百晓学者学者目录

于淼

教授、研究员，复旦大学

精选作品

期刊论文

2024

An integrated view of the structure and function of the human 4D nucleome

J. Dekker, B. A. Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Li-Yan Yang, J. Gibcus, Nils Krietenstein, O. Rando, Jie Xu, D. Janssens, S. Henikoff, A. Kukalev, Andréa Willemin, Warren Winick-Ng, Rieke Kempfer, Ana Pombo, Miao Yu, Pradeep Kumar, Liguo Zhang, Andrew S. Belmont, Takayo Sasaki, T. van Schaik, Laura Brueckner, Daan Peric-Hupkes, B. van Steensel, Ping Wang, Haoxi Chai, Minji Kim, Yijun Ruan, Ran Zhang, Sofia A. Quinodoz, Prashant Bhat, M. Guttman, Wenxin Zhao, Shu Chien, Yuan Liu, Sergey V. Venev, D. Plewczyński, Ibai Irastorza Azcarate, Dominik Szabó, Christoph J. Thieme, Teresa Szczepińska, Mateusz Chiliński, Kaustav Sengupta, Mattia Conte, Andrea Esposito, Alex Abraham, Ruochi Zhang, Yuchuan Wang, Xingzhao Wen, Qiuyang Wu, Yang Yang, Jie Liu, Lorenzo Boninsegna, Aslı Yıldırım, Yu-Xiang Zhan, A. Chiariello, Simona Bianco, Lindsay Lee, Ming Hu, Yun Li, R. J. Barnett, Ashley L. Cook, Daniel J. Emerson, Claire Marchal, Peiyao Zhao, Peter Park, Burak H. Alver, Andrew J. Schroeder, Rahi Navelkar, Clara Bakker, William Ronchetti, Shannon R. Ehmsen, Alexander D. Veit, N. Gehlenborg, Ting Wang, Dao-Feng Li, Xiao-Tao Wang, Mario Nicodemi, Bing Ren, Sheng Zhong, Jennifer E. Phillips-Cremins, David M. Gilbert, Katherine Pollard, Frank Alber, Jian Ma, W. S. Noble, Feng Yue

bioRxiv

DOI

2023

SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity

Bethany R. Fixsen, Claudia Z. Han, Yi Zhou, N. Spann, P. Saisan, Zeyang Shen, Christopher D. Balak, Mashito Sakai, Isidoro Cobo, I. Holtman, A. Warden, G. Ramirez, J. Collier, Martina P. Pasillas, Miao Yu, Rong Hu, Bin Li, S. Belhocine, D. Gosselin, N. Coufal, B. Ren, Christopher K. Glass

Nature Immunology

DOI

2022

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

Miao Yu, Nathan R. Zemke, Zi-Yin Chen, Ivan Juric, Rong Hu, R. Raviram, Armen Abnousi, Rongxin Fang, Yan-Xiao Zhang, David U. Gorkin, Y. Li, Yuan Zhao, Lindsay Lee, Shreya Mishra, A. Schmitt, Yun-Jiang Qiu, D. Dickel, A. Visel, L. Pennacchio, Ming Hu, B. Ren

bioRxiv

DOI

2021

SnapHiC: a computational pipeline to identify chromatin loops from single cell Hi-C data

Miao Yu, Armen Abnousi, Yan-Xiao Zhang, Guoqiang Li, Lindsay Lee, Zi-Yin Chen, Rongxin Fang, Taylor M. Lagler, Yu-Chen Yang, Jia Wen, Quan Sun, Yun Li, B. Ren, Ming Hu

Nature Methods

DOI

2021

Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath

Xingjie Ren, Meng-Chi Wang, Bing-Kun Li, Kirsty Jamieson, Lina Zheng, Ian R. Jones, Bin Li, M. Takagi, Jerry C Lee, Lenka Maliskova, Tsz-Wai Tam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, B. Ren, Wei Wang, Yin Shen

bioRxiv

DOI

2021

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

Riccardo Calandrelli, Xingzhao Wen, J. L. Charles Richard, Zhifei Luo, Tri C. Nguyen, Chienju Chen, Zhijie Qi, Shuang-Hong Xue, Weizhong Chen, Zhangming Yan, Weixin Wu, K. Zaleta-Rivera, Rong Hu, Miao Yu, Yuchuan Wang, Wenbo Li, Jian Ma, B. Ren, Sheng Zhong

bioRxiv

DOI

2021

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Miao Yu, Ivan Juric, Armen Abnousi, Ming Hu, B. Ren

Methods in molecular biology

DOI

2021

Publisher Correction: Chromothripsis drives the evolution of gene amplification in cancer

Ofer Shoshani, Simon F. Brunner, R. Yaeger, P. Ly, Yael Nechemia-Arbely, D. H. Kim, Rongxin Fang, Guillaume A. Castillon, Miao Yu, J. Li, Ying Sun, Mark Ellisman, B. Ren, P. Campbell, D. Cleveland

Nature

DOI

2021

Promoter-proximal CTCF-binding promotes long-range-enhancer dependent gene activation

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, M. Nicodemi, Hui-Min Zhao, B. Ren

Nature Structural & Molecular Biology

DOI

2021

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Hui Huang, Quan-Sheng Zhu, Adam P. Jussila, Yuanyuan Han, Bogdan Bintu, Colin Kern, Mattia Conte, Yan-Xiao Zhang, Simona Bianco, A. Chiariello, Miao Yu, Rong Hu, Melodi Tastemel, Ivan Juric, Ming Hu, M. Nicodemi, X. Zhuang, B. Ren

Nature Genetics

DOI

2021

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

Qi-Ling Zhou, Miao Yu, Roberto Tirado-Magallanes, Bin Li, Lingshi Kong, M. Guo, Zi-Hui Tan, Sanghoon Lee, L. Chai, A. Numata, T. Benoukraf, M. Fullwood, Motomi Osato, B. Ren, D. Tenen

Nature Communications

DOI

2020

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

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, M. Nicodemi, Hui-Min Zhao, B. Ren

bioRxiv

DOI

2020

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

Qiancheng You, Anthony Youzhi Cheng, Xiaoqiong Gu, B. Harada, Miao Yu, Tong Wu, B. Ren, Z. Ouyang, Chuan He

Nature Biotechnology

DOI

2020

Chromothripsis drives the evolution of gene amplification in cancer

Ofer Shoshani, Simon F. Brunner, R. Yaeger, P. Ly, Yael Nechemia-Arbely, D. H. Kim, Rongxin Fang, Guillaume A. Castillon, Miao Yu, J. Li, Ying Sun, Mark Ellisman, B. Ren, P. Campbell, D. Cleveland

Nature

DOI

2019

Circular ecDNA promotes accessible chromatin and high oncogene expression

Si-Han Wu, Kristen M. Turner, Nam Nguyen, R. Raviram, M. Erb, J. Santini, J. Luebeck, Utkrisht Rajkumar, Ya-Rui Diao, Bin Li, Wenjing Zhang, Nathan M. Jameson, M. Corces, Jeffrey M. Granja, Xingqi Chen, C. Coruh, Armen Abnousi, Jack Houston, Zhen Ye, Rong Hu, Miao Yu, Hoon Kim, Julie A. Law, R. Verhaak, Ming Hu, F. Furnari, Howard Y. Chang, B. Ren, V. Bafna, P. Mischel

Nature

DOI

2019

Brain cell type-specific enhancer-promoter interactome maps and disease risk association

A. Nott, I. Holtman, N. Coufal, J. Schlachetzki, Miao Yu, Rong Hu, Claudia Z. Han, Monique Pena, Jiayang Xiao, Yin Wu, Zahara Keulen, Martina P. Pasillas, Carolyn O’Connor, C. Nickl, Simon T. Schafer, Zeyang Shen, R. Rissman, J. Brewer, D. Gosselin, D. Gonda, M. Levy, M. Rosenfeld, Graham P. McVicker, F. Gage, B. Ren, C. Glass

Science

DOI

2019

Joint profiling of DNA methylation and chromatin architecture in single cells

Guoqiang Li, Yaping Liu, Yan-Xiao Zhang, Naoki Kubo, Miao Yu, Rongxin Fang, Manolis Kellis, B. Ren

Nature Methods

DOI

2019

Lineage-specific control of promoter-enhancer interactions by CTCF during neural cell differentiation

Naoki Kubo, Haruhiko Ishii, Rong Hu, Franz Meitinger, Xiong Xiong, James D. Hocker, David U. Gorkin, Miao Yu, Bin Li, Jesse R. Dixon, Ming Hu, A. Desai, Hui-Min Zhao, B. Ren

2019

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

Chenxu Zhu, Miao Yu, Hui Huang, Ivan Juric, Armen Abnousi, Rong Hu, J. Lucero, M. Behrens, Ming Hu, Bing Ren

Nature Structural & Molecular Biology

DOI

2018

Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function

Verena M. Link, Sascha H. Duttke, H. Chun, I. Holtman, Emma Westin, M. Hoeksema, Yohei Abe, Dylan Skola, C. Romanoski, Jenhan Tao, Gregory J. Fonseca, T. Troutman, N. Spann, Tobias Strid, Mashito Sakai, Miao Yu, Rong Hu, Rongxin Fang, D. Metzler, B. Ren, C. Glass

Cell

DOI

2018

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Ivan Juric, Miao Yu, Armen Abnousi, R. Raviram, Rongxin Fang, Yuan Zhao, Yan-Xiao Zhang, Yun-Jiang Qiu, Yu-Chen Yang, Yun Li, B. Ren, Ming Hu

bioRxiv

DOI

2016

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

Rongxin Fang, Miao Yu, Guoqiang Li, S. Chee, Tristin Liu, A. Schmitt, Bing Ren

Cell Research

DOI

2016

近接ライゲーション支援ChIP‐seqによる長距離クロマチン相互作用のマッピング【Powered by NICT】

Rongxin Fang, Miao Yu, Guo-Qiang Li, Chee Sora, Liu Tristin, D. SchmittAnthony, Bing Ren

研究方向

非编码调控元件及靶基因识别三维基因组与疾病相关非编码变异调控

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