Publications

Topographic structure and function of locus coeruleus noradrenaline neurons

2026.

Nature. Su, Zhixiao; Kosillo, Polina; Jung, Kanghoon; Chen, Shuonan; Summers, Mathew T.; Piet, Alex; Hou, Han; Hagihara, Kenta M.; Friedmann, Drew; Ho-Shing, Olivia; Becker, Matthew I.; Chartrand, Thomas; Yin, Xinxin; Grotz, Peter; Hilton-VanOsdall, Ella; Lee, Margaret; Javeri, Rajvi; Tuggle, Samantha L.; Ouellette, Naveen; Myers, Holly; Baka, Judith; Laiton, Camilo; Wulf, Kaelin; Rohde, John; Buccino, Alessio P.; Arshadi, Cameron; Wang, Di; Seshamani, Sharmishtaa; Vasquez, Sonya; Eng, Carolyn M.; Ollerenshaw, Douglas R.; Dee, Nick; Casper, Tamara; Ho, Windy; Jungert, Matthew; Jordan, Atlas; Phillips, Elliot; Chakka, Anish Bhaswanth; Nasirova, Kamiliam; Blake, Krista; McCutcheon, Audrey; Koch, Megan; Vergara, Maria Camila; Smith, Kimberly A.; Jarsky, Tim; Lusk, Nicholas; Rue, Mara C. P.; Chen, Xiaoyin; Siegle, Joshua H.; Glaser, Adam K.; Lee, Brian R.; Svoboda, Karel; Isogai, Yoh; Chandrashekar, Jayaram V.; Cohen, Jeremiah Y. PMID: 42749800; DOI: 10.1038/s41586-026-11026-0

Spatial dynamics of brain development and neuroinflammation

2025.

Nature. Zhang, Di; Rubio Rodríguez-Kirby, Leslie A.; Lin, Yingxin; Wang, Wenqi; Song, Mengyi; Wang, Li; Wang, Lijun; Kanatani, Shigeaki; Jimenez-Beristain, Tony; Dang, Yonglong; Zhong, Mei; Kukanja, Petra; Bao, Shuozhen; Wang, Shaohui; Chen, Xinyi Lisa; Gao, Fu; Wang, Dejiang; Xu, Hang; Ma, Cong; Lou, Xing; Liu, Yang; Chen, Jinmiao; Sestan, Nenad; Uhlén, Per; Kriegstein, Arnold; Zhao, Hongyu; Castelo-Branco, Gonçalo; Fan, Rong. PMID: 41193846; DOI: 10.1038/s41586-025-09663-y

A comparative atlas of single-cell chromatin accessibility in the human brain

2023.

Science. Li, Yang Eric; Preissl, Sebastian; Miller, Michael; Johnson, Nicholas D.; Wang, Zihan; Jiao, Henry; Zhu, Chenxu; Wang, Zhaoning; Xie, Yang; Poirion, Olivier; Kern, Colin; Pinto-Duarte, Antonio; Tian, Wei; Siletti, Kimberly; Emerson, Nora; Osteen, Julia; Lucero, Jacinta; Lin, Lin; Yang, Qian; Zhu, Quan; Zemke, Nathan; Espinoza, Sarah; Yanny, Anna Marie; Nyhus, Julie; Dee, Nick; Casper, Tamara; Shapovalova, Nadiya; Hirschstein, Daniel; Hodge, Rebecca D.; Linnarsson, Sten; Bakken, Trygve; Levi, Boaz; Keene, C. Dirk; Shang, Jingbo; Lein, Ed; Wang, Allen; Behrens, M. Margarita; Ecker, Joseph R.; Ren, Bing. DOI: 10.1126/science.adf7044

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

2023.

