Chongzhi Zang Lab  

Publications


Google Scholar profile


Selected Publications

* indicates authors with equal contributions.
  1. Universal correction of enzymatic sequence bias
    Andre L. Martins, Ninad M. Walavalkar, Warren D. Anderson, Chongzhi Zang, Michael J. Guertin
    Submitted

  2. Prior to joining UVA

  3. High-dimensional genomic data bias correction and data integration using MANCIE
    Chongzhi Zang*, Tao Wang*, Ke Deng, Bo Li, Sheng’en Hu, Qian Qin, Tengfei Xiao, Shihua Zhang, Clifford A. Meyer, Housheng Hansen He, Myles Brown, Jun S. Liu, Yang Xie, X. Shirley Liu
    Nature Communications 7, 11305 (2016)

  4. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
    Su Wang*, Chongzhi Zang*, Tengfei Xiao, Jingyu Fan, Shenglin Mei, Qian Qin, Qiu Wu, Xujuan Li, Kexin Xu, Housheng Hansen He, Myles Brown, Clifford A. Meyer, X. Shirley Liu
    Genome Research 26, 1417–1429 (2016)

  5. Cistrome Data Browser: an integrated data portal for ChIP-Seq and chromatin accessibility data in human and mouse
    Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A. Meyer, X. Shirley Liu
    Nucleic Acids Research 45 (D1), D658–D662 (2016)

  6. NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
    Chongzhi Zang*, Annouck Luyten*, Christina Chen, X. Shirley Liu, Ramesh A. Shivdasani
    Scientific Reports 6, 30255 (2016)

  7. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
    Qian Qin, Shenglin Mei, Qiu Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Han Xu, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
    BMC Bioinformatics 17, 404 (2016)

  8. Integrative analysis reveals the transcriptional collaboration between EZH2 and E2F1 in the regulation of cancer-related gene expression
    Han Xu*, Kexin Xu*, Housheng H. He, Chongzhi Zang, Chen-Hao Chen, Yiwen Chen, Qian Qin, Su Wang, Chenfei Wang, Sheng’en Hu, Fugen Li, Henry Long, Myles Brown, X. Shirley Liu
    Molecular Cancer Research 14, 163–172 (2016)

  9. Partitioning heritability by functional annotation using genome-wide association summary statistics
    Hilary K. Finucane, Brendan Bulik-Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po-Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Farh, Stephan Ripke, Felix R. Day, ReproGen Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Shaun Purcell, Eli Stahl, Sara Lindstrom, John R. B. Perry, Yukinori Okada, Soumya Raychaudhuri, Mark J. Daly, Nick Patterson, Benjamin M. Neale, Alkes L. Price
    Nature Genetics 47, 1228–1235 (2015)

  10. Network analysis of gene essentiality in functional genomics experiments
    Peng Jiang, Hongfang Wang, Wei Li, Chongzhi Zang, Bo Li, Yinling J. Wong, Clifford Meyer, Jun S. Liu, Jon C. Aster, X. Shirley Liu
    Genome Biology 16, 239 (2015)

  11. The role of Notch receptors in transcriptional regulation
    Hongfang Wang, Chongzhi Zang, X. Shirley Liu, Jon C. Aster
    Journal of Cellular Physiology 230, 982–988 (2015)

  12. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers
    Hongfang Wang*, Chongzhi Zang*, Len Taing, Kelly Arnett, Yinling Joey Wong, Warren S. Pear, Stephen C. Blacklow, X. Shirley Liu, Jon C. Aster
    Proceedings of the National Academy of Sciences USA 111, 715–710 (2014)

  13. Active enhancers are delineated de novo during hematopoiesis with limited lineage fidelity among specified primary blood cells
    Annouck Luyten*, Chongzhi Zang*, X. Shirley Liu, Ramesh A. Shivdasani
    Genes and Development 28, 1827–1839 (2014)

  14. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
    Housheng Hansen He, Clifford A. Meyer, Sheng’en Shawn Hu, Mei-Wei Chen, Chongzhi Zang, Yin Liu, Prakash K. Rao, Teng Fei, Han Xu, Henry Long, X. Shirley Liu, Myles Brown
    Nature Methods 11, 73–78 (2014)

  15. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
    Alexander Gusev, S. Hong Lee, Gosia Trynka, Hilary Finucane, Bjarni J. Vilhjálmsson, Han Xu, Chongzhi Zang, Stephan Ripke, Brendan Bulik-Sullivan, Eli Stahl, Schizophrenia Working Group of the Psychiatric Genomics Consortium, SWE-SCZ Consortium, Anna K. Kähler, Christina M. Hultman, Shