Publications

A comparative atlas of single-cell chromatin accessibility in the human brain

Published in bioRxiv, 2022

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Recommended citation: Yang Eric Li, Sebastian Preissl, Michael Miller, Nicholas D. Johnson, Zihan Wang, Henry Jiao, Chenxu Zhu, Zhaoning Wang, Yang Xie, Olivier Poirion, Colin Kern, Antonio Pinto-Duarte, Wei Tian, Kimberly Siletti, Nora Emerson, Julia Osteen, Jacinta Lucero, Lin Lin, Qian Yang, Quan Zhu, Sarah Espinoza, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya Shapovalova, Daniel Hirschstein, Rebecca D. Hodge, Sten Linnarsson, Trygve Bakken, Boaz 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." bioRxiv, 2022. doi: https://doi.org/10.1101/2022.11.09.515833

Systematic analysis of binding of transcription factors to noncoding variants

Published in Nature, 2021

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Recommended citation: Yan, Jian, Qiu, Yunjiang, Dos Santos, Andr{\'e} M Ribeiro, Yin, Yimeng, Li, Yang E, Vinckier, Nick, Nariai, Naoki, Benaglio, Paola, Raman, Anugraha, ..., Taipale, Jussi & Ren, Bing "Systematic analysis of binding of transcription factors to noncoding variants." Nature, 2021.

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

Published in Nature Methods, 2021

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Recommended citation: Zhu, Chenxu, Zhang, Yanxiao, Li, Yang Eric, Lucero, Jacinta, Behrens, M Margarita, Ren, Bing, "Joint profiling of histone modifications and transcriptome in single cells from mouse brain." Nature Methods, 2021.

DNA methylation atlas of the mouse brain at single-cell resolution

Published in Nature, 2021

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Recommended citation: Liu, Hanqing, Zhou, Jingtian, Tian, Wei, Luo, Chongyuan, Bartlett, Anna, Aldridge, Andrew, Lucero, Jacinta, Li, Yang Eric, ..., Ecker Joseph R. "DNA methylation atlas of the mouse brain at single-cell resolution." Nature, 2021.

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Published in Nature communications, 2021

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Recommended citation: Fang, Rongxin, Preissl, Sebastian, Li, Yang, Hou, Xiaomeng, Lucero, Jacinta, Wang, Xinxin, Motamedi, Amir, Shiau, Andrew K, Zhou, Xinzhu, Xie, Fangming, ..., Ren, Bing "Comprehensive analysis of single cell ATAC-seq data with SnapATAC." Nature communications, 2021.

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Published in Nature, 2021

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Recommended citation: Bakken, Trygve E, Jorstad, Nikolas L, Hu, Qiwen, Lake, Blue B, Tian, Wei, ..., Li, Yang, ..., Lein, Ed S. "Comparative cellular analysis of motor cortex in human, marmoset and mouse." Nature, 2021.

Cardiac cell type–specific gene regulatory programs and disease risk association

Published in Science advances, 2021

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Recommended citation: Hocker, James D, Poirion, Olivier B, Zhu, Fugui, Buchanan, Justin, ..., Li, Yang E, ..., others, "Cardiac cell type--specific gene regulatory programs and disease risk association." Science advances, 2021.

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Published in Nature, 2021

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Recommended citation: Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S, Aldridge, Andrew I, Ament, Seth A, Bartlett, Anna, Behrens, M Margarita, ..., Li, Yang Eric, ..., Zeng, Hongkui & Mukamel Eran A. "A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex." Nature, 2021.

A single-cell atlas of chromatin accessibility in the human genome

Published in Cell, 2021

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Recommended citation: Zhang, Kai, Hocker, James D, Miller, Michael, Hou, Xiaomeng, Chiou, Joshua, Poirion, Olivier B, Qiu, Yunjiang, Li, Yang E, Gaulton, Kyle J, Wang, Allen, ..., Bing, Ren "A single-cell atlas of chromatin accessibility in the human genome." Cell, 2021.

A multimodal cell census and atlas of the mammalian primary motor cortex

Published in Nature, 2021

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Recommended citation: Network, BRAIN Initiative Cell Census, "A multimodal cell census and atlas of the mammalian primary motor cortex." Nature, 2021.