Nature. Yao, Zizhen; van Velthoven, Cindy T. J.; Kunst, Michael; Zhang, Meng; McMillen, Delissa; Lee, Changkyu; Jung, Won; Goldy, Jeff; Abdelhak, Aliya; Aitken, Matthew; Baker, Katherine; Baker, Pamela; Barkan, Eliza; Bertagnolli, Darren; Bhandiwad, Ashwin; Bielstein, Cameron; Bishwakarma, Prajal; Campos, Jazmin; Carey, Daniel; Casper, Tamara; Chakka, Anish Bhaswanth; Chakrabarty, Rushil; Chavan, Sakshi; Chen, Min; Clark, Michael; Close, Jennie; Crichton, Kirsten; Daniel, Scott; DiValentin, Peter; Dolbeare, Tim; Ellingwood, Lauren; Fiabane, Elysha; Fliss, Timothy; Gee, James; Gerstenberger, James; Glandon, Alexandra; Gloe, Jessica; Gould, Joshua; Gray, James; Guilford, Nathan; Guzman, Junitta; Hirschstein, Daniel; Ho, Windy; Hooper, Marcus; Huang, Mike; Hupp, Madie; Jin, Kelly; Kroll, Matthew; Lathia, Kanan; Leon, Arielle; Li, Su; Long, Brian; Madigan, Zach; Malloy, Jessica; Malone, Jocelin; Maltzer, Zoe; Martin, Naomi; McCue, Rachel; McGinty, Ryan; Mei, Nicholas; Melchor, Jose; Meyerdierks, Emma; Mollenkopf, Tyler; Moonsman, Skyler; Nguyen, Thuc Nghi; Otto, Sven; Pham, Trangthanh; Rimorin, Christine; Ruiz, Augustin; Sanchez, Raymond; Sawyer, Lane; Shapovalova, Nadiya; Shepard, Noah; Slaughterbeck, Cliff; Sulc, Josef; Tieu, Michael; Torkelson, Amy; Tung, Herman; Valera Cuevas, Nasmil; Vance, Shane; Wadhwani, Katherine; Ward, Katelyn; Levi, Boaz; Farrell, Colin; Young, Rob; Staats, Brian; Wang, Ming-Qiang Michael; Thompson, Carol L.; Mufti, Shoaib; Pagan, Chelsea M.; Kruse, Lauren; Dee, Nick; Sunkin, Susan M.; Esposito, Luke; Hawrylycz, Michael J.; Waters, Jack; Ng, Lydia; Smith, Kimberly; Tasic, Bosiljka; Zhuang, Xiaowei; Zeng, Hongkui. DOI: 10.1038/s41586-023-06812-z

A single-cell genomic atlas for maturation of the human cerebellum during early childhood

2023.

Science Translational Medicine. Ament, Seth A.; Cortes-Gutierrez, Marcia; Herb, Brian R.; Mocci, Evelina; Colantuoni, Carlo; McCarthy, Margaret M. DOI: 10.1126/scitranslmed.ade1283

A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

2023.

Nature. Winter, Carla C.; Jacobi, Anne; Su, Junfeng; Chung, Leeyup; van Velthoven, Cindy T. J.; Yao, Zizhen; Lee, Changkyu; Zhang, Zicong; Yu, Shuguang; Gao, Kun; Duque Salazar, Geraldine; Kegeles, Evgenii; Zhang, Yu; Tomihiro, Makenzie C.; Zhang, Yiming; Yang, Zhiyun; Zhu, Junjie; Tang, Jing; Song, Xuan; Donahue, Ryan J.; Wang, Qing; McMillen, Delissa; Kunst, Michael; Wang, Ning; Smith, Kimberly A.; Romero, Gabriel E.; Frank, Michelle M.; Krol, Alexandra; Kawaguchi, Riki; Geschwind, Daniel H.; Feng, Guoping; Goodrich, Lisa V.; Liu, Yuanyuan; Tasic, Bosiljka; Zeng, Hongkui; He, Zhigang. DOI: 10.1038/s41586-023-06817-8

Comparative transcriptomics reveals human-specific cortical features

2023.

