Publications
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
2021.
Cell. Yao, Zizhen; van Velthoven, Cindy T.J.; Nguyen, Thuc Nghi; Goldy, Jeff; Sedeno-Cortes, Adriana E.; Baftizadeh, Fahimeh; Bertagnolli, Darren; Casper, Tamara; Chiang, Megan; Crichton, Kirsten; Ding, Song-Lin; Fong, Olivia; Garren, Emma; Glandon, Alexandra; Gouwens, Nathan W.; Gray, James; Graybuck, Lucas T.; Hawrylycz, Michael J.; Hirschstein, Daniel; Kroll, Matthew; Lathia, Kanan; Lee, Changkyu; Levi, Boaz; McMillen, Delissa; Mok, Stephanie; Pham, Thanh; Ren, Qingzhong; Rimorin, Christine; Shapovalova, Nadiya; Sulc, Josef; Sunkin, Susan M.; Tieu, Michael; Torkelson, Amy; Tung, Herman; Ward, Katelyn; Dee, Nick; Smith, Kimberly A.; Tasic, Bosiljka; Zeng, Hongkui. PMID: 34004146; DOI: 10.1016/j.cell.2021.04.021A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
2021.
Nature. Yao, Zizhen; Liu, Hanqing; Xie, Fangming; Fischer, Stephan; Adkins, Ricky S.; Aldridge, Andrew I.; Ament, Seth A.; Bartlett, Anna; Behrens, M. Margarita; Van den Berge, Koen; Bertagnolli, Darren; de Bézieux, Hector Roux; Biancalani, Tommaso; Booeshaghi, A. Sina; Bravo, Héctor Corrada; Casper, Tamara; Colantuoni, Carlo; Crabtree, Jonathan; Creasy, Heather; Crichton, Kirsten; Crow, Megan; Dee, Nick; Dougherty, Elizabeth L.; Doyle, Wayne I.; Dudoit, Sandrine; Fang, Rongxin; Felix, Victor; Fong, Olivia; Giglio, Michelle; Goldy, Jeff; Hawrylycz, Mike; Herb, Brian R.; Hertzano, Ronna; Hou, Xiaomeng; Hu, Qiwen; Kancherla, Jayaram; Kroll, Matthew; Lathia, Kanan; Li, Yang Eric; Lucero, Jacinta D.; Luo, Chongyuan; Mahurkar, Anup; McMillen, Delissa; Nadaf, Naeem M.; Nery, Joseph R.; Nguyen, Thuc Nghi; Niu, Sheng-Yong; Ntranos, Vasilis; Orvis, Joshua; Osteen, Julia K.; Pham, Thanh; Pinto-Duarte, Antonio; Poirion, Olivier; Preissl, Sebastian; Purdom, Elizabeth; Rimorin, Christine; Risso, Davide; Rivkin, Angeline C.; Smith, Kimberly; Street, Kelly; Sulc, Josef; Svensson, Valentine; Tieu, Michael; Torkelson, Amy; Tung, Herman; Vaishnav, Eeshit Dhaval; Vanderburg, Charles R.; van Velthoven, Cindy; Wang, Xinxin; White, Owen R.; Huang, Z. Josh; Kharchenko, Peter V.; Pachter, Lior; Ngai, John; Regev, Aviv; Tasic, Bosiljka; Welch, Joshua D.; Gillis, Jesse; Macosko, Evan Z.; Ren, Bing; Ecker, Joseph R.; Zeng, Hongkui; Mukamel, Eran A. PMID: 34616066; DOI: 10.1038/s41586-021-03500-8An atlas of cortical arealization identifies dynamic molecular signatures
2021.
Nature. Bhaduri, Aparna; Sandoval-Espinosa, Carmen; Otero-Garcia, Marcos; Oh, Irene; Yin, Raymund; Eze, Ugomma C.; Nowakowski, Tomasz J.; Kriegstein, Arnold R. PMID: 34616070; DOI: 10.1038/s41586-021-03910-8An atlas of gene regulatory elements in adult mouse cerebrum
2021.
Nature. Li, Yang Eric; Preissl, Sebastian; Hou, Xiaomeng; Zhang, Ziyang; Zhang, Kai; Qiu, Yunjiang; Poirion, Olivier B.; Li, Bin; Chiou, Joshua; Liu, Hanqing; Pinto-Duarte, Antonio; Kubo, Naoki; Yang, Xiaoyu; Fang, Rongxin; Wang, Xinxin; Han, Jee Yun; Lucero, Jacinta; Yan, Yiming; Miller, Michael; Kuan, Samantha; Gorkin, David; Gaulton, Kyle J.; Shen, Yin; Nunn, Michael; Mukamel, Eran A.; Behrens, M. Margarita; Ecker, Joseph R.; Ren, Bing. PMID: 34616068; DOI: 10.1038/s41586-021-03604-1Comparative cellular analysis of motor cortex in human, marmoset and mouse
2021.
