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Z

Zizhen Yao

Allen Institute for Brain Science

60H-index
151Paper Count
2.4WCitation Count
Published Papers 40
Publication Date
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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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Genoarchitecture and input–output organization of the mouse basal ganglia and thalamic parafascicular nucleus
errNature Neuroscience
IF20
err2026-04-28
err0
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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The new frontier in understanding human and mammalian brain development
errNature
IF48.5
err2025-11-05
err0
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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errSave
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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errSave
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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errSave
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
errCELL GENOMICS
IF9
err2023-07-01
err4
errOAAI
errXie, Fangming; Armand, Ethan J.; Yao, Zizhen; Liu, Hanqing; Bartlett, Anna; Behrens, M. Margarita; Li, Yang Eric; Lucero, Jacinta D.; Luo, Chongyuan; Nery, Joseph R.; Pinto-Duarte, Antonio; Poirion, Olivier B.; Preissl, Sebastian; Rivkin, Angeline C.; Tasic, Bosiljka; Zeng, Hongkui; Ren, Bing; Ecker, Joseph R.; Mukamel, Eran A.
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Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-20
err70
errOAAI
errMacQuarrie, Kyle L.; Yao, Zizhen; Fong, Abraham P.; Diede, Scott J.; Rudzinski, Erin R.; Hawkins, Douglas S.; Tapscott, Stephen J.
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Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types (vol 40, 111176, 2022)
errCELL REPORTS
IF6.9
err2022-11-01
err2
errOAAI
errNandi, Anirban; Chartrand, Thomas; Van Geit, Werner; Buchin, Anatoly; Yao, Zizhen; Lee, Soo Yeun; Wei, Yina; Kalmbach, Brian; Lee, Brian; Lein, Ed; Berg, Jim; Sumbul, Uygar; Koch, Christof; Tasic, Bosiljka; Anastassiou, Costas A.
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Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types
errCELL REPORTS
IF6.9
err2022-08-01
err14
errOAAI
errNandi, Anirban; Chartrand, Thomas; Van Geit, Werner; Buchin, Anatoly; Yao, Zizhen; Lee, Soo Yeun; Wei, Yina; Kalmbach, Brian; Lee, Brian; Lein, Ed; Berg, Jim; Sumbul, Uygar; Koch, Christof; Tasic, Bosiljka; Anastassiou, Costas A.
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Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
errELIFE
IF0
err2021-09-02
err40
errOAAI
errBakken, Trygve E.; van Velthoven, Cindy T. J.; Menon, Vilas; Hodge, Rebecca D.; Yao, Zizhen; Thuc Nghi Nguyen; Graybuck, Lucas T.; Horwitz, Gregory D.; Bertagnolli, Darren; Goldy, Jeff; Yanny, Anna Marie; Garren, Emma; Parry, Sheana; Casper, Tamara; Shehata, Soraya, I; Barkan, Eliza R.; Szafer, Aaron; Levi, Boaz P.; Dee, Nick; Smith, Kimberly A.; Sunkin, Susan M.; Bernard, Amy; Phillips, John; Hawrylycz, Michael J.; Koch, Christof; Murphy, Gabe J.; Lein, Ed; Zeng, Hongkui; Tasic, Bosiljka
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Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex
errCOMMUNICATIONS BIOLOGY
IF5.1
err2021-06-02
err22
errOAAI
errvan der Veen, Bastiaan; Kapanaiah, Sampath K. T.; Kilonzo, Kasyoka; Steele-Perkins, Peter; Jendryka, Martin M.; Schulz, Stefanie; Tasic, Bosiljka; Yao, Zizhen; Zeng, Hongkui; Akam, Thomas; Nicholson, Janet R.; Liss, Birgit; Nissen, Wiebke; Pekcec, Anton; Kaetzel, Dennis
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errSave
Enhancer viruses for combinatorial cell-subclass-specific labeling
errNEURON
IF15
err2021-05-01
err82
errOAAI
errGraybuck, Lucas T.; Daigle, Tanya L.; Sedeno-Cortes, Adriana E.; Walker, Miranda; Kalmbach, Brian; Lenz, Garreck H.; Morin, Elyse; Thuc Nghi Nguyen; Garren, Emma; Bendrick, Jacqueline L.; Kim, Tae Kyung; Zhou, Thomas; Mortrud, Marty; Yao, Shenqin; Siverts, La' Akea; Larsen, Rachael; Gore, Bryan B.; Szelenyi, Eric R.; Trader, Cameron; Balaram, Pooja; van Velthoven, Cindy T. J.; Chiang, Megan; Mich, John K.; Dee, Nick; Goldy, Jeff; Cetin, Ali H.; Smith, Kimberly; Way, Sharon W.; Esposito, Luke; Yao, Zizhen; Gradinaru, Viviana; Sunkin, Susan M.; Lein, Ed; Levi, Boaz P.; Ting, Jonathan T.; Zeng, Hongkui; Tasic, Bosiljka
