KA, Kim DK, Ramakrishnan C, Shenoy KV, Sussillo D, Deisseroth K. "Brain-wide neural dynamics in dynamic foraging" Computational and Systems Neuroscience (COSYNE) 2024, 2-011, Lisbon, Portugal, 1-Mar-2024 [Poster]

[33] Jo YJ*, Liu TX*, O'Shea DJ*, Shi J, Shenoy TC, Patron KA, Kim DK, Ramakrishnan C, Shenoy KV, Sussillo D, Deisseroth K. "Brain-wide neural dynamics in dynamic foraging" Janelia Conference on Bridging Diverse Perspectives on the Mechanistic Basis of Foraging, P15, Janelia Research Campus, Ashburn, VA, 26-Feb-2024 [Poster]

[32] Inoue M, Wang PY, Kim YS, Jo YJ, Burne EFX, Drinnenberg A, Quirin S, Ramakrishnan C, Lo MK, Tajima S, Kato HE, Deisseroth K. "All-optical observation and control of communication between cell-types during behavior via structure-guided design of K+-selective channelrhodopsins" Society for Neuroscience 2023, 513.23, Washington, DC, 15-Nov-2023 [Poster]

[31] Wang PY*, Drinnenberg A*, Jo YJ*, Kim YS, Inoue M, Burne EFX, Ramakrishnan C, Quirin S, Kato HE, Deisseroth K. "Two-photon optogenetics using engineered potassium-selective channelrhodopsins" Society for Neuroscience 2023, 513.21, Washington, DC, 15-Nov-2023 [Poster]

[30] Jo YJ*, Liu TX*, O'Shea DJ, Shi J, Shenoy TC, Patron KA, Kim DK, Ramakrishnan C, Shenoy KV, Sussillo D, Deisseroth K. "Brain-wide neural dynamics in dynamic foraging" Society for Neuroscience 2023, 513.20, Washington, DC, 15-Nov-2023 [Poster]

[29] Kim YS, Tajima S, Wang PY, Jo YJ, Byrne EFX, Kishi K, Ramakrishnan C, Inoue M, Kato HE, Deisseroth K. "Structural basis and neuroscience applications for selectivity and kinetic variants of potassium-selective channelrhodopsins" Society for Neuroscience 2023, 513.16, Washington, DC, 15-Nov-2023 [Poster]

[28] Kim G, Ahn D, Kang M, Park J, Ryu DH, Jo YJ, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park YK. "Rapid identification of individual bacterial pathogens using three-dimensional quantitative phase imaging and artificial neural network" SPIE Photonics West 2023, 12389-7, San Francisco, CA, 28-Jan-2023 [Talk]

[27] Chen R, Hsueh B, Tang DD, Raffiee M, Jo YJ, Kim YS, Inoue M, Ramakrishnan C, Tan L, Zeineh MM, Goubran M, Deisseroth K. "Cardiogenic control of affective behavioral states" Society for Neuroscience 2022, 499.18, San Diego, CA, 15-Nov-2022 [Poster]

[26] Jo YJ, Sylwestrak EL, Vesuna S, Quirin S, Drinnenberg A, Liu TX, Shi J, Kim DK, Ramakrishnan C, Chen R, Shenoy KV, Sussillo D, Deisseroth K. "Data-driven identification and perturbation of multi-regional and cell-type-specific neural population dynamics in reward history computation" Society for Neuroscience 2022, 499.16, San Diego, CA, 15-Nov-2022 [Poster]

[25] Kim YS, Wang PY, Byrne EFX, Jo YJ, Ramakrishnan C, Quirin S, Kato HE, Deisseroth K. "Structure-guided design of pump-like channelrhodopsins with properties enabling markedly improved optogenetic control in the brain" Society for Neuroscience 2022, 499.01, San Diego, CA, 15-Nov-2022 [Poster]

[24] Jo YJ, Cho H, Park WS, Kim G, Ryu DH, Kim YS, Lee M, Park S, Lee MJ, Joo H, Jo HH, Lee S, Lee S, Min HS, Heo WD, Park YK. "Label-free multiplexed microtomography of endogenous subcellular dynamics using generalizable deep learning" Conference on Lasers and Electro-Optics (CLEO) 2022, ATh2I.6, San Jose, CA, 19-May-2022 [Virtual Talk]

[23] Jo YJ. "Conferring biochemical specificity on quantitative phase imaging" SPIE Photonics West 2022, PC119700F, San Francisco, CA, 2-Mar-2022 [Invited Virtual Talk]

[22] Kim YS, Ahn D, Ryu DH, Cho H, Dao K, Kim K, Park JY, Yu Y, Jo YJ, Min HS, Kang SJ, Shin EC, Park YK. "Utilizing optical diffraction tomography and artificial intelligence to identify white blood cells" SPIE Photonics West 2020, 11249-87, San Francisco, CA, 3-Feb-2020 [Poster]

[21] Kim G, Ahn D, Kang M, Jo YJ, Ryu DH, Kim H, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park YK. "Rapid label-free identification of individual bacterial pathogens using optical diffraction tomography and convolutional neural network" SPIE Photonics West 2020, 11249-83, San Francisco, CA, 3-Feb-2020 [Poster]

[20] Ryu DH, Choi G, Jo YJ, Kim YS, Park WS, Min HS, Park YK. "Deep-learning-based noise reduction using unpaired dataset in optical diffraction tomography" SPIE Photonics West 2020, 11249-44, San Francisco, CA, 3-Feb-2020 [Talk]

