The first marathon day
Finally finished my first half marathon at Oct 24, 2021. 
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The Mt. San Gorgonio
Yeah! Conquer the 2nd highest summit in southern california. 
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The first marathon day
Finally finished my first half marathon at Oct 24, 2021.
The Mt. San Gorgonio
Yeah! Conquer the 2nd highest summit in southern california.
publications
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
A comparative atlas of single-cell chromatin accessibility in the human brain
Published in bioRxiv, 2022
Link to preprint on bioRxiv Use Google Scholar for full citation
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
talks
Exploring Single-cell Epigenetic Cell Atlas through Cis-element Atlas (CATlas) web portal
Published:
An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
Published:
I was invited to introduce our current effort on the comprehensive analysis of gene regulatory programs in the mouse brain, which can assist in interpreting noncoding risk variants that contribute to various neurological diseases and traits in humans.
Comprehensive Analysis of Gene Regulation in Adult Mouse Cerebrum
Published:
I was invited to introduce our current effort on the comprehensive analysis of gene regulatory programs in the mouse brain, and the general analysis techniques of single-cell sequencing data.
teaching
Teaching Assistant, Bioinformatics in Action
Graduate course, MOE Key Lab of Bioinformatics, School of Life Sciences Tsinghua University, 2018
BRAIN Data Standards Grant Workshop
Workshop, The 7th annual Brain Research through Advancing Innovative Neurotechnologies (BRAIN)® Initiative Investigators Meeting, 2021
Exploring Single-cell Epigenetic Cell Atlas through Cis-element Atlas (CATlas) web portal
Workshop, BICCN Data Exploration Workshop - 2021, 2021
Comprehensive Analysis of Single Cell Epigenomic Data
Invited lecture, Cold Spring Harbor Laboratory (CSHL), 2021
tools
Genetic Variants Allelic TF Binding Database (GVATdb)
Published:
A web server for searching SNPs with differential Transcription factors (TF) binding.
This database characterizes the allelic binding of 95,886 common human single nucleotide polymorphisms (SNPs, MAF>1% in Eeuropean and Asian populations) to 270 distinct transcription factors (TFs). The SNPs were chosen from neighboring regions (<=500 kb) of 83 risk loci of type 2 diabetes (T2D) that were identified in several genome wide association studies (GWAS). The data were generated using SNP-SELEX. website link
RBPgroup
Published:
This web-based database provides the RNA binding sites and regulatory elements.
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We develop a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. website link
Cis-element Atlas (CATlas)
Published:
A web portal for single-cell epigenetic datasets in human and mouse.
You can explore cell clusters and annotations identified from single-cell ATAC-seq, as well as genomic tracks. We also offer the downloading of candidate enhancer linked to putative target genes at cell-type resolution. For detail about the experimental or computational pipeline, please refer to our recent work published on Nature and preprint on bioRxiv.
We hope you find this data resource useful. Please write us with experiences and suggestions. We would love stories about how people are using it in their work.