Bing Ren

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 92

Top Venues

Nature

Nature methods

Nature communications

Nature biotechnology

Ludwig Institute for Cancer Research

Harvard University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Ludwig Institute for Cancer Research Oct 01 2001

United States

Member

Education History

Harvard University Sep 01 1992 - Jun 01 1998

United States

PHD :: Molecular and Cellular Biology

Publications

Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Nathan Daniel Jayne, Zhengyu Liang, Do-Hwan Lim, Poshen Benson Chen, Cristina Diaz, Kei-Ichiro Arimoto, Lingbo Xia, Mengdan Liu, Bing Ren, Xiang-Dong Fu, Dong-Er Zhang
RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks. Blood advances 8 (10) (2024)
Jie Xu, Bing Ren
Built to be imperfect. Nature cell biology 26 (8) (2024)
Nathan Daniel Jayne, Zhengyu Liang, Do-Hwan Lim, Poshen Benson Chen, Cristina Diaz, Kei-Ichiro Arimoto, Lingbo Xia, Mengdan Liu, Bing Ren, Xiang-Dong Fu, Dong-Er Zhang
RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks. Blood advances 8 (10) (2024)
Nathan R Zemke, Ethan J Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R Nery, Rosa Gomez Castanon, Anna Bartlett, Julia K Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S Indralingam, Jonathan A Rink, Yang Xie, Michael Miller, Fenna M Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A McCarroll, Edward M Callaway, Ting Wang, Ed S Lein, M Margarita Behrens, Joseph R Ecker, Bing Ren
Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature (2024)
Ibai Irastorza-Azcarate, Alexander Kukalev, Rieke Kempfer, Christoph J Thieme, Guido Mastrobuoni, Julia Markowski, Gesa Loof, Thomas M Sparks, Emily Brookes, Kedar Nath Natrajan, Stephan Sauer, Amanda G Fisher, Mario Nicodemi, Bing Ren, Roland F Schwarz, Stefan Kempa, Ana Pombo
Extensive folding variability between homologous chromosomes in mammalian cells. bioRxiv : the preprint server for biology (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods (2024)
Elena M Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V Strunnikov, Bing Ren, Victor V Lobanenkov
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome biology 25 (1) (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods (2024)
Nelson J Johansen, Niklas Kempynck, Nathan R Zemke, Saroja Somasundaram, Seppe De Winter, Marcus J Hooper, Deepanjali Dwivedi, Ruchi Lohia, Fabien Wehbe, Bocheng Li, Darina Abaffyová, Ethan J Armand, Julie De Man, Eren Can Eksi, Nikolai Hecker, Gert Hulselmans, Vasileios Konstantakos, David Mauduit, John K Mich, Gabriele Partel, Tanya L Daigle, Boaz P Levi, Kai Zhang, Yoshiaki Tanaka, Jonathan M Werner, Jonathan T Ting, Yoav Ben-Simon, Jeremy A Miller, Joseph R Ecker, Bing Ren, Stein Aerts, Ed S Lein, Bosiljka Tasic, Trygve E Bakken
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv : the preprint server for biology (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods (2024)
Jie Xu, Bing Ren
Built to be imperfect. Nature cell biology (2024)
Elena M Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V Strunnikov, Bing Ren, Victor V Lobanenkov
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome biology 25 (1) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Nathan Daniel Jayne, Zhengyu Liang, Do-Hwan Lim, Poshen Benson Chen, Cristina Diaz, Kei-Ichiro Arimoto, Lingbo Xia, Mengdan Liu, Bing Ren, Xiang-Dong Fu, Dong-Er Zhang
RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks. Blood advances 8 (10) (2024)
Elena M Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V Strunnikov, Bing Ren, Victor V Lobanenkov
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome biology 25 (1) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Elie N Farah, Robert K Hu, Colin Kern, Qingquan Zhang, Ting-Yu Lu, Qixuan Ma, Shaina Tran, Bo Zhang, Daniel Carlin, Alexander Monell, Andrew P Blair, Zilu Wang, Jacqueline Eschbach, Bin Li, Eugin Destici, Bing Ren, Sylvia M Evans, Shaochen Chen, Quan Zhu, Neil C Chi
