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publications

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.

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.

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 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.

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.

talks

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.

teaching

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.

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.