Publications

Founding research for our technology

Dae Hee Yun, Young-Gyun Park, Jae Hun Cho, Lee Kamentsky, Nicholas B. Evans, Alex Albanese, Katherine Xie, Justin Swaney, Chang Ho Sohn, Yuxuan Tian, Qiangge Zhang, Gabi Drummond, Webster Guan, Nicholas DiNapoli, Heejin Choi, Hae-Yoon Jung, Luzdary Ruelas, Guoping Feng, and Kwanghun Chung. “Ultrafast Immunostaining of Organ-Scale Tissues for Scalable Proteomic Phenotyping.” bioRxiv (June 2019).

Justin Swaney, Lee Kamentsky, Nicholas B Evans, Katherine Xie, Young-Gyun Park, Gabrielle Drummond, Dae Hee Yun, and Kwanghun Chung. “Scalable Image Processing Techniques for Quantitative Analysis of Volumetric Biological Images from Light-Sheet Microscopy.” bioRxiv (March 2019).

Young-Gyun Park, Chang Ho Sohn, Ritchie Chen, Margaret McCue, Dae Hee Yun, Gabrielle T. Drummond, Taeyun Ku, Nicholas B. Evans, Hayeon Caitlyn Oak, Wendy Trieu, Heejin Choi, Xin Jin, Varoth Lilascharoen, Ji Wang, Matthias C. Truttmann, Helena W. Qi , Hidde L. Ploegh, Todd R. Golub, Shih-Chi Chen, Matthew P. Frosch, Heather J. Kulik, Byung Kook Lim, and Kwanghun Chung. “Protection of Tissue Physicochemical Properties Using Polyfunctional Crosslinkers.” Nature Biotechnology 37 (December 2018).

Sung-Yon Kim, Jae Hun Cho, Evan Murray, Naveed Bakh, Heejin Choi, Kimberly Ohn, Luzdary Ruelas, Austin Hubbert, Meg McCue, Sara L. Vassallo, Philipp J. Keller, and Kwanghun Chung. “Stochastic electrotransport selectively enhances the transport of highly electromobile molecules.” PNAS (November 2015).

Taeyun Ku, Justin Swaney, Jeong-Yoon Park, Alexandre Albanese, Evan Murray, Jae Hun Cho, Young-Gyun Park, Vamsi Mangena, Jiapei Chen, and Kwanghun Chung. “Multiplexed and Scalable Super-Resolution Imaging of Three-Dimensional Protein Localization in Size-Adjustable Tissues.” Nature Biotechnology 34, no. 9 (September 2016).

Raju Tomer, Li Ye, Brian Hsueh, and Karl Deisseroth. “Advanced CLARITY for Rapid and High-Resolution Imaging of Intact Tissues.” Nature Protocols 9, no. 7 (July 2014).

Studies utilizing our technology

Lutz Menzel, Maria Zschummel, Tadhg Crowley, Vedran Franke, Michael Grau, Carolin Ulbricht, Anja Hauser, Volker Siffrin, Marc Bajénoff, Sophie E Acton, Altuna Akalin, Georg Lenz, Gerald Willimsky, Uta E Höpken, Armin Rehm. “Lymphocyte access to lymphoma is impaired by high endothelial venule regression.” Cell Reports 37, 4 (October 2021).

Nicholas N. Foster, Joshua Barry, Laura Korobkova, Luis Garcia, Lei Gao, Marlene Becerra, Yasmine Sherafat, Bo Peng, Xiangning Li, Jun-Hyeok Choi, Lin Gou, Brian Zingg, Sana Azam, Darrick Lo, Neda Khanjani, Bin Zhang, Jim Stanis, Ian Bowman, Kaelan Cotter, Chunru Cao, Seita Yamashita, Amanda Tugangui, Anan Li, Tao Jiang, Xueyan Jia, Zhao Feng, Sarvia Aquino, Hyun-Seung Mun, Muye Zhu, Anthony Santarelli, Nora L. Benavidez, Monica Song, Gordon Dan, Marina Fayzullina, Sarah Ustrell, Tyler Boesen, David L. Johnson, Hanpeng Xu, Michael S. Bienkowski, X. William Yang, Hui Gong, Michael S. Levine, Ian Wickersham, Qingming Luo, Joel D. Hahn, Byung Kook Lim, Li I. Zhang, Carlos Cepeda, Houri Hintiryan, and Hong-Wei Dong. “The Mouse Cortico-Basal Ganglia-Thalamic Network.” Nature (October 2021).