Nature. Bakken, Trygve E.; Jorstad, Nikolas L.; Hu, Qiwen; Lake, Blue B.; Tian, Wei; Kalmbach, Brian E.; Crow, Megan; Hodge, Rebecca D.; Krienen, Fenna M.; Sorensen, Staci A.; Eggermont, Jeroen; Yao, Zizhen; Aevermann, Brian D.; Aldridge, Andrew I.; Bartlett, Anna; Bertagnolli, Darren; Casper, Tamara; Castanon, Rosa G.; Crichton, Kirsten; Daigle, Tanya L.; Dalley, Rachel; Dee, Nick; Dembrow, Nikolai; Diep, Dinh; Ding, Song-Lin; Dong, Weixiu; Fang, Rongxin; Fischer, Stephan; Goldman, Melissa; Goldy, Jeff; Graybuck, Lucas T.; Herb, Brian R.; Hou, Xiaomeng; Kancherla, Jayaram; Kroll, Matthew; Lathia, Kanan; van Lew, Baldur; Li, Yang Eric; Liu, Christine S.; Liu, Hanqing; Lucero, Jacinta D.; Mahurkar, Anup; McMillen, Delissa; Miller, Jeremy A.; Moussa, Marmar; Nery, Joseph R.; Nicovich, Philip R.; Niu, Sheng-Yong; Orvis, Joshua; Osteen, Julia K.; Owen, Scott; Palmer, Carter R.; Pham, Thanh; Plongthongkum, Nongluk; Poirion, Olivier; Reed, Nora M.; Rimorin, Christine; Rivkin, Angeline; Romanow, William J.; Sedeño-Cortés, Adriana E.; Siletti, Kimberly; Somasundaram, Saroja; Sulc, Josef; Tieu, Michael; Torkelson, Amy; Tung, Herman; Wang, Xinxin; Xie, Fangming; Yanny, Anna Marie; Zhang, Renee; Ament, Seth A.; Behrens, M. Margarita; Bravo, Hector Corrada; Chun, Jerold; Dobin, Alexander; Gillis, Jesse; Hertzano, Ronna; Hof, Patrick R.; Höllt, Thomas; Horwitz, Gregory D.; Keene, C. Dirk; Kharchenko, Peter V.; Ko, Andrew L.; Lelieveldt, Boudewijn P.; Luo, Chongyuan; Mukamel, Eran A.; Pinto-Duarte, António; Preissl, Sebastian; Regev, Aviv; Ren, Bing; Scheuermann, Richard H.; Smith, Kimberly; Spain, William J.; White, Owen R.; Koch, Christof; Hawrylycz, Michael; Tasic, Bosiljka; Macosko, Evan Z.; McCarroll, Steven A.; Ting, Jonathan T.; Zeng, Hongkui; Zhang, Kun; Feng, Guoping; Ecker, Joseph R.; Linnarsson, Sten; Lein, Ed S. PMID: 34616062; DOI: 10.1038/s41586-021-03465-8DNA methylation atlas of the mouse brain at single-cell resolution
2021.
Nature. Liu, Hanqing; Zhou, Jingtian; Tian, Wei; Luo, Chongyuan; Bartlett, Anna; Aldridge, Andrew; Lucero, Jacinta; Osteen, Julia K.; Nery, Joseph R.; Chen, Huaming; Rivkin, Angeline; Castanon, Rosa G.; Clock, Ben; Li, Yang Eric; Hou, Xiaomeng; Poirion, Olivier B.; Preissl, Sebastian; Pinto-Duarte, Antonio; O’Connor, Carolyn; Boggeman, Lara; Fitzpatrick, Conor; Nunn, Michael; Mukamel, Eran A.; Zhang, Zhuzhu; Callaway, Edward M.; Ren, Bing; Dixon, Jesse R.; Behrens, M. Margarita; Ecker, Joseph R. PMID: 34616061; DOI: 10.1038/s41586-020-03182-8Enhancer viruses for combinatorial cell-subclass-specific labeling
2021.
Neuron. Graybuck, Lucas T.; Daigle, Tanya L.; Sedeño-Cortés, Adriana E.; Walker, Miranda; Kalmbach, Brian; Lenz, Garreck H.; Morin, Elyse; Nguyen, Thuc Nghi; 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. PMID: 33789083; DOI: 10.1016/j.neuron.2021.03.011Epigenomic diversity of cortical projection neurons in the mouse brain
2021.
Nature. Zhang, Zhuzhu; Zhou, Jingtian; Tan, Pengcheng; Pang, Yan; Rivkin, Angeline C.; Kirchgessner, Megan A.; Williams, Elora; Lee, Cheng-Ta; Liu, Hanqing; Franklin, Alexis D.; Miyazaki, Paula Assakura; Bartlett, Anna; Aldridge, Andrew I.; Vu, Minh; Boggeman, Lara; Fitzpatrick, Conor; Nery, Joseph R.; Castanon, Rosa G.; Rashid, Mohammad; Jacobs, Matthew W.; Ito-Cole, Tony; O’Connor, Carolyn; Pinto-Duartec, António; Dominguez, Bertha; Smith, Jared B.; Niu, Sheng-Yong; Lee, Kuo-Fen; Jin, Xin; Mukamel, Eran A.; Behrens, M. Margarita; Ecker, Joseph R.; Callaway, Edward M. PMID: 34616065; DOI: 10.1038/s41586-021-03223-wHuman neocortical expansion involves glutamatergic neuron diversification
2021.
