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Hongkui Zeng

Allen Institute for Brain Science

94H-index
377Paper Count
5.5WCitation Count
Published Papers 107
Publication Date
Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
errNature
IF48.5
err2026-07-01
err0
errOAAI
errStaci A. Sorensen; Nathan W. Gouwens; Yun Wang; Matt Mallory; Agata Budzillo; Rachel Dalley; Brian R. Lee; Olga Gliko; Hsien-chi Kuo; Xiuli Kuang; Rusty Mann; Leila Ahmadinia; Lauren Alfiler; Fahimeh Baftizadeh; Katherine S. Baker; Sarah Bannick; Darren Bertagnolli; Kris Bickley; Phil Bohn; Jasmine Bomben; Chris Bowman; Gabriella Boyer; Krissy Brouner; Dillan Brown; Alex Cahoon; Natalie Chen; Chao Chen; Kai Chen; Maggie Chvilicek; Forrest Collman; Tanya L. Daigle; Tim Dawes; Rebecca de Frates; Nick Dee; Maxwell DePartee; Tom Egdorf; Laila El-Hifnawi; Rachel Enstrom; Luke Esposito; Colin Farrell; Rohan Gala; Clare Gamlin; Amanda Gary; Andrew Glomb; Olena Gerasymchuk; Jeff Goldy; Hong Gu; Kristen Hadley; Mike Hawrylycz; Alex Henry; Dijon Hill; Karla E. Hirokawa; Zili Huang; Katelyn Johnson; Zoe Juneau; Sara Kebede; Lisa Kim; Lauren Kruse; Changkyu Lee; Arielle L. Leon; Phil Lesnar; Quinn Lheureux; Anan Li; Yaoyao Li; Elizabeth Liang; Katie Link; Michelle Maxwell; Medea McGraw; Delissa A. McMillen; Alice Mukora; Lindsay Ng; Thomas Ochoa; Aaron Oldre; Daniel Park; Christina Alice Pom; Zoran Popovich; Lydia Potekhina; Ram Rajanbabu; Shea Ransford; Melissa R. Reding; Augustin Ruiz; David Sandman; Martin Schroedter; Josh Sevigny; Lyudmila Shulga; La’Akea Siverts; Cliff R. Slaughterbeck; Kimberly A. Smith; Michelle Stoecklin; Josef Sulc; Susan M. Sunkin; Michael Tieu; Jonathan T. Ting; Jessica Trinh; Ramel Velasco; Sara Vargas; Dave Vumbaco; Miranda Walker; Micheal Wang; Adrian Wanner; Jack Waters; Mirah Wells; Grace Williams; Julia A. Wilson; Wei Xiong; Ed S. Lein; Jim Berg; Brian E. Kalmbach; Shenqin Yao; Hui Gong; Qingming Luo; Quanxin Wang; Lydia Ng; Uygar Sümbül; Zizhen Yao; Tim Jarsky; Bosiljka Tasic; Hongkui Zeng
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Brain-wide topographic coordination of rotating waves
errScience
IF45.8
err2026-06-18
err0
PREAI
errZhiwen Ye; Alexander E. Ladd; Nancy MacKenzie; Ljuvica Kolich; Anna J. Li; Daniel Birman; Matthew S. Bull; Tanya L. Daigle; Bosiljka Tasic; Hongkui Zeng; Nicholas A. Steinmetz
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Genoarchitecture and input–output organization of the mouse basal ganglia and thalamic parafascicular nucleus
err2026-04-28
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errOAAI
errQuanxin Wang; Ashwin Bhandiwad; Nathan W. Gouwens; Shenqin Yao; Yun Wang; Xiuli Kuang; Anan Li; Xiangning Li; Rachel Dalley; Hsien-Chi Kuo; Phil Lesnar; Wenjie Xu; Matt Mallory; Yaoyao Li; Laila El-Hifnawi; Leila Ahmadinia; Ben Ouellette; Lauren Kruse; Lydia Ng; Hui Gong; Qingming Luo; Michael Kunst; Cindy T. J. van Velthoven; Zizhen Yao; Staci A. Sorensen; Hongkui Zeng
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Psilocybin triggers an activity-dependent rewiring of large-scale cortical networks
errCell
IF42.5
err2025-12-05
err0
PREAI