Spatially organized cellular communities form the developing human heart. Nature 627 (8005) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods (2024)
Nathan Daniel Jayne, Zhengyu Liang, Do-Hwan Lim, Poshen Benson Chen, Cristina Diaz, Kei-Ichiro Arimoto, Lingbo Xia, Mengdan Liu, Bing Ren, Xiang-Dong Fu, Dong-Er Zhang
RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks. Blood advances 8 (10) (2024)
Elena M Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V Strunnikov, Bing Ren, Victor V Lobanenkov
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome biology 25 (1) (2024)
Kai Zhang, Nathan R Zemke, Ethan J Armand, Bing Ren
A fast, scalable and versatile tool for analysis of single-cell omics data. Nature methods 21 (2) (2024)
Kyle J Gaulton, Sebastian Preissl, Bing Ren
Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nature reviews. Genetics (2023)
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah C Johnsen, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek K Arora, David B Solit, Byron H Lee
KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer. Cancer research 83 (6) (2023)
Bojing Blair Jia, Adam Jussila, Colin Kern, Quan Zhu, Bing Ren
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature biotechnology (2023)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng, Chongyuan Luo, Jesse R Dixon, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. bioRxiv : the preprint server for biology (2023)
Shiwei Liu, Pu Zheng, Cosmos Yuqi Wang, Bojing Blair Jia, Nathan R Zemke, Bing Ren, Xiaowei Zhuang
Cell-type-specific 3D-genome organization and transcription regulation in the brain. bioRxiv : the preprint server for biology (2023)
Nathan R Zemke, Ethan J Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R Nery, Rosa Gomez Castanon, Anna Bartlett, Julia K Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S Indralingam, Jonathan A Rink, Yang Xie, Michael Miller, Fenna M Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A McCarroll, Edward M Callaway, Ting Wang, Ed S Lein, M Margarita Behrens, Joseph R Ecker, Bing Ren
Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 624 (7991) (2023)
Kyle J Gaulton, Sebastian Preissl, Bing Ren
Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nature reviews. Genetics (2023)
Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, António Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren
Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature 624 (7991) (2023)
Bojing Blair Jia, Adam Jussila, Colin Kern, Quan Zhu, Bing Ren
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature biotechnology (2023)
Riccardo Calandrelli, Xingzhao Wen, John Lalith Charles Richard, Zhifei Luo, Tri C Nguyen, Chien-Ju Chen, Zhijie Qi, Shuanghong Xue, Weizhong Chen, Zhangming Yan, Weixin Wu, Kathia Zaleta-Rivera, Rong Hu, Miao Yu, Yuchuan Wang, Wenbo Li, Jian Ma, Bing Ren, Sheng Zhong
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nature communications 14 (1) (2023)
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah C Johnsen, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek K Arora, David B Solit, Byron H Lee
KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and drives cell proliferation in bladder cancer. Cancer research (2023)
Bojing Blair Jia, Adam Jussila, Colin Kern, Quan Zhu, Bing Ren
Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature biotechnology (2023)
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah C Johnsen, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek K Arora, David B Solit, Byron H Lee
KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer. Cancer research 83 (6) (2023)
Bojing Blair Jia, Adam Jussila, Colin Kern, Quan Zhu, Bing Ren
Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature biotechnology (2023)
