Epigenomics and Gene Regulation

Integrative modeling of transcription factor binding, chromatin accessibility, and cis-regulation across human and mouse.

A long-running thread of the lab is integrative modeling of gene regulation from large-scale chromatin data. We build databases, pipelines, and statistical models that connect transcription factor binding, histone modification, and chromatin accessibility to downstream gene expression and disease.

This direction underlies the Cistrome Data Browser ecosystem (Mei et al., 2017)(Zheng et al., 2019), the ChiLin quality-control and analysis pipeline for ChIP-seq and DNase-seq (Qin et al., 2016), the Lisa framework for inferring transcriptional regulators from public chromatin data (Qin et al., 2020), the CR Cistrome resource for chromatin regulators (Wang et al., 2014), and our cis-regulatory modeling work using H3K27ac compendia (Wang et al., 2016). We have also contributed to the ENCODE consortium’s expanded encyclopedia of regulatory elements in the human and mouse genomes (ENCODE Project Consortium, 2020). We continue to extend these methods to single-cell, spatial, and disease-context regulomes.

References

2020

Genome Biol

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Qian Qin, J Fan, R Zheng, and 8 more authors

Genome Biology*Co-first authors , 2020

Bib HTML

@article{Qin2020Lisa,
  title = {{Lisa}: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and {ChIP-seq} data},
  author = {Qin, Qian and Fan, J and Zheng, R and Wan, C and Mei, S and Wu, Q and Sun, H and Brown, M and Zhang, J and Meyer, C A and Liu, X S},
  journal = {Genome Biology},
  volume = {21},
  number = {1},
  pages = {32},
  year = {2020},
}

Nature

Expanded encyclopaedias of DNA elements in the human and mouse genomes

ENCODE Project Consortium

Nature, 2020

Bib HTML

@article{ENCODE2020Expanded,
  title = {Expanded encyclopaedias of {DNA} elements in the human and mouse genomes},
  author = {{ENCODE Project Consortium}},
  journal = {Nature},
  volume = {583},
  number = {7818},
  pages = {699--710},
  year = {2020},
}

2019

NAR

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

R Zheng, C Wan, S Mei, and 8 more authors

Nucleic Acids Research, 2019

Bib HTML

@article{Zheng2019CistromeDataBrowser,
  title = {{Cistrome Data Browser}: expanded datasets and new tools for gene regulatory analysis},
  author = {Zheng, R and Wan, C and Mei, S and Qin, Qian and Wu, Q and Sun, H and Chen, C H and Brown, M and Zhang, X and Meyer, C A and Liu, X S},
  journal = {Nucleic Acids Research},
  volume = {47},
  number = {D1},
  pages = {D729--D735},
  year = {2019},
}

2017

NAR

Cistrome Data Browser: a data portal for ChIP-seq and chromatin accessibility data in human and mouse

S Mei, Qian Qin, Q Wu, and 11 more authors

Nucleic Acids Research*Co-first authors , 2017

Bib HTML

@article{Mei2017CistromeDataBrowser,
  title = {{Cistrome Data Browser}: a data portal for {ChIP-seq} and chromatin accessibility data in human and mouse},
  author = {Mei, S and Qin, Qian and Wu, Q and Sun, H and Zheng, R and Zang, C and Zhu, M and Wu, J and Shi, X and Taing, L and Liu, T and Brown, M and Meyer, C A and Liu, X S},
  journal = {Nucleic Acids Research},
  volume = {45},
  number = {D1},
  pages = {D658--D662},
  year = {2017},
}

2016

BMC Bioinformatics

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

Qian Qin, S Mei, Q Wu, and 14 more authors

BMC Bioinformatics*Co-first authors , 2016

Bib HTML

@article{Qin2016ChiLin,
  title = {{ChiLin}: a comprehensive {ChIP-seq} and {DNase-seq} quality control and analysis pipeline},
  author = {Qin, Qian and Mei, S and Wu, Q and Sun, H and Li, L and Taing, L and Chen, S and Li, F and Liu, T and Zang, C and Xu, H and Chen, Y and Meyer, C A and Zhang, Y and Brown, M and Long, H W and Liu, X S},
  journal = {BMC Bioinformatics},
  volume = {17},
  number = {1},
  pages = {404},
  year = {2016},
}

Genome Res

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles

S Wang, C Zang, T Xiao, and 10 more authors

Genome Research, 2016

Bib HTML

@article{Wang2016H3K27ac,
  title = {Modeling cis-regulation with a compendium of genome-wide histone {H3K27ac} profiles},
  author = {Wang, S and Zang, C and Xiao, T and Fan, J and Mei, S and Qin, Qian and Wu, Q and Li, X and Xu, K and He, H H and Brown, M and Meyer, C A and Liu, X S},
  journal = {Genome Research},
  volume = {26},
  number = {10},
  pages = {1417--1429},
  year = {2016},
}

2014

NAR

CR Cistrome: a ChIP-seq database for chromatin regulators and histone modification linkages in human and mouse

Q Wang, J Huang, H Sun, and 9 more authors

Nucleic Acids Research, 2014

Bib HTML

@article{Wang2014CRCistrome,
  title = {{CR Cistrome}: a {ChIP-seq} database for chromatin regulators and histone modification linkages in human and mouse},
  author = {Wang, Q and Huang, J and Sun, H and Liu, J and Wang, J and Wang, Q and Qin, Qian and Mei, S and Zhao, C and Yang, X and Liu, X S and Zhang, Y},
  journal = {Nucleic Acids Research},
  volume = {42},
  number = {Database issue},
  pages = {D450--D458},
  year = {2014},
}