Rodrigo Muñoz-Castañeda, Brian Zingg, Katherine S. Matho, Xiaoyin Chen, Quanxin Wang, Nicholas N. Foster, Anan Li, Arun Narasimhan, Karla E. Hirokawa, Bingxing Huo, Samik Bannerjee, Laura Korobkova, Chris Sin Park, Young-Gyun Park, Michael S. Bienkowski, Uree Chon, Diek W. Wheeler, Xiangning Li, Yun Wang, Maitham Naeemi, Peng Xie, Lijuan Liu, Kathleen Kelly, Xu An, Sarojini M. Attili, Ian Bowman, Anastasiia Bludova, Ali Cetin, Liya Ding, Rhonda Drewes, Florence D’Orazi, Corey Elowsky, Stephan Fischer, William Galbavy, Lei Gao, Jesse Gillis, Peter A. Groblewski, Lin Gou, Joel D. Hahn, Joshua T. Hatfield, Houri Hintiryan, Jason Huang, Hideki Kondo, Xiuli Kuang, Philip Lesnar, Xu Li, Yaoyao Li, Mengkuan Lin, Darrick Lo, Judith Mizrachi, Stephanie Mok, Philip R. Nicovich, Ramesh Palaniswamy, Jason Palmer, Xiaoli Qi, Elise Shen, Yu-Chi Sun, Huizhong Tao, Wayne Wakemen, Yimin Wang, Shenqin Yao, Jin Yuan, Huiqing Zhan, Muye Zhu, Lydia Ng, Li I. Zhang, Byung Kook Lim, Michael Hawrylycz, Hui Gong, James C. Gee, Yongsoo Kim, Kwanghun Chung, X William Yang, Hanchuan Peng, Qingming Luo, Partha P. Mitra, Anthony M. Zador, Hongkui Zeng, Giorgio A. Ascoli, Z Josh Huang, Pavel Osten, Julie A. Harris, and Hong-Wei Dong. “Cellular Anatomy of the Mouse Primary Motor Cortex.” Nature (October 2021).

Alexander J Knights, Shanshan Liu, Yingxu Ma, Victoria S Nudell, Eric Perkey, Matthew J Sorensen, Robert T Kennedy, Ivan Maillard, Li Ye, Heejin Jun, and Jun Wu. “Acetylcholine-synthesizing macrophages in subcutaneous fat are regulated by β2-adrenergic signaling.” The EMBO Journal e106061 (August 2021).

Camilla Olianti, Francesco Giardini, Erica Lazzeri, Irene Costantini, Ludovico Silvestri, Raffaele Coppini, Elisabetta Cerbai, Francesco S. Pavone, and Leonardo Sacconi. “Optical clearing in cardiac imaging: A comparative study.” Progress in Biophysics and Molecular Biology (August 2021).

Nora L. Benavidez, Michael S. Bienkowski, Muye Zhu, Luis H. Garcia, Marina Fayzullina, Lei Gao, Ian Bowman, Lin Gou, Neda Khanjani, Kaelan R. Cotter, Laura Korobkova, Marlene Becerra, Chunru Cao, Monica Y. Song, Bin Zhang, Seita Yamashita, Amanda J. Tugangui, Brian Zingg, Kasey Rose, Darrick Lo, Nicholas N. Foster, Tyler Boesen, Hyun-Seung Mun, Sarvia Aquino, Ian R. Wickersham, Giorgio A. Ascoli, Houri Hintiryan, and Hong-Wei Dong. “Organization of the inputs and outputs of the mouse superior colliculus.” Nature Communications 12, 4004 (June 2021).