An atlas of gene regulatory elements in adult mouse cerebrum

Published in Nature, 2021

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Recommended citation: Li, Yang Eric, Preissl, Sebastian, Hou, Xiaomeng, Zhang, Ziyang, Zhang, Kai, Qiu, Yunjiang, Poirion, Olivier B, Li, Bin, Chiou, Joshua, Liu, Hanqing, others, "An atlas of gene regulatory elements in adult mouse cerebrum." Nature, 2021.

Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer

Published in Cell research, 2020

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Recommended citation: Teng, Shuaishuai, Li, Yang Eric, Yang, Ming, Qi, Rui, Huang, Yiming, Wang, Qianyu, Zhang, Yanmei, Chen, Shanwen, Li, Shasha, Lin, Kequan, ..., Lu, Zhi John & Wang, Dong "Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer." Cell research, 2020.

Recurrently deregulated lncRNAs in hepatocellular carcinoma

Published in Nature communications, 2017

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Recommended citation: Yang, Yang, Chen, Lei, Gu, Jin, Zhang, Hanshuo, Yuan, Jiapei, Lian, Qiuyu, Lv, Guishuai, ..., Li, Yang, ..., Zhang, Michael Q. & Lu, Zhi John "Recurrently deregulated lncRNAs in hepatocellular carcinoma." Nature communications, 2017.

Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites

Published in Genome biology, 2017

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Recommended citation: Li, Yang Eric, Xiao, Mu, Shi, Binbin, Yang, Yu-Cheng T, Wang, Dong, Wang, Fei, Marcia, Marco, Lu, Zhi John, "Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA--protein binding sites." Genome biology, 2017.

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

Published in Nucleic acids research, 2016

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Recommended citation: Yang Wu, Rihao Qu, Yiming Huang, Binbin Shi, Mengrong Liu, Yang Li, Zhi Lu, "RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data." Nucleic acids research, 2016.

CLIPdb: a CLIP-seq database for protein-RNA interactions

Published in BMC genomics, 2015

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Recommended citation: Yu-Cheng Yang, Chao Di, Boqin Hu, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu, Zhi Lu, "CLIPdb: a CLIP-seq database for protein-RNA interactions." BMC genomics, 2015.

Amphibians crossing the bering land bridge: evidence from holarctic treefrogs (Hyla, Hylidae, Anura)

Published in Molecular phylogenetics and evolution, 2015

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Recommended citation: Jia-Tang Li, Ji-Shan Wang, Hui-Huang Nian, Spartak Litvinchuk, Jichao Wang, Yang Li, Ding-Qi Rao, Sebastian Klaus, "Amphibians crossing the bering land bridge: evidence from holarctic treefrogs (Hyla, Hylidae, Anura)." Molecular phylogenetics and evolution, 2015.

A common set of distinct features that characterize noncoding RNAs across multiple species

Published in Nucleic acids research, 2015

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Recommended citation: Long Hu, Chao Di, Mingxuan Kai, Yu-Cheng Yang, Yang Li, Yunjiang Qiu, Xihao Hu, Kevin Yip, Michael Zhang, Zhi Lu, "A common set of distinct features that characterize noncoding RNAs across multiple species." Nucleic acids research, 2015.

Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene

Published in Proceedings of the National Academy of Sciences, 2013

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Recommended citation: Jia-Tang Li, Yang Li, Sebastian Klaus, Ding-Qi Rao, David Hillis, Ya-Ping Zhang, "Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene." Proceedings of the National Academy of Sciences, 2013.

Study on setting up experiments of bdellovibrio bacteriovorus in innovative microbiology experimental teaching

Published in Experimental Technology and Management, 2012

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Recommended citation: Hong, Wang, Yang, Li, Jie, Zhang, Wenjing, Fang, Yan, Li, Heng, Xu, Jian, Zhao, "Study on setting up experiments of bdellovibrio bacteriovorus in innovative microbiology experimental teaching." Experimental Technology and Management, 2012.

Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia)

Published in Zoologica Scripta, 2012

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Recommended citation: Li, Jia-Tang, Li, Yang, Murphy, Robert W, Rao, Ding-Qi, Zhang, Ya-Ping, "Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia)." Zoologica Scripta, 2012.

Yang E. Li

Publications