Wei Tian, Jingtian Zhou, Anna Bartlett, Qiurui Zeng, Hanqing Liu, Rosa Gomez Castanon, Mia Kenworthy, Jordan Altshul, Cynthia Valadon, Andrew I Aldridge, Joseph R Nery, Huaming Chen, Jiaying Xu, Nicholas D Johnson, Jacinta Lucero, Julia K Osteen, Nora Emerson, Jonathan A Rink, Jasper Lee, Yang Eric Li, Kimberly Siletti, Michelle Liem, Naomi Claffey, Carolyn O'Connor, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya V Shapovalova, Daniel Hirschstein, Song-Lin Ding, Rebecca D Hodge, Boaz P Levi, C Dirk Keene, Sten Linnarsson, Ed S Lein, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA methylation and 3D genome architecture in the human brain. Science (New York, N.Y.) 382 (6667) (2023)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng, Chongyuan Luo, Jesse R Dixon, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. bioRxiv : the preprint server for biology (2023)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jonathan A Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R Dixon, Hongkui Zeng, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature 624 (7991) (2023)
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah C Johnsen, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek K Arora, David B Solit, Byron H Lee
KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer. Cancer research 83 (6) (2023)
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah C Johnsen, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek K Arora, David B Solit, Byron H Lee
KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer. Cancer research 83 (6) (2023)
Yang Xie, Chenxu Zhu, Zhaoning Wang, Melodi Tastemel, Lei Chang, Yang Eric Li, Bing Ren
Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nature structural & molecular biology (2023)
Yang Eric Li, Sebastian Preissl, Michael Miller, Nicholas D Johnson, Zihan Wang, Henry Jiao, Chenxu Zhu, Zhaoning Wang, Yang Xie, Olivier B Poirion, Colin Kern, António Pinto-Duarte, Wei Tian, Kimberly Siletti, Nora Emerson, Julia Osteen, Jacinta Lucero, Lin Lin, Qian Yang, Quan Zhu, Nathan R Zemke, Sarah Espinoza, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya V Shapovalova, Daniel Hirschstein, Rebecca D Hodge, Sten Linnarsson, Trygve E Bakken, Boaz P Levi, C Dirk Keene, Jingbo Shang, Ed S Lein, Allen Wang, M Margarita Behrens, Joseph R Ecker, Bing Ren
A comparative atlas of single-cell chromatin accessibility in the human brain. Science (New York, N.Y.) 382 (6667) (2023)
Bojing Blair Jia, Adam Jussila, Colin Kern, Quan Zhu, Bing Ren
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature biotechnology (2023)
Shiwei Liu, Pu Zheng, Cosmos Yuqi Wang, Bojing Blair Jia, Nathan R Zemke, Bing Ren, Xiaowei Zhuang
Cell-type-specific 3D-genome organization and transcription regulation in the brain. bioRxiv : the preprint server for biology (2023)
Romina D'Aurizio, Orazio Catona, Mattia Pitasi, Yang Eric Li, Bing Ren, Silvia Kirsten Nicolis
Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease. International journal of molecular sciences 23 (14) (2022)
Zhipeng Meng, Fu-Long Li, Cao Fang, Benjamin Yeoman, Yunjiang Qiu, Ying Wang, Xiaomin Cai, Kimberly C Lin, Di Yang, Min Luo, Vivian Fu, Xiaoxiao Ma, Yarui Diao, Filippo G Giancotti, Bing Ren, Adam J Engler, Kun-Liang Guan
The Hippo pathway mediates Semaphorin signaling. Science advances 8 (21) (2022)
Sebastian Preissl, Kyle J Gaulton, Bing Ren
Characterizing cis-regulatory elements using single-cell epigenomics. Nature reviews. Genetics (2022)
Jian Yan, Yunjiang Qiu, André M Ribeiro Dos Santos, Yimeng Yin, Yang Eric Li, Nick Vinckier, Naoki Nariai, Paola Benaglio, Anugraha Raman, Xiaoyu Li, Shicai Fan, Joshua Chiou, Fulin Chen, Kelly A Frazer, Kyle J Gaulton, Bjoern Gaertner, Jussi Taipale, Bing Ren
Systematic analysis of binding of transcription factors to noncoding variants. Nature 591 (7848) (2021)
Chenxu Zhu, Yanxiao Zhang, Yang Eric Li, Jacinta Lucero, M Margarita Behrens, Bing Ren
Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nature methods 18 (3) (2021)
Qi-Ling Zhou, Miao Yu, Roberto Tirado-Magallanes, Bin Li, Lingshi Kong, Mingrui Guo, Zi Hui Tan, Sanghoon Lee, Li Chai, Akihiko Numata, Touati Benoukraf, Melissa Jane Fullwood, Motomi Osato, Bing Ren, Daniel Geoffrey Tenen
ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nature communications 12 (1) (2021)
Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Xinzhu Zhou, Fangming Xie, Eran A Mukamel, Kai Zhang, Yanxiao Zhang, M Margarita Behrens, Joseph R Ecker, Bing Ren
Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature communications 12 (1) (2021)
James D Hocker, Olivier B Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang Eric Li, Yanxiao Zhang, Elie N Farah, Allen Wang, Andrew D McCulloch, Kyle J Gaulton, Bing Ren, Neil C Chi, Sebastian Preissl
Cardiac cell type-specific gene regulatory programs and disease risk association. Science advances 7 (20) (2021)
Hui Huang, Quan Zhu, Adam Jussila, Yuanyuan Han, Bogdan Bintu, Colin Kern, Mattia Conte, Yanxiao Zhang, Simona Bianco, Andrea Maria Chiariello, Miao Yu, Rong Hu, Melodi Tastemel, Ivan Juric, Ming Hu, Mario Nicodemi, Xiaowei Zhuang, Bing Ren
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains. Nature genetics 53 (7) (2021)
Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian R Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova, Tsz Wai Tam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, Bing Ren, Wei Wang, Yin Shen
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science advances 7 (38) (2021)
Ryan J Geusz, Allen Wang, Dieter K Lam, Nicholas K Vinckier, Konstantinos-Dionysios Alysandratos, David A Roberts, Jinzhao Wang, Samy Kefalopoulou, Araceli Ramirez, Yunjiang Qiu, Joshua Chiou, Kyle J Gaulton, Bing Ren, Darrell N Kotton, Bjoern Gaertner
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nature communications 12 (1) (2021)
Trygve E Bakken, Nikolas L Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian E Kalmbach, Megan Crow, Rebecca D Hodge, Fenna M Krienen, Staci A Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D Aevermann, Andrew I Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G Castanon, Kirsten Crichton, Tanya L Daigle, Rachel Dalley, Nick Dee, Nikolai C Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T Gray, Brian R Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S Liu, Hanqing Liu, Jacinta D Lucero, Anup A Mahurkar, Delissa McMillen, Jeremy A Miller, Marmar Moussa, Joseph R Nery, Philip R Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K Osteen, Scott Owen, Carter R Palmer, Trangthanh H Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M Reed, Christine Rimorin, Angeline Rivkin, William J Romanow, Adriana E Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R Hof, Thomas Höllt, Gregory D Horwitz, C Dirk Keene, Peter V Kharchenko, Andrew L Ko, Boudewijn P F Lelieveldt, Chongyuan Luo, Eran A Mukamel, António Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly A Smith, William J Spain, Owen R White, Christof Koch, Michael J Hawrylycz, Bosiljka Tasic, Evan Z Macosko, Steven A McCarroll, Jonathan T Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R Ecker, Sten Linnarsson, Ed S Lein
Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598 (7879) (2021)
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldridge, Seth A Ament, Anna Bartlett, M Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bezieux, Tommaso Biancalani, Ali Sina Booeshaghi, Héctor Corrada Bravo, Tamara Casper, Carlo Colantuoni, Jonathan Crabtree, Heather H Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle G Giglio, Jeff Goldy, Michael J Hawrylycz, Brian R Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D Lucero, Chongyuan Luo, Anup A Mahurkar, Delissa McMillen, Naeem M Nadaf, Joseph R Nery, Thuc Nghi Nguyen, Sheng-Yong Niu, Vasilis Ntranos, Joshua Orvis, Julia K Osteen, Trangthanh H Pham, António Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C Rivkin, Kimberly A Smith, Kelly Street, Josef Sulc, Valentine Svensson, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Charles R Vanderburg, Cindy T J van Velthoven, Xinxin Wang, Owen R White, Z Josh Huang, Peter V Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D Welch, Jesse Gillis, Evan Z Macosko, Bing Ren, Joseph R Ecker, Hongkui Zeng, Eran A Mukamel
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598 (7879) (2021)
