Publications
Brain-wide correspondence of neuronal epigenomics and distant projections.
Zhou J, Zhang Z, Wu M, Liu H, Pang Y, Bartlett A, Peng Z, Ding W, Rivkin A, Lagos WN, Williams E, Lee CT, Miyazaki PA, Aldridge A, Zeng Q, Salinda JLA, Claffey N, Liem M, Fitzpatrick C, Boggeman L, Yao Z, Smith KA, Tasic B, Altshul J, Kenworthy MA, Valadon C, Nery JR, Castanon RG, Patne NS, Vu M, Rashid M, Jacobs M, Ito T, Osteen J, Emerson N, Lee J, Cho S, Rink J, Huang HH, Pinto-Duartec A, Dominguez B, Smith JB, O’Connor C, Zeng H, Chen S, Lee KF, Mukamel EA, Jin X, Margarita Behrens M, Ecker JR, Callaway EM
Brain-wide correspondence of neuronal epigenomics and distant projections. Nature. 2023 Dec; 624(7991):355-365.
PMID: 38092919
Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections
Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Angeline Rivkin, Will N. Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew Aldridge, Qiurui Zeng, J.L. Angelo Salinda, Naomi Claffey, Michelle Liem, Conor Fitzpatrick, Lara Boggeman, Zizhen Yao, Kimberly A. Smith, Bosiljka Tasic, Jordan Altshul, Mia A. Kenworthy, Cynthia Valadon, Joseph R. Nery, Rosa G. Castanon, Neelakshi S. Patne, Minh Vu, Mohammad Rashid, Matthew Jacobs, Tony Ito, Julia Osteen, Nora Emerson, Jasper Lee, Silvia Cho, Jon Rink, Hsiang-Hsuan Huang, António Pinto-Duartec, Bertha Dominguez, Jared B. Smith, Carolyn O’Connor, Hongkui Zeng, Kuo-Fen Lee, Eran A. Mukamel, Xin Jin, M. Margarita Behrens, Joseph R. Ecker, Edward M. Callaway
Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections. BioRXiv. 2023 May; 10.1101/2023.05.01.538832
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.
Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2022 Mar 09; 2(3).
PMID: 35419551
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
Chongyuan Luo, Hanqing Liu, Fangming Xie, Ethan J Armand, Kimberly Siletti, Trygve E Bakken, Rongxin Fang, Wayne I Doyle, Tim Stuart, Rebecca D Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R Nery, David A Davis, Deborah C Mash, Rahul Satija, Jesse R Dixon, Sten Linnarsson, Ed Lein, M Margarita Behrens, Bing Ren, Eran A Mukamel, Joseph R Ecker
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell genomics. 2022 Mar 9;2(3):100107.
PMID: 35419551
A multimodal cell census and atlas of the mammalian primary motor cortex
Principal manuscript editors, Analysis coordination, Integrated data analysis Armand Ethan Yao Zizhen, ATAC-seq data generation and processing Fang Rongxin Hou XiaomengLucero Jacinta D. Osteen Julia K. Pinto-Duarte Antonio Poirion Olivier Preissl Sebastian Wang Xinxin , Epi-retro-seq data generation and processing Dominguez Bertha Ito-Cole Tony Jacobs Matthew Jin Xin Lee Cheng-Ta Lee Kuo-Fen Miyazaki Paula Assakura Pang Yan Rashid Mohammad Smith Jared B. Vu Minh Williams Elora, OLST/STPT and other data generation Narasimhan Arun Palaniswamy Ramesh, Morphology, connectivity and imaging analysis Banerjee Samik Ding Liya Huilgol Dhananjay Huo Bingxing Kuo Hsien-Chi Laturnus Sophie Li Xu Mitra Partha P. Mizrachi Judith Wang Quanxin Xie Peng Xiong Feng Yu Yang , Spatially resolved single-cell transcriptomics (MERFISH) Eichhorn Stephen W. Transgenic tools Allen Shona Hockemeyer Dirk Lee Angus Y. Veldman Matthew B.Brain Image Library (BIL) archive Hood Greg, DANDI archive Dichter Benjamin Grauer Michae Helba Brian, Brain Cell Data Center (BCDC) Bandrowski Anita Barkas Nikolaos Carlin Benjamin D’Orazi Florence D. Degatano Kylee Gillespie Thomas H. Khajouei Farzaneh Konwar Kishori Thompson Carol, Project management Kelly Kathleen Mok Stephanie Sunkin Susan
A multimodal cell census and atlas of the mammalian primary motor cortex Nature. 2021 Oct;598(7879):86-102.