Nature. Berg, Jim; Sorensen, Staci A.; Ting, Jonathan T.; Miller, Jeremy A.; Chartrand, Thomas; Buchin, Anatoly; Bakken, Trygve E.; Budzillo, Agata; Dee, Nick; Ding, Song-Lin; Gouwens, Nathan W.; Hodge, Rebecca D.; Kalmbach, Brian; Lee, Changkyu; Lee, Brian R.; Alfiler, Lauren; Baker, Katherine; Barkan, Eliza; Beller, Allison; Berry, Kyla; Bertagnolli, Darren; Bickley, Kris; Bomben, Jasmine; Braun, Thomas; Brouner, Krissy; Casper, Tamara; Chong, Peter; Crichton, Kirsten; Dalley, Rachel; de Frates, Rebecca; Desta, Tsega; Lee, Samuel Dingman; D’Orazi, Florence; Dotson, Nadezhda; Egdorf, Tom; Enstrom, Rachel; Farrell, Colin; Feng, David; Fong, Olivia; Furdan, Szabina; Galakhova, Anna A.; Gamlin, Clare; Gary, Amanda; Glandon, Alexandra; Goldy, Jeff; Gorham, Melissa; Goriounova, Natalia A.; Gratiy, Sergey; Graybuck, Lucas; Gu, Hong; Hadley, Kristen; Hansen, Nathan; Heistek, Tim S.; Henry, Alex M.; Heyer, Djai B.; Hill, DiJon; Hill, Chris; Hupp, Madie; Jarsky, Tim; Kebede, Sara; Keene, Lisa; Kim, Lisa; Kim, Mean-Hwan; Kroll, Matthew; Latimer, Caitlin; Levi, Boaz P.; Link, Katherine E.; Mallory, Matthew; Mann, Rusty; Marshall, Desiree; Maxwell, Michelle; McGraw, Medea; McMillen, Delissa; Melief, Erica; Mertens, Eline J.; Mezei, Leona; Mihut, Norbert; Mok, Stephanie; Molnar, Gabor; Mukora, Alice; Ng, Lindsay; Ngo, Kiet; Nicovich, Philip R.; Nyhus, Julie; Olah, Gaspar; Oldre, Aaron; Omstead, Victoria; Ozsvar, Attila; Park, Daniel; Peng, Hanchuan; Pham, Trangthanh; Pom, Christina A.; Potekhina, Lydia; Rajanbabu, Ramkumar; Ransford, Shea; Reid, David; Rimorin, Christine; Ruiz, Augustin; Sandman, David; Sulc, Josef; Sunkin, Susan M.; Szafer, Aaron; Szemenyei, Viktor; Thomsen, Elliot R.; Tieu, Michael; Torkelson, Amy; Trinh, Jessica; Tung, Herman; Wakeman, Wayne; Waleboer, Femke; Ward, Katelyn; Wilbers, René; Williams, Grace; Yao, Zizhen; Yoon, Jae-Geun; Anastassiou, Costas; Arkhipov, Anton; Barzo, Pal; Bernard, Amy; Cobbs, Charles; de Witt Hamer, Philip C.; Ellenbogen, Richard G.; Esposito, Luke; Ferreira, Manuel; Gwinn, Ryder P.; Hawrylycz, Michael J.; Hof, Patrick R.; Idema, Sander; Jones, Allan R.; Keene, C. Dirk; Ko, Andrew L.; Murphy, Gabe J.; Ng, Lydia; Ojemann, Jeffrey G.; Patel, Anoop P.; Phillips, John W.; Silbergeld, Daniel L.; Smith, Kimberly; Tasic, Bosiljka; Yuste, Rafael; Segev, Idan; de Kock, Christiaan P. J.; Mansvelder, Huibert D.; Tamas, Gabor; Zeng, Hongkui; Koch, Christof; Lein, Ed S. PMID: 34616067; DOI: 10.1038/s41586-021-03813-8Phenotypic variation of transcriptomic cell types in mouse motor cortex
2021.
Nature. Scala, Federico; Kobak, Dmitry; Bernabucci, Matteo; Bernaerts, Yves; Cadwell, Cathryn René; Castro, Jesus Ramon; Hartmanis, Leonard; Jiang, Xiaolong; Laturnus, Sophie; Miranda, Elanine; Mulherkar, Shalaka; Tan, Zheng Huan; Yao, Zizhen; Zeng, Hongkui; Sandberg, Rickard; Berens, Philipp; Tolias, Andreas S. PMID: 33184512; DOI: 10.1038/s41586-020-2907-3