Science. Jorstad, Nikolas L.; Song, Janet H. T.; Exposito-Alonso, David; Suresh, Hamsini; Castro-Pacheco, Nathan; Krienen, Fenna M.; Yanny, Anna Marie; Close, Jennie; Gelfand, Emily; Long, Brian; Seeman, Stephanie C.; Travaglini, Kyle J.; Basu, Soumyadeep; Beaudin, Marc; Bertagnolli, Darren; Crow, Megan; Ding, Song-Lin; Eggermont, Jeroen; Glandon, Alexandra; Goldy, Jeff; Kiick, Katelyn; Kroes, Thomas; McMillen, Delissa; Pham, Trangthanh; Rimorin, Christine; Siletti, Kimberly; Somasundaram, Saroja; Tieu, Michael; Torkelson, Amy; Feng, Guoping; Hopkins, William D.; Höllt, Thomas; Keene, C. Dirk; Linnarsson, Sten; McCarroll, Steven A.; Lelieveldt, Boudewijn P.; Sherwood, Chet C.; Smith, Kimberly; Walsh, Christopher A.; Dobin, Alexander; Gillis, Jesse; Lein, Ed S.; Hodge, Rebecca D.; Bakken, Trygve E. DOI: 10.1126/science.ade9516

Interindividual variation in human cortical cell type abundance and expression

2023.

Science. Johansen, Nelson; Somasundaram, Saroja; Travaglini, Kyle J.; Yanny, Anna Marie; Shumyatcher, Maya; Casper, Tamara; Cobbs, Charles; Dee, Nick; Ellenbogen, Richard; Ferreira, Manuel; Goldy, Jeff; Guzman, Junitta; Gwinn, Ryder; Hirschstein, Daniel; Jorstad, Nikolas L.; Keene, C. Dirk; Ko, Andrew; Levi, Boaz P.; Ojemann, Jeffrey G.; Pham, Thanh; Shapovalova, Nadiya; Silbergeld, Daniel; Sulc, Josef; Torkelson, Amy; Tung, Herman; Smith, Kimberly; Lein, Ed S.; Bakken, Trygve E.; Hodge, Rebecca D.; Miller, Jeremy A. PMID: 37824649; DOI: 10.1126/science.adf2359

Single-cell analysis of chromatin accessibility in the adult mouse brain

2023.

Nature. Zu, Songpeng; Li, Yang Eric; Wang, Kangli; Armand, Ethan J.; Mamde, Sainath; Amaral, Maria Luisa; Wang, Yuelai; Chu, Andre; Xie, Yang; Miller, Michael; Xu, Jie; Wang, Zhaoning; Zhang, Kai; Jia, Bojing; Hou, Xiaomeng; Lin, Lin; Yang, Qian; Lee, Seoyeon; Li, Bin; Kuan, Samantha; Liu, Hanqing; Zhou, Jingtian; Pinto-Duarte, Antonio; Lucero, Jacinta; Osteen, Julia; Nunn, Michael; Smith, Kimberly A.; Tasic, Bosiljka; Yao, Zizhen; Zeng, Hongkui; Wang, Zihan; Shang, Jingbo; Behrens, M. Margarita; Ecker, Joseph R.; Wang, Allen; Preissl, Sebastian; Ren, Bing. DOI: 10.1038/s41586-023-06824-9

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

2023.

Nature. Liu, Hanqing; Zeng, Qiurui; Zhou, Jingtian; Bartlett, Anna; Wang, Bang-An; Berube, Peter; Tian, Wei; Kenworthy, Mia; Altshul, Jordan; Nery, Joseph R.; Chen, Huaming; Castanon, Rosa G.; Zu, Songpeng; Li, Yang Eric; Lucero, Jacinta; Osteen, Julia K.; Pinto-Duarte, Antonio; Lee, Jasper; Rink, Jon; Cho, Silvia; Emerson, Nora; Nunn, Michael; O’Connor, Carolyn; Wu, Zhanghao; Stoica, Ion; Yao, Zizhen; Smith, Kimberly A.; Tasic, Bosiljka; Luo, Chongyuan; Dixon, Jesse R.; Zeng, Hongkui; Ren, Bing; Behrens, M. Margarita; Ecker, Joseph R. DOI: 10.1038/s41586-023-06805-y