Joseph R. Luchsinger, Tracy L. Fetterly, Kellie M. Williford, Gregory J. Salimando, Marie A. Doyle, Jose Maldonado, Richard B. Simerly, Danny G. Winder, and Samuel W. Centanni. “Delineation of an insula-BNST circuit engaged by struggling behavior that regulates avoidance in mice.” Nature Communications 12, 3561 (June 2021).

Houri Hintiryan, Ian Bowman, David L. Johnson, Laura Korobkova, Muye Zhu, Neda Khanjani, Lin Gou, Lei Gao, Seita Yamashita, Michael S. Bienkowski, Luis Garcia, Nicholas N. Foster, Nora L. Benavidez, Monica Y. Song, Darrick Lo, Kaelan R. Cotter, Marlene Becerra, Sarvia Aquino, Chunru Cao, Ryan P. Cabeen, Jim Stanis, Marina Fayzullina, Sarah A. Ustrell, Tyler Boesen, Amanda J. Tugangui, Zheng-Gang Zhang, Bo Peng, Michael S. Fanselow, Peyman Golshani, Joel D. Hahn, Ian R. Wickersham, Giorgio A. Ascoli, Li I. Zhang, and Hong-Wei Dong. “Connectivity characterization of the mouse basolateral amygdalar complex.” Nature Communications 12 (May 2021).

Ashley R. Helseth, Ricardo Hernandez-Martinez, Victoria L. Hall, Matthew L. Oliver, Brandon D. Turner, Zachary F. Caffall, Joseph E. Rittiner, Miranda K. Shipman, Connor S. King, Viviana Gradinaru, Charles Gerfen, Mauro Costa-Mattioli, and Nicole Calakos. “Cholinergic neurons constitutively engage the ISR fordopamine modulation and skill learning in mice.” Science 372, Issue 6540 (April 2021).

Patrick Sweeney, Michelle N. Bedenbaugh, Jose Maldonado, Pauline Pan, Katelyn Fowler, Savannah Y. Williams, Luis E. Gimenez, Masoud Ghamari-Langroudi, Griffin Downing, Yijun Gui, Colleen K. Hadley, Stephen T. Joy, Anna K. Mapp, Richard B. Simerly, and Roger D. Cone. “The melanocortin-3 receptor is a pharmacological target for the regulation of anorexia.” Science Translational Medicine 13 (April 2021).

Ankit Bharat, Tiago N Machuca, Melissa Querrey, Chitaru Kurihara, Rafael Garza-Castillon Jr, Samuel Kim, Adwaiy Manerikar, Andres Pelaez, Mauricio Pipkin, Abbas Shahmohammadi, Mindaugas Rackauskas, Suresh Rao KG, K R Balakrishnan, Apar Jindal, Lara Schaheen, Samad Hashimi, Bhuvin Buddhdev, Ashwini Arjuna, Lorenzo Rosso, Alessandro Palleschi, Christian Lang, Peter Jaksch, G R Scott Budinger, Mario Nosotti, and Konrad Hoetzenecker. “Early Outcomes After Lung Transplantation for Severe COVID-19: A Series of the First Consecutive Cases from Four Countries.” The Lancet Respiratory Medicine (March 2021).

Alexandre Albanese, Justin M. Swaney, Dae Hee Yun, Nicholas B. Evans, Jenna M. Antonucci, Silvia Velasco, Chang Ho Sohn, Paola Arlotta, Lee Gehrke, and Kwanghun Chung. “Multiscale 3D Phenotyping of Human Cerebral Organoids.” Scientific Reports 10 (December 2020).

Ankit Bharat, Melissa Querrey, Nikolay S. Markov, Samuel Kim, Chitaru Kurihara, Rafael Garza-Castillon Adwaiy Manerikar, Ali Shilatifard, Rade Tomic, Yuliya Politanska, Hiam Abdala-Valencia, Anjana V. Yeldandi, Jon W. Lomasney, Alexander V. Misharin, and G.R. Scott Budinger. “Lung Transplantation for Patients with Severe COVID-19.” Science Translational Medicine 30 (November 2020).

Madelyn R. Lorenz, Jennifer M. Brazill, Alec Beeve, Ivana Shen, and Erica L. Scheller. “A Neuroskeletal Atlas of the Mouse Limb.” bioRxiv (September 2020).