[19] Lee M, Lee YH, Song J, Kim G, Jo YJ, Min HS, Kim CH, Park YK. "Deep learning framework enables 3D label-free tracking of immunological synapse using optical diffraction tomography" SPIE Photonics West 2020, 11249-33, San Francisco, CA, 3-Feb-2020 [Talk]

[18] Kim G, Ahn D, Kang M, Jo YJ, Ryu DH, Kim H, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park YK. "Rapid Identification of Sepsis Pathogens Using Deep Learning and Optical Diffraction Tomography" ASM Microbe 2019, P516, San Francisco, CA, 22-Jun-2019 [Poster]

[17] Chang T, Jo YJ, Min HS, Choi G, Park YK. "Compensation of aberration and noise of single quantitative phase image using deep learning" SPIE Photonics West 2019, 10887-63, San Francisco, CA, 4-Feb-2019 [Poster]

[16] Ryu DH, Choi G, Jo YJ, Kim YS, Min HS, Park YK. "Deep Learning Approach to Coherent Noise Reduction in Optical Diffraction Tomography" Annual Biophotonics Conference 2018, Tissue Biophotonics - 13, Asia Culture Center, Gwangju, Republic of Korea, 27-Oct-2018 [Poster]  *ABC 2018 Student Poster Award

[15] Chang T, Jo YJ, Min HS, Choi G, Park YK. "Deep Learning Aberration Compensation in Quantitative Phase Imaging" Annual Biophotonics Conference 2018, MIS - 24, Asia Culture Center, Gwangju, Republic of Korea, 27-Oct-2018 [Poster]

[14] Kim G, Jo YJ, Cho H, Choi G, Kim BS, Min HS, Park YK. "Automated Identification of Bacteria using Three-Dimensional Holographic Imaging and Convolutional Neural Network" IEEE Photonics Conference 2018, ME3.3, Reston, VA, 1-Oct-2018 [Talk]

[13] Park YK, Jo YJ. "Rapid and label-free optical screening of anthrax spores using quantitative phase imaging and deep neural network" ASM Microbe 2018, CPHM11-376, Atlanta, GA, 8-Jun-2018 [Poster]

[12] Jo YJ, Jung JH, Park YK. "HoloConvNet: A deep learning framework for holographic screening of anthrax spores" SPIE Photonics West 2018, 10503-70, San Francisco, CA, 29-Jan-2018 [Poster]

[11] Jo YJ, Yoon J, Park YK. "Tomographic cell type classifiers for label-free sorting of lymphocytes" SPIE Photonics West 2018, 10503-69, San Francisco, CA, 29-Jan-2018 [Poster]

[10] Park YK, Jo YJ. "Artificial intelligence and quantitative phase imaging" SPIE Photonics West 2018, 10503-20, San Francisco, CA, 29-Jan-2018 [Talk]

[9] Yoon J, Kim K, Kim M, Jo YJ, Kang SJ, Park YK. "Label-free analysis and identification of white blood cell population using optical diffraction tomography" Asia Communications and Photonics Conference 2015, ASu2A.159, Hong Kong, 22-Nov-2015 [Poster]

[8] Yu H, Lee P, Jo YJ, Jeong Y, Tuchin VV, Park YK. "Hybrid application of complex wavefront shaping optical coherence tomography and optical clearing agents for the penetration depth enhancement" Asia Communications and Photonics Conference 2015, ASu2A.158, Hong Kong, 22-Nov-2015 [Poster]

[7] Yoon J, Kim K, Kim M, Jo YJ, Kang SJ, Park YK. "Identification of white blood cell population using optical diffraction tomography" Annual Biophotonics Conference 2015, Cellular Biophotonics - 26, Korea University, Seoul, Republic of Korea, 30-Oct-2015 [Poster]

[6] Yu H, Jo YJ, Park YK. "Combined effect of complex wavefront shaping and optical clearing agent on the suppression of multiple light scattering in optical coherence tomography" SPIE Photonics West 2015, 9336-97, San Francisco, CA, 09-Feb-2015 [Poster] 

[5] Jo YJ, Jung JH, Park H, Park YK. "Single-bacterial identification based on holographic machine learning" SPIE Photonics West 2015, 9336-95, San Francisco, CA, 09-Feb-2015 [Poster] 

[4] Jo YJ, Jung JH, Park H, Park YK. "Optical holographic identification of bacterial species at the single-bacterium level" Asia Communications and Photonics Conference 2014, ATh3A.210, Shanghai, China, 13-Nov-2014 [Poster]

[3] Jo YJ, Jung JH, Park H, Park YK. "Single-bacterial profiling and identification based on quantitative phase imaging" Biophysical Society 58th Annual Meeting, 3051-Pos, San Francisco, CA, 18-Feb-2014 [Poster] 

[2] Jo YJ, Jung JH, Lee JW, Shin SA, Kim Y, Nam KT, Park JH, Park YK. "Rapid and label-free identification of individual bacterium with Fourier transform light scattering" SPIE Photonics West 2014, 8952-29, San Francisco, CA, 02-Feb-2014 [Talk]

[1] Jo YJ, Lee JW, Park JH, Park YK. "Optical diagnosis of bacteria by quantitative phase imaging techniques" SPIE 2013 Nano-Bio Sensing, Imaging & Spectroscopy, OA 1-2, Jeju, Republic of Korea, 21-Feb-2013 [Talk]