Joint profiling of histone modifications and transcriptome in single cells from mouse brain
Zhu, Chenxu, Zhang, Yanxiao, Li, Yang Eric, Lucero, Jacinta, Behrens, M. Margarita, Ren, Bing
Published in Nature methods (01.03.2021)
Published in Nature methods (01.03.2021)
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Journal Article
Comparative cellular analysis of motor cortex in human, marmoset and mouse
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, Crichton, Kirsten, Daigle, Tanya L., Dalley, Rachel, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T., Herb, Brian R., Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Liu, Christine S., 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., 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.
Published in Nature (London) (07.10.2021)
Published in Nature (London) (07.10.2021)
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Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease
D’Aurizio, Romina, Catona, Orazio, Pitasi, Mattia, Li, Yang Eric, Ren, Bing, Nicolis, Silvia Kirsten
Published in International journal of molecular sciences (19.07.2022)
Published in International journal of molecular sciences (19.07.2022)
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A comparative atlas of single-cell chromatin accessibility in the human brain
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
Published in Science (American Association for the Advancement of Science) (13.10.2023)
Published in Science (American Association for the Advancement of Science) (13.10.2023)
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Droplet-based single-cell joint profiling of histone modifications and transcriptomes
Xie, Yang, Zhu, Chenxu, Wang, Zhaoning, Tastemel, Melodi, Chang, Lei, Li, Yang Eric, Ren, Bing
Published in Nature structural & molecular biology (01.10.2023)
Published in Nature structural & molecular biology (01.10.2023)
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A multimodal cell census and atlas of the mammalian primary motor cortex
Callaway, Edward M., Dong, Hong-Wei, Ecker, Joseph R., Hawrylycz, Michael J., Huang, Z. Josh, Lein, Ed S., Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A., Behrens, M. Margarita, Chun, Jerold, Feng, Guoping, Gee, James C., Ghosh, Satrajit S., Halchenko, Yaroslav O., Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E., Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J., Tickle, Timothy L., Yang, X. William, Zhang, Kun, Bakken, Trygve E., Berens, Philipp, Daigle, Tanya L., Harris, Julie A., Jorstad, Nikolas L., Kalmbach, Brian E., Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S., Mukamel, Eran A., Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T., Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L., Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D., Hu, Lijuan, Keene, C. Dirk, Krienen, Fenna M., Kroll, Matthew, Lake, Blue B., Lathia, Kanan, Linnarsson, Sten, Liu, Christine S., Macosko, Evan Z., McCarroll, Steven A., McMillen, Delissa, Nadaf, Naeem M., Nguyen, Thuc Nghi, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M., Regev, Aviv, Rimorin, Christine, Romanow, William J., Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy T. J., Vanderburg, Charles R., Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D., Osteen, Julia K., Pinto-Duarte, Antonio, Poirion, Olivier
Published in Nature (London) (07.10.2021)
Published in Nature (London) (07.10.2021)
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Journal Article
DNA methylation atlas of the mouse brain at single-cell resolution
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.
Published in Nature (London) (07.10.2021)
Published in Nature (London) (07.10.2021)
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A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
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.
Published in Nature (London) (07.10.2021)
Published in Nature (London) (07.10.2021)
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An atlas of gene regulatory elements in adult mouse cerebrum
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
Published in Nature (London) (07.10.2021)
Published in Nature (London) (07.10.2021)
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Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer
Teng, Shuaishuai, Li, Yang Eric, Yang, Ming, Qi, Rui, Huang, Yiming, Wang, Qianyu, Zhang, Yanmei, Chen, Shanwen, Li, Shasha, Lin, Kequan, Cao, Yang, Ji, Qunsheng, Gu, Qingyang, Cheng, Yujing, Chang, Zai, Guo, Wei, Wang, Pengyuan, Garcia-Bassets, Ivan, Lu, Zhi John, Wang, Dong
Published in Cell research (01.01.2020)
Published in Cell research (01.01.2020)
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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
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.
