表观基因组学与基因调控

整合建模人类和小鼠中的转录因子结合、染色质可及性和顺式调控。

课题组长期关注从大规模染色质数据中进行基因调控整合建模。我们构建数据库、分析流程和统计模型，将转录因子结合、组蛋白修饰和染色质可及性与下游基因表达和疾病表型连接起来。

这一方向支撑了 Cistrome Data Browser 生态系统 (Mei et al., 2017)(Zheng et al., 2019)、用于 ChIP-seq 和 DNase-seq 的 ChiLin 质量控制与分析流程 (Qin et al., 2016)、从公共染色质数据推断转录调控因子的 Lisa 框架 (Qin et al., 2020)、面向 chromatin regulators 的 CR Cistrome 资源 (Wang et al., 2014)，以及基于 H3K27ac 数据集合的顺式调控建模工作 (Wang et al., 2016)。我们也参与了 ENCODE consortium 对人类和小鼠基因组调控元件百科的扩展工作 (ENCODE Project Consortium, 2020)。未来我们将继续把这些方法扩展到单细胞、空间和疾病场景下的 regulome 分析。

参考文献

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},
}