Naoki Kubo, Haruhiko Ishii, Xiong Xiong, Simona Bianco, Franz Meitinger, Rong Hu, James D Hocker, Mattia Conte, David U Gorkin, Miao Yu, Bin Li, Jesse R Dixon, Ming Hu, Mario Nicodemi, Huimin Zhao, Bing Ren
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nature structural & molecular biology 28 (2) (2021)
Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier B Poirion, Bin Li, Joshua Chiou, Hanqing Liu, António Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Michael Miller, Samantha Kuan, David Gorkin, Kyle J Gaulton, Yin Shen, Michael Nunn, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker, Bing Ren
An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598 (7879) (2021)
Miao Yu, Armen Abnousi, Yanxiao Zhang, Guoqiang Li, Lindsay Lee, Ziyin Chen, Rongxin Fang, Taylor M Lagler, Yuchen Yang, Jia Wen, Quan Sun, Yun Li, Bing Ren, Ming Hu
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nature methods 18 (9) (2021)
Hanqing Liu, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew I Aldridge, Jacinta Lucero, Julia K Osteen, Joseph R Nery, Huaming Chen, Angeline Rivkin, Rosa G Castanon, Ben Clock, Yang Eric Li, Xiaomeng Hou, Olivier B Poirion, Sebastian Preissl, António Pinto-Duarte, Carolyn O'Connor, Lara Boggeman, Conor Fitzpatrick, Michael Nunn, Eran A Mukamel, Zhuzhu Zhang, Edward M Callaway, Bing Ren, Jesse R Dixon, M Margarita Behrens, Joseph R Ecker
DNA methylation atlas of the mouse brain at single-cell resolution. Nature 598 (7879) (2021)
Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A Williams, Diane Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker
Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature 583 (7818) (2020)
null null, Michael Paul Snyder, Thomas R Gingeras, Jill E Moore, Zhiping Weng, Mark B Gerstein, Bing Ren, Ross Cameron Hardison, John A Stamatoyannopoulos, Brenton R Graveley, Elise A Feingold, Michael J Pazin, Michael Pagan, Daniel A Gilchrist, Benjamin C Hitz, J Michael Cherry, Bradley E Bernstein, Eric M Mendenhall, Daniel R Zerbino, Adam Frankish, Paul Flicek, Richard M Myers
Perspectives on ENCODE. Nature 583 (7818) (2020)
Qiancheng You, Anthony Youzhi Cheng, Xi Gu, Bryan T Harada, Miao Yu, Tong Wu, Bing Ren, Zhengqing Ouyang, Chuan He
Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nature biotechnology 39 (2) (2020)
null null, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John L Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael Paul Snyder, Bradley E Bernstein, Barbara Wold, Ross Cameron Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Nishigandha Phalke
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583 (7818) (2020)
Ofer Shoshani, Simon F Brunner, Rona Yaeger, Peter Ly, Yael Nechemia-Arbely, Dong Hyun Kim, Rongxin Fang, Guillaume A Castillon, Miao Yu, Julia S Z Li, Ying Sun, Mark H Ellisman, Bing Ren, Peter J Campbell, Don W Cleveland
Chromothripsis drives the evolution of gene amplification in cancer. Nature 591 (7848) (2020)
Peng He, Brian A Williams, Diane Trout, Georgi K Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A Pennacchio, Diane E Dickel, Axel Visel, Bing Ren, Ross Cameron Hardison, Yu Zhang, Barbara J Wold
The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature 583 (7818) (2020)
Marios Arvanitis, Emmanouil Tampakakis, Yanxiao Zhang, Wei Wang, Adam Auton, null null, Diptavo Dutta, Stephanie A Glavaris, Ali R Keramati, Nilanjan Chatterjee, Neil C Chi, Bing Ren, Wendy S Post, Alexis J Battle
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. Nature communications 11 (1) (2020)
Alex Wells, David Heckerman, Ali Torkamani, Li Yin, Jonathan Sebat, Bing Ren, Amalio Telenti, Julia di Iulio
Ranking of non-coding pathogenic variants and putative essential regions of the human genome. Nature communications 10 (1) (2019)