Published in Nature (London) (14.12.2023)
Published in Nature (London) (14.12.2023)
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Conserved and divergent gene regulatory programs of the mammalian neocortex
Zemke, Nathan R., Armand, Ethan J., Wang, Wenliang, Lee, Seoyeon, Zhou, Jingtian, Li, Yang Eric, Liu, Hanqing, Tian, Wei, Nery, Joseph R., Castanon, Rosa G., Bartlett, Anna, Osteen, Julia K., Li, Daofeng, Zhuo, Xiaoyu, Xu, Vincent, Chang, Lei, Dong, Keyi, Indralingam, Hannah S., Rink, Jonathan A., Xie, Yang, Miller, Michael, Krienen, Fenna M., Zhang, Qiangge, Taskin, Naz, Ting, Jonathan, Feng, Guoping, McCarroll, Steven A., Callaway, Edward M., Wang, Ting, Lein, Ed S., Behrens, M. Margarita, Ecker, Joseph R., Ren, Bing
Published in Nature (London) (14.12.2023)
Published in Nature (London) (14.12.2023)
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Single-cell analysis of chromatin accessibility in the adult mouse brain
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
Published in Nature (London) (14.12.2023)
Published in Nature (London) (14.12.2023)
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Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity
Raviram, Ramya, Raman, Anugraha, Preissl, Sebastian, Ning, Jiangfang, Wu, Shaoping, Koga, Tomoyuki, Zhang, Kai, Brennan, Cameron W, Zhu, Chenxu, Luebeck, Jens, Van Deynze, Kinsey, Han, Jee Yun, Hou, Xiaomeng, Ye, Zhen, Mischel, Anna K, Li, Yang Eric, Fang, Rongxin, Baback, Tomas, Mugford, Joshua, Han, Claudia Z, Glass, Christopher K, Barr, Cathy L, Mischel, Paul S, Bafna, Vineet, Escoubet, Laure, Ren, Bing, Chen, Clark C
Published in Proceedings of the National Academy of Sciences - PNAS (16.05.2023)
Published in Proceedings of the National Academy of Sciences - PNAS (16.05.2023)
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Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex
Zemke, Nathan R., Armand, Ethan J., Wang, Wenliang, Lee, Seoyeon, Zhou, Jingtian, Li, Yang Eric, Liu, Hanqing, Tian, Wei, Nery, Joseph R., Castanon, Rosa G., Bartlett, Anna, Osteen, Julia K., Li, Daofeng, Zhuo, Xiaoyu, Xu, Vincent, Chang, Lei, Dong, Keyi, Indralingam, Hannah S., Rink, Jonathan A., Xie, Yang, Miller, Michael, Krienen, Fenna M., Zhang, Qiangge, Taskin, Naz, Ting, Jonathan, Feng, Guoping, McCarroll, Steven A., Callaway, Edward M., Wang, Ting, Lein, Ed S., Behrens, M. Margarita, Ecker, Joseph R., Ren, Bing
Published in Nature (London) (25.01.2024)
Published in Nature (London) (25.01.2024)
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DDDR-24. INTEGRATED ANALYSIS OF SINGLE CELL CHROMATIN ACCESSIBILITY AND RNA EXPRESSION IDENTIFIED COMMON VULNERABILITY DESPITE GLIOBLASTOMA HETEROGENEITY
Raviram, Ramya, Raman, Anugraha, Preissl, Sebastian, Wu, Shaoping, Koga, Tomoyuki, Zhu, Chenxu, Luebeck, Jens, Van Deynze, Kinsey, Han, Jee Yun, Hou, Xioameng, Ye, Zhen, Mischel, Anna, Li, Yang Eric, Fang, Rongxin, Baback, Tomas, Mugford, Joshua, Han, Claudia, Glass, Christopher, Barr, Cathy, Mischel, Paul, Bafna, Vineet, Escoubet, Laura, Ren, Bing, Chen, Clark
Published in Neuro-oncology (Charlottesville, Va.) (14.11.2022)
Published in Neuro-oncology (Charlottesville, Va.) (14.11.2022)
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Comparative cellular analysis of motor cortex in human, marmoset and mouse (vol 598, pg 111, 2021)
Bakken, TE, Jorstad, NL, Hu, Q, Lake, BB, Tian, W, Kalmbach, BE, Crow, M, Hodge, RD, Krienen, FM, Sorensen, SA
Published in NATURE (07.04.2022)
Published in NATURE (07.04.2022)
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Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse
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, Crichton, Kirsten, Daigle, Tanya L., Dalley, Rachel, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T., Herb, Brian R., Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Liu, Christine S., 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., Lelieveldt, Boudewijn P., Luo, Chongyuan, Mukamel, Eran A., Pinto-Duarte, António, Preiss, 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.
Published in Nature (London) (07.04.2022)
Published in Nature (London) (07.04.2022)
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Journal Article
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
Xie, 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.
Published in Cell genomics (12.07.2023)
Published in Cell genomics (12.07.2023)
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