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Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis
errCELL REPORTS
IF6.9
err2020-05-01
err43
errOAAI
errDing, Song-Lin; Yao, Zizhen; Hirokawa, Karla E.; Thuc Nghi Nguyen; Graybuck, Lucas T.; Fong, Olivia; Bohn, Phillip; Ngo, Kiet; Smith, Kimberly A.; Koch, Christof; Phillips, John W.; Lein, Ed S.; Harris, Julie A.; Tasic, Bosiljka; Zeng, Hongkui
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errSave
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
errELIFE
IF0
err2019-11-11
err102
errOAAI
errSmith, Stephen J.; Sumbul, Uygar; Graybuck, Lucas T.; Collman, Forrest; Seshamani, Sharmishtaa; Gala, Rohan; Gliko, Olga; Elabbady, Leila; Miller, Jeremy A.; Bakken, Trygve E.; Rossier, Jean; Yao, Zizhen; Lein, Ed; Zeng, Hongkui; Tasic, Bosiljka; Hawrylycz, Michael
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MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle
errELIFE
IF0
err2019-02-21
err61
errOAAI
errHodge, Brian A.; Zhang, Xiping; Gutierrez-Monreal, Miguel A.; Cao, Yi; Hammers, David W.; Yao, Zizhen; Wolff, Christopher A.; Du, Ping; Kemler, Denise; Judge, Andrew R.; Esser, Karyn A.
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Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation (vol 93, pg 1035, 2017)
errNEURON
IF15
err2017-11-01
err3
errOAAI
errClose, Jennie L.; Yao, Zizhen; Levi, Boaz P.; Miller, Jeremy A.; Bakken, Trygve E.; Menon, Vilas; Ting, Jonathan T.; Wall, Abigail; Krostag, Anne-Rachel; Thomsen, Elliot R.; Nelson, Angel M.; Mich, John K.; Hodge, Rebecca D.; Shehata, Soraya I.; Glass, Ian A.; Bort, Susan; Shapovalova, Nadiya V.; Ngo, N. Kiet; Grimley, Joshua S.; Phillips, John W.; Thompson, Carol L.; Ramanathan, Sharad; Lein, Ed
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errSave
The identification and functional annotation of RNA structures conserved in vertebrates
errGENOME RESEARCH
IF5.5
err2017-05-09
err68
errOAAI
errSeemann, Stefan E.; Mirza, Aashiq H.; Hansen, Claus; Bang-Berthelsen, Claus H.; Garde, Christian; Christensen-Dalsgaard, Mikkel; Torarinsson, Elfar; Yao, Zizhen; Workman, Christopher T.; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L.; Gorodkin, Jan
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errSave
Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation
errNEURON
IF15
err2017-03-01
err47
errOAAI
errClose, Jennie L.; Yao, Zizhen; Levi, Boaz P.; Miller, Jeremy A.; Bakken, Trygve E.; Menon, Vilas; Ting, Jonathan T.; Wall, Abigail; Krostag, Anne-Rachel; Thomsen, Elliot R.; Nelson, Angel M.; Mich, John K.; Hodge, Rebecca D.; Shehata, Soraya I.; Glass, Ian A.; Bort, Susan; Shapovalova, Nadiya V.; Ngo, N. Kiet; Grimley, Joshua S.; Phillips, John W.; Thompson, Carol L.; Ramanathan, Sharad; Lein, Ed
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errSave
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
errELIFE
IF0
err2017-01-23
err57
errOAAI
errGray, Lucas T.; Yao, Zizhen; Thuc Nghi Nguyen; Kim, Tae Kyung; Zeng, Hongkui; Tasic, Bosilijka
errShare
errSave
A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development
errCELL STEM CELL
IF20.4
err2017-01-01
err112
errOAAI
errYao, Zizhen; Mich, John K.; Ku, Sherman; Menon, Vilas; Krostag, Anne-Rachel; Martinez, Refugio A.; Furchtgott, Leon; Mulholland, Heather; Bort, Susan; Fuqua, Margaret A.; Gregor, Ben W.; Hodge, Rebecca D.; Jayabalu, Anu; May, Ryan C.; Melton, Samuel; Nelson, Angelique M.; Ngo, N. Kiet; Shapovalova, Nadiya V.; Shehata, Soraya I.; Smith, Michael W.; Tait, Leah J.; Thompson, Carol L.; Thomsen, Elliot R.; Ye, Chaoyang; Glass, Ian A.; Kaykas, Ajamete; Yao, Shuyuan; Phillips, John W.; Grimley, Joshua S.; Levi, Boaz P.; Wang, Yanling; Ramanathan, Sharad
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errSave

Research Directions

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Co-authors
Cooperation Journals
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Daniel H. Geschwind
H-index: 188 · Papers: 966
J
Joseph R. Ecker
H-index: 168 · Papers: 535
C
Christof Koch
H-index: 160 · Papers: 1.1K
B
Bing Ren
H-index: 131 · Papers: 543
S
Stephen M. Schwartz
H-index: 125 · Papers: 853
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