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins, Xian Fan, Jia Wen, Robert E Handsaker, Susan Fairley, Zev N Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M Wenger, Alex R Hastie, Danny Antaki, Thomas Anantharaman, Peter A Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T Chuang, Christine C Lambert, Deanna M Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M Munson, Fábio C P Navarro, Bradley J Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W C Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C J Spierings, Alistair Ward, AnneMarie E Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy-Gallego, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B Gerstein, Pui-Yan Kwok, Peter M Lansdorp, Gabor T Marth, Jonathan Sebat, Xing-Hua Shi, Ali Bashir, Kai Ye, Scott E Devine, Michael E Talkowski, Ryan E Mills, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee
Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature communications 10 (1) (2019)
Yael Nechemia-Arbely, Karen H Miga, Ofer Shoshani, Aaron Aslanian, Moira A McMahon, Ah Young Lee, Daniele Fachinetti, John Yates Iii, Bing Ren, Don W Cleveland
DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres. Nature cell biology 21 (6) (2019)
Lucas Patel, Rhea Kang, Scott C Rosenberg, Yunjiang Qiu, Ramya Raviram, Sora Chee, Rong Hu, Bing Ren, Francesca Cole, Kevin D Corbett
Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nature structural & molecular biology 26 (3) (2019)
Guoqiang Li, Yaping Liu, Yanxiao Zhang, Naoki Kubo, Miao Yu, Rongxin Fang, Manolis Kellis, Bing Ren
Joint profiling of DNA methylation and chromatin architecture in single cells. Nature methods 16 (10) (2019)
David U Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony D Schmitt, Amina Noor, Joshua Chiou, Kyle J Gaulton, Jonathan Sebat, Yun Li, Kasper D Hansen, Bing Ren
Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome biology 20 (1) (2019)
Yanxiao Zhang, Ting Li, Sebastian Preissl, Maria Luisa Amaral, Jonathan D Grinstein, Elie N Farah, Eugin Destici, Yunjiang Qiu, Rong Hu, Ah Young Lee, Sora Chee, Kaiyue Ma, Zhen Ye, Quan Zhu, Hui Huang, Rongxin Fang, Leqian Yu, Juan Carlos Izpisua Belmonte, Jun Wu, Sylvia M Evans, Neil C Chi, Bing Ren
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nature genetics 51 (9) (2019)
Chenxu Zhu, Miao Yu, Hui Huang, Ivan Juric, Armen Abnousi, Rong Hu, Jacinta Lucero, M Margarita Behrens, Ming Hu, Bing Ren
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nature structural & molecular biology 26 (11) (2019)
Inkyung Jung, Anthony Schmitt, Yarui Diao, Andrew J Lee, Tristin Liu, Dongchan Yang, Catherine Tan, Junghyun Eom, Marilynn Chan, Sora Chee, Zachary Chiang, Changyoun Kim, Eliezer Masliah, Cathy L Barr, Bin Li, Samantha Kuan, Dongsup Kim, Bing Ren
A compendium of promoter-centered long-range chromatin interactions in the human genome. Nature genetics 51 (10) (2019)
William W Greenwald, Joshua Chiou, Jian Yan, Yunjiang Qiu, Ning Dai, Allen Wang, Naoki Nariai, Anthony Aylward, Jee Yun Han, Nikita Kadakia, Laura Regue, Mei-Lin Okino, Frauke Drees, Dana Kramer, Nicholas Vinckier, Liliana Minichiello, David U Gorkin, Joseph Avruch, Kelly A Frazer, Maike Sander, Bing Ren, Kyle J Gaulton
Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nature communications 10 (1) (2019)
Sebastian Preissl, Rongxin Fang, Hui Huang, Yuan Zhao, Ramya Raviram, David U Gorkin, Yanxiao Zhang, Brandon C Sos, Veena Afzal, Diane E Dickel, Samantha Kuan, Axel Visel, Len A Pennacchio, Kun Zhang, Bing Ren
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature neuroscience 21 (3) (2018)
Julia di Iulio, Istvan Bartha, Emily H M Wong, Hung-Chun Yu, Victor Lavrenko, Dongchan Yang, Inkyung Jung, Michael A Hicks, Naisha Shah, Ewen F Kirkness, Martin M Fabani, William H Biggs, Bing Ren, J Craig Venter, Amalio Telenti
The human noncoding genome defined by genetic diversity. Nature genetics 50 (3) (2018)
Andrea Local, Hui Huang, Claudio P Albuquerque, Namit Singh, Ah Young Lee, Wei Wang, Chaochen Wang, Judy E Hsia, Andrew K Shiau, Kai Ge, Kevin D Corbett, Dong Wang, Huilin Zhou, Bing Ren
Identification of H3K4me1-associated proteins at mammalian enhancers. Nature genetics 50 (1) (2017)

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