Iliodora V. Pop, Felipe Espinosa, Megan Goyal, Bishakha Mona, Mark A. Landy, Osita W. Ogujiofor, Kevin M. Dean, Channabasavaiah B. Gurumurthy, and Helen C. Lai. “Evidence for Genetically Distinct Direct and Indirect Spinocerebellar Pathways Mediating Proprioception.” bioRxiv (August 2020).

Tzofi Klinghoffer, Peter Morales, Young-Gyun Park, Nicholas Evans, Kwanghun Chung, and Laura J. Brattain. “Self-Supervised Feature Extraction for 3D Axon Segmentation.” arXiv (April 2020).

Osita W. Ogujiofor, Iliodora V. Pop, Felipe Espinosa, Razaq O. Durodoye, Michael L. Viacheslavov, Rachel Jarvis, Mark A. Landy, Gordon Fishell, Robert P. Machold, and Helen C. Lai. “Motor Neurons Involved in Fine Motor Control Are Labeled by Tracing Atoh1-Lineage Neurons in the Spinal Cord.” bioRxiv (March 2020).

Nora L. Benavidez, Michael S. Bienkowski, Neda Khanjani, Ian Bowman, Marina Fayzullina, Luis Garcia, Lei Gao, Laura Korobkova, Lin Gou, Kaelan Cotter, Marlene Becerra, Sarvia Aquino, Chunru Cao, Nicholas N. Foster, Monica Y. Song, Bin Zhang, Seita Yamashita, Muye Zhu, Darrick Lo, Tyler Boesen, Brian Zingg, Anthony Santarelli, Ian R. Wickersham, Giorgio A. Ascoli, Houri Hintiryan, and Hong-Wei Dong. “The Mouse Cortico-Tectal Projectome.” bioRxiv (March 2020).

Jiaming Guo, Camille Artur, Tasha Womack, Jason L. Eriksen, and David Mayerich. “Multiplex Protein-Specific Microscopy with Ultraviolet Surface Excitation.” Biomedical Optics Express 11, no. 1 (January 2020).

Han-Eol Park, Dongkil Choi, Ji Su Park, Changgon Sim, Sohyun Park, Sunah Kang, Hyunsoo Lim, Myungsun Lee, Jaeyoun Kim, Jinyoung Pac, Kunsoo Rhee, Junho Lee, Yunjong Lee, Yan Lee, and Sung-Yon Kim. “Scalable and Isotropic Expansion of Tissues with Simply Tunable Expansion Ratio.” Advanced Science 1901673 (September 2019).

Eric M. Trautmann, Daniel J. O’Shea, Xulu Sun, James H. Marshel, Ailey Crow, Brian Hsueh, Sam Vesuna, Lucas Cofer, Gergő Bohner, Will Allen, Isaac Kauvar, Sean Quirin, Matthew MacDougall, Yuzhi Chen, Matthew P. Whitmire, Charu Ramakrishnan, Maneesh Sahani, Eyal Seidemann, Stephen I. Ryu, Karl Deisseroth, and Krishna V. Shenoy. “Dendritic Calcium Signals in Rhesus Macaque Motor Cortex Drive an Optical Brain-Computer Interface.” bioRxiv (September 2019).

Hideya Sakaguchi, Yuki Ozaki, Tomoka Ashida, Takayoshi Matsubara, Naotaka Oishi, Shunsuke Kihara, and Jun Takahashi. “Self-Organized Synchronous Calcium Transients in a Cultured Human Neural Network Derived from Cerebral Organoids.” Stem Cell Reports 13, no. 3 (September 2019).

Chui-Wei Wong, Hao-Wei Han, Yu-Wen Tien, and Shan-hui Hsu. “Biomaterial Substrate-Derived Compact Cellular Spheroids Mimicking the Behavior of Pancreatic Cancer and Microenvironment.” Biomaterials 213 (August 2019).