PMID: 34616075
DNA methylation atlas of the mouse brain at single-cell resolution.
Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, Poirion OB, Preissl S, Pinto-Duarte A, O’Connor C, Boggeman L, Fitzpatrick C, Nunn M, Mukamel EA, Zhang Z, Callaway EM, Ren B, Dixon JR, Behrens MM, Ecker JR
DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 2021 10; 598(7879):120-128.
PMID: 34616061
Epigenomic diversity of cortical projection neurons in the mouse brain.
Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs MW, Ito-Cole T, O’Connor C, Pinto-Duartec A, Dominguez B, Smith JB, Niu SY, Lee KF, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM
Epigenomic diversity of cortical projection neurons in the mouse brain. Nature. 2021 10; 598(7879):167-173.
PMID: 34616065
A multimodal cell census and atlas of the mammalian primary motor cortex.
Ricky S Adkins, Andrew I Aldridge, Shona Allen, Seth A Ament, Xu An, Ethan Armand, Giorgio A Ascoli, Trygve E Bakken, Anita Bandrowski, Samik Banerjee, Nikolaos Barkas, Anna Bartlett, Helen S Bateup, M Margarita Behrens, Philipp Berens, Jim Berg, Matteo Bernabucci, Yves Bernaerts, Darren Bertagnolli, Tommaso Biancalani, Lara Boggeman, A Sina Booeshaghi, Ian Bowman, Héctor Corrada Bravo, Cathryn René Cadwell, Edward M Callaway, Benjamin Carlin, Carolyn O'Connor, Robert Carter, Tamara Casper, Rosa G Castanon, Jesus Ramon Castro, Rebecca K Chance, Apaala Chatterjee, Huaming Chen, Jerold Chun, Carlo Colantuoni, Jonathan Crabtree, Heather Creasy, Kirsten Crichton, Megan Crow, Florence D D'Orazi, Tanya L Daigle, Rachel Dalley, Nick Dee, Kylee Degatano, Benjamin Dichter, Dinh Diep, Liya Ding, Song-Lin Ding, Bertha Dominguez, Hong-Wei Dong, Weixiu Dong, Elizabeth L Dougherty, Sandrine Dudoit, Joseph R Ecker, Stephen W Eichhorn, Rongxin Fang, Victor Felix, Guoping Feng, Zhao Feng, Stephan Fischer, Conor Fitzpatrick, Olivia Fong, Nicholas N Foster, William Galbavy, James C Gee, Satrajit S Ghosh, Michelle Giglio, Thomas H Gillespie, Jesse Gillis, Melissa Goldman, Jeff Goldy, Hui Gong, Lin Gou, Michael Grauer, Yaroslav O Halchenko, Julie A Harris, Leonard Hartmanis, Joshua T Hatfield, Mike Hawrylycz, Brian Helba, Brian R Herb, Ronna Hertzano, Houri Hintiryan, Karla E Hirokawa, Dirk Hockemeyer, Rebecca D Hodge, Greg Hood, Gregory D Horwitz, Xiaomeng Hou, Lijuan Hu, Qiwen Hu, Z Josh Huang, Bingxing Huo, Tony Ito-Cole, Matthew Jacobs, Xueyan Jia, Shengdian Jiang, Tao Jiang, Xiaolong Jiang, Xin Jin, Nikolas L Jorstad, Brian E Kalmbach, Jayaram Kancherla, C Dirk Keene, Kathleen Kelly, Farzaneh Khajouei, Peter V Kharchenko, Gukhan Kim, Andrew L Ko, Dmitry Kobak, Kishori Konwar, Daniel J Kramer, Fenna M Krienen, Matthew Kroll, Xiuli Kuang, Hsien-Chi Kuo, Blue B Lake, Rachael Larsen, Kanan Lathia, Sophie Laturnus, Angus Y Lee, Cheng-Ta Lee, Kuo-Fen Lee, Ed S Lein, Phil Lesnar, Anan Li, Xiangning Li, Xu Li, Yang Eric Li, Yaoyao Li, Yuanyuan Li, Byungkook Lim, Sten Linnarsson, Christine S Liu, Hanqing Liu, Lijuan Liu, Jacinta D Lucero, Chongyuan Luo, Qingming Luo, Evan Z Macosko, Anup Mahurkar, Maryann E Martone, Katherine S Matho, Steven A McCarroll, Carrie McCracken, Delissa McMillen, Elanine Miranda
A multimodal cell census and atlas of the mammalian primary motor cortex. Biorxiv. 2020.10. 19.343129
PMID: 34616075
Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population.