errQuan Jiang; Ling-Xiao Shao; Shenqin Yao; Neil K. Savalia; Amelia D. Gilbert; Pasha A. Davoudian; Jack D. Nothnagel; Guilian Tian; Tin Shing Hung; Hei Ming Lai; Kevin T. Beier; Hongkui Zeng; Alex C. Kwan
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Roadmap for direct and indirect translation of optogenetics into discoveries and therapies for humans
err2025-11-18
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PREAI
errChristian Lüscher; Valentina Emiliani; Nita Farahany; Aryn Gittis; Viviana Gradinaru; Katherine A. High; Botond Roska; José-Alain Sahel; Ofer Yizhar; Hongkui Zeng; Karl Deisseroth
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The new frontier in understanding human and mammalian brain development
errNature
IF48.5
err2025-11-05
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PREAI
errTomasz J. Nowakowski; Patricia R. Nano; Katherine S. Matho; Xiaoyin Chen; Emily K. Corrigan; Wubin Ding; Yuan Gao; Matthew Heffel; Jaikishan Jayakumar; Harris S. Kaplan; Fae N. Kronman; Rothem Kovner; Camiel C. A. Mannens; Mengyi Song; Marilyn R. Steyert; Sridevi Venkatesan; Jenelle L. Wallace; Li Wang; Jonathan M. Werner; Di Zhang; Guohua Yuan; Guolong Zuo; Seth A. Ament; Carlo Colantuoni; Catherine Dulac; Rong Fan; Jesse Gillis; Arnold R. Kriegstein; Fenna M. Krienen; Yongsoo Kim; Sten Linnarsson; Partha P. Mitra; Alex A. Pollen; Nenad Sestan; Daniel J. Tward; Cindy T. J. van Velthoven; Zizhen Yao; Aparna Bhaduri; Hongkui Zeng
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Transcriptomic and spatial organization of telencephalic GABAergic neurons
errNature
IF48.5
err2025-11-05
err0
errOAAI
errCindy T. J. van Velthoven; Yuan Gao; Michael Kunst; Changkyu Lee; Delissa McMillen; Anish Bhaswanth Chakka; Tamara Casper; Michael Clark; Rushil Chakrabarty; Scott Daniel; Tim Dolbeare; Rebecca Ferrer; Jessica Gloe; Jeff Goldy; Junitta Guzman; Carliana Halterman; Windy Ho; Mike J. Huang; Katelyn James; Rachel McCue; Beagan Nguy; Trangthanh Cardenas; Kara Ronellenfitch; Emma D. Thomas; Amy Torkelson; Chelsea M. Pagan; Lauren Kruse; Nick Dee; Lydia Ng; Jack Waters; Kimberly A. Smith; Bosiljka Tasic; Zizhen Yao; Hongkui Zeng
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Continuous cell-type diversification in mouse visual cortex development
errNature
IF48.5
err2025-11-05
err0
errOAAI
errYuan Gao; Cindy T. J. van Velthoven; Changkyu Lee; Emma D. Thomas; Rémi Mathieu; Angela P. Ayala; Stuard Barta; Darren Bertagnolli; Jazmin Campos; Trangthanh Cardenas; Daniel Carey; Tamara Casper; Anish Bhaswanth Chakka; Rushil Chakrabarty; Megan Chiang; Lindsey Ching; Michael Clark; Marie J. Desierto; Rebecca Ferrer; Jessica Gloe; Jeff Goldy; Nathan Guilford; Junitta Guzman; Carliana R. Halterman; Samantha D. Hastings; Daniel Hirschstein; Windy Ho; Katelyn James; Zoe Juneau; Naomi Martin; Rachel McCue; Emma Meyerdierks; Amanda C. Mitchell; Josh S. Nagra; Beagan Nguy; Thuc Nghi Nguyen; Paul Olsen; Alana A. Oyama; Nick Pena; Jacob Quon; Qingzhong Ren; Augustin Ruiz; Nadiya V. Shapovalova; Josef Sulc; Amy Torkelson; Alex Tran; Herman Tung; Nasmil Valera Cuevas; Justin Wang; Jeanelle Ariza; Delissa A. M. McMillen; Jack Waters; Michael Kunst; Kara Ronellenfitch; Boaz Levi; Michael J. Hawrylycz; Chelsea Pagan; Nick Dee; Kimberly A. Smith; Bosiljka Tasic; Zizhen Yao; Hongkui Zeng
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epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain
err2025-10-29
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errOAAI
errJosephine K. Liwang; Fae N. Kronman; Hyun-Jae Pi; Yuan-Ting Wu; Daniel J. Vanselow; Steffy B. Manjila; Deniz Parmaksiz; Donghui Shin; Yoav Ben-Simon; Michael Taormina; Sharon W. Way; Hongkui Zeng; Bosiljka Tasic; Lydia Ng; Yongsoo Kim
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Data-driven fine-grained region discovery in the mouse brain with transformers
err2025-10-07
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errOAAI
errAlex J. Lee; Alma Dubuc; Michael Kunst; Shenqin Yao; Nicholas Lusk; Lydia Ng; Hongkui Zeng; Bosiljka Tasic; Reza Abbasi-Asl
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The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales
err2025-09-30
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errOAAI
errKaitlin M. Stouffer; Xiaoyin Chen; Hongkui Zeng; Benjamin Charlier; Laurent Younes; Alain Trouvé; Michael I. Miller
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Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals
errCell
IF42.5
err2025-08-21
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errOAAI
errSimon Haziza; Radosław Chrapkiewicz; Yanping Zhang; Vasily Kruzhilin; Jane Li; Jizhou Li; Geoffroy Delamare; Rachel Swanson; György Buzsáki; Madhuvanthi Kannan; Ganesh Vasan; Michael Z. Lin; Hongkui Zeng; Tanya L. Daigle; Mark J. Schnitzer
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Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals
errCell
IF42.5
err2025-07-16
err0
errOAAI
errSimon Haziza; Radosław Chrapkiewicz; Yanping Zhang; Vasily Kruzhilin; Jane Li; Jizhou Li; Geoffroy Delamare; Rachel Swanson; György Buzsáki; Madhuvanthi Kannan; Ganesh Vasan; Michael Z. Lin; Hongkui Zeng; Tanya L. Daigle; Mark J. Schnitzer
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Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling
errCell
IF42.5
err2025-06-19
err0
errOAAI
errRichard Drexler; Antonia Drinnenberg; Avishai Gavish; Belgin Yalçin; Kiarash Shamardani; Abigail E. Rogers; Rebecca Mancusi; Vrunda Trivedi; Kathryn R. Taylor; Yoon Seok Kim; Pamelyn J. Woo; Neeraj Soni; Minhui Su; Alexandre Ravel; Eva Tatlock; Alexandra Midler; Samuel H. Wu; Charu Ramakrishnan; Ritchie Chen; Alberto E. Ayala-Sarmiento; David Rincon Fernandez Pacheco; La'Akea Siverts; Tanya L. Daigle; Bosiljka Tasic; Hongkui Zeng; Joshua J. Breunig; Karl Deisseroth; Michelle Monje
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Connectomics of predicted Sst transcriptomic types in mouse visual cortex
errNATURE
IF48.5
err2025-04-09
err5
errOAAI
errGamlin, Clare R.; Schneider-Mizell, Casey M.; Mallory, Matthew; Elabbady, Leila; Gouwens, Nathan; Williams, Grace; Mukora, Alice; Dalley, Rachel; Bodor, Agnes L.; Brittain, Derrick; Buchanan, JoAnn; Bumbarger, Daniel J.; Joyce, Emily; Kapner, Daniel; Kinn, Sam; Mahalingam, Gayathri; Seshamani, Sharmishtaa; Takeno, Marc; Torres, Russel; Yin, Wenjing; Nicovich, Philip R.; Bae, J. Alexander; Castro, Manuel A.; Dorkenwald, Sven; Halageri, Akhilesh; Jia, Zhen; Jordan, Chris; Kemnitz, Nico; Lee, Kisuk; Li, Kai; Lu, Ran; Macrina, Thomas; Mitchell, Eric; Mondal, Shanka Subhra; Mu, Shang; Nehoran, Barak; Popovych, Sergiy; Silversmith, William; Turner, Nicholas L.; Wong, William; Wu, Jingpeng; Yu, Szi-chieh; Berg, Jim; Jarsky, Tim; Lee, Brian; Seung, H. Sebastian; Zeng, Hongkui; Reid, R. Clay; Collman, Forrest; da Costa, Nuno Macarico
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Neuronal diversity and stereotypy at multiple scales through whole brain morphometry
err2024-11-26
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errOAAI
errLiu, Yufeng; Jiang, Shengdian; Zhao, Sujun; Li, Yingxin; Zhixi, Yun; Zhao, Zuo-Han; Zhang, Lingli; Wang, Gaoyu; Chen, Xin; Manubens-Gil, Linus; Hang, Yuning; Gong, Qiaobo; Li, Yuanyuan; Qian, Penghao; Qu, Lei; Garcia-Forn, Marta; Wang, Wei; De Rubeis, Silvia; Wu, Zhuhao; Osten, Pavel; Gong, Hui; Hawrylycz, Michael; Mitra, Partha; Dong, Hongwei; Luo, Qingming; Ascoli, Giorgio A.; Zeng, Hongkui; Liu, Lijuan; Peng, Hanchuan
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BRAINSTEM NEUROMODULATORY NEURONS PROMOTE GLIOMA GROWTH LOCALLY AND VIA LONG-RANGE PROJECTIONS TO MIDLINE AND CORTICAL STRUCTURES
err2024-11-11
err0
PREAI
errDrexler, Richard; Drinnenberg, Antonia; Gavish, Avishai; Yalcin, Belgin; Shamardani, Kiarash; Rogers, Abigail; Mancusi, Rebecca; Taylor, Kathryn; Kim, Yoon Seok; Woo, Pamelyn; Ravel, Alexandre; Tatlock, Eva; Jokhai, Rayyan; Ayala-Sarmiento, Alberto; Rincon-Fernandez, David; Ramakrishnan, Charu; Siverts, La'Akea; Daigle, Tanya; Tasic, Bosiljka; Zeng, Hongkui; Breunig, Joshua; Loh, Kyle; Deisseroth, Karl; Monje, Michelle
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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets (vol 20, pg 824, 2023)
err2024-08-02
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errOAAI
errManubens-Gil, Linus; Zhou, Zhi; Chen, Hanbo; Ramanathan, Arvind; Liu, Xiaoxiao; Liu, Yufeng; Bria, Alessandro; Gillette, Todd; Ruan, Zongcai; Yang, Jian; Radojevic, Miroslav; Zhao, Ting; Cheng, Li; Qu, Lei; Liu, Siqi; Bouchard, Kristofer E.; Gu, Lin; Cai, Weidong; Ji, Shuiwang; Roysam, Badrinath; Wang, Ching-Wei; Yu, Hongchuan; Sironi, Amos; Iascone, Daniel Maxim; Zhou, Jie; Bas, Erhan; Conde-Sousa, Eduardo; Aguiar, Paulo; Li, Xiang; Li, Yujie; Nanda, Sumit; Wang, Yuan; Muresan, Leila; Fua, Pascal; Ye, Bing; He, Hai-yan; Staiger, Jochen F.; Peter, Manuel; Cox, Daniel N.; Simonneau, Michel; Oberlaender, Marcel; Jefferis, Gregory; Ito, Kei; Gonzalez-Bellido, Paloma; Kim, Jinhyun; Rubel, Edwin; Cline, Hollis T.; Zeng, Hongkui; Nern, Aljoscha; Chiang, Ann-Shyn; Yao, Jianhua; Roskams, Jane; Livesey, Rick; Stevens, Janine; Liu, Tianming; Dang, Chinh; Guo, Yike; Zhong, Ning; Tourassi, Georgia; Hill, Sean; Hawrylycz, Michael; Koch, Christof; Meijering, Erik; Ascoli, Giorgio A.; Peng, Hanchuan
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High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy
err2024-07-27
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errOAAI
errGliko, Olga; Mallory, Matt; Dalley, Rachel; Gala, Rohan; Gornet, James; Zeng, Hongkui; Sorensen, Staci A.; Sumbul, Uygar
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