Irene Costantini, Giacomo Mazzamuto, Annunziatina Laurino, Erica Lazzeri, Leonardo Sacconi, Mattia Neri, Andrea Simonetto, Matteo Roffilli, Ludovico Silvestri, and Francesco S. Pavone. “Three-Dimensional Analysis of Human Brain Cytoarchitectonics by Means of a SWITCH/TDE-Combined Clearing Method.” Proceedings Volume 11076, Advances in Microscopic Imaging II 110760B (July 2019).

Dheeraj S. Roy, Young-Gyun Park, Sachie K. Ogawa, Jae H. Cho, Heejin Choi, Lee Kamensky, Jared Martin, Kwanghun Chung, and Susumu Tonegawa. “Brain-Wide Mapping of Contextual Fear Memory Engram Ensembles Supports the Dispersed Engram Complex Hypothesis.” bioRxiv (June 2019).

Antonia Lichtenegger, Johanna Gesperger, Barbara Kiesel, Martina Muck, Pablo Eugui, Danielle J. Harper, Matthias Salas, Marco Augustin, Conrad W. Merkle, Christoph K. Hitzenberger, Georg Widhalm, Adelheid Wöhrer, and Bernhard Baumann. “Revealing Brain Pathologies with Multimodal Visible Light Optical Coherence Microscopy and Fluorescence Imaging.” Journal of Biomedical Optics 24, no. 6 (June 2019).

Anthony J. Martorell, Abigail L. Paulson, Ho-Jun Suk, Fatema Abdurrob, Gabrielle T. Drummond, Webster Guan, Jennie Z. Young, David Nam-Woo Kim, Oleg Kritskiy, Scarlett J. Barker, Vamsi Mangena, Stephanie M. Prince, Emery N. Brown, Kwanghun Chung, Edward S. Boyden, Annabelle C. Singer, and Li-Huei Tsai. “Multi-sensory Gamma Stimulation Ameliorates Alzheimer’s-Associated Pathology and Improves Cognition.” Cell 177 (April 2019).

Turgay Saritas, Victor G. Puelles, Xiao-Tong Su, James A. McCormick, Paul A. Welling, and David H. Ellison. “Optical Clearing in the Kidney Reveals Potassium-Mediated Tubule Remodeling.” Cell Reports 25 (December 2018).

Tomoyuki Mano, Alexandre Albanese, Hans-Ulrich Dodt, Ali Erturk, Viviana Gradinaru, Jennifer B. Treweek, Atsushi Miyawaki, Kwanghun Chung, and Hiroki R. Ueda. “Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy.” Journal of Neuroscience 38, no. 44 (October 2018).

Antonia Lichtenegger, Martina Muck, Pablo Eugui, Danielle J. Harper, Marco Augustin, Konrad Leskovar, Christoph K. Hitzenberger, Adelheid Woehrer, and Bernhard Baumann. “Assessment of Pathological Features in Alzheimer’s Disease Brain Tissue with a Large Field-of-View Visible-Light Optical Coherence Microscope.” Neurophotonics 5, no. 3 (July 2018).

William E. Allen, Laura A. DeNardo, Michael Z. Chen, Cindy D. Liu, Kyle M. Loh, Lief E. Fenno, Charu Ramakrishnan, Karl Deisseroth, and Liqun Luo. “Thirst-Associated Preoptic Neurons Encode an Aversive Motivational Drive.” Science 357, no. 6356 (September 2017).

Jian Ren, Heejin Choi, Kwanghun Chung, and Brett E. Bouma. “Label-Free Volumetric Optical Imaging of Intact Murine Brains.” Scientific Reports 7, no. 46306 (April 2017).

Christina K. Kim, Avishek Adhikari, and Karl Deisseroth. “Integration of Optogenetics with Complementary Methodologies in Systems Neuroscience.” Nature Reviews Neuroscience 18, no. 4 (April 2017).

Rebecca Gail Canter, Wen-Chin Huang, Heejin Choi, Jun Wang, Lauren Ashley Watson, Christine G. Yao, Fatema Abdurrob, Stephanie M. Bousleiman, Jennie Z. Young, David A. Bennett, Ivana Delalle, Kwanghun Chung, & Li-Huei Tsai. “3D Mapping Reveals Network-specific Amyloid Progression and Subcortical Susceptibility.” bioRxiv (March 2017).