Kim EJ, Zhang Z, Huang L, Ito-Cole T, Jacobs MW, Juavinett AL, Senturk G, Hu M, Ku M, Ecker JR, Callaway EM
Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. Neuron. 2020 07 22; 107(2):274-282.e6.
PMID: 32396852
Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants.
Chongyuan Luo, Hanqing Liu, Fangming Xie, Ethan J Armand, Kimberly Siletti, Trygve E Bakken, Rongxin Fang, Wayne I Doyle, Rebecca D Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R Nery, David A Davis, Deborah C Mash, Jesse R Dixon, Sten Linnarsson, Ed Lein, M Margarita Behrens, Bing Ren, Eran A Mukamel, Joseph R Ecker
Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants. Biorxiv . 2019.12. 11.873398
PMID: 35419551
Epigenetic silencing of a multifunctional plant stress regulator.
Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, Schmitz RJ, Lewsey MG, Chory J, Ecker JR
Epigenetic silencing of a multifunctional plant stress regulator. Elife. 2019 08 16; 8.
PMID: 31418686
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.
Wanamaker SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O’Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 08; 14(8):819-825.
PMID: 28650476
Functional Human Oocytes Generated by Transfer of Polar Body Genomes.
Ma H, O’Neil RC, Marti Gutierrez N, Hariharan M, Zhang ZZ, He Y, Cinnioglu C, Kayali R, Kang E, Lee Y, Hayama T, Koski A, Nery J, Castanon R, Tippner-Hedges R, Ahmed R, Van Dyken C, Li Y, Olson S, Battaglia D, Lee DM, Wu DH, Amato P, Wolf DP, Ecker JR, Mitalipov S
Functional Human Oocytes Generated by Transfer of Polar Body Genomes. Cell Stem Cell. 2017 01 05; 20(1):112-119.
PMID: 27840020
Molecular Criteria for Defining the Naive Human Pluripotent State.
Theunissen TW, Friedli M, He Y, Planet E, O’Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R
Molecular Criteria for Defining the Naive Human Pluripotent State. Cell Stem Cell. 2016 10 06; 19(4):502-515.
PMID: 27424783
Histone modifications predispose genome regions to breakage and translocation.
Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T
Histone modifications predispose genome regions to breakage and translocation. Genes Dev. 2015 Jul 01; 29(13):1393-402.
PMID: 26104467
An alternative pluripotent state confers interspecies chimaeric competency.
Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC
An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21; 521(7552):316-21.
PMID: 25945737
The accessible chromatin landscape of the human genome.
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA
The accessible chromatin landscape of the human genome. Nature. 2012 Sep 06; 489(7414):75-82.
PMID: 22955617
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011 Oct; 21(10):1757-67.
PMID: 21750106
Decreased stability of photosystem I in dgd1 mutant of Arabidopsis thaliana.
Guo J, Zhang Z, Bi Y, Yang W, Xu Y, Zhang L
Decreased stability of photosystem I in dgd1 mutant of Arabidopsis thaliana. FEBS Lett. 2005 Jul 04; 579(17):3619-24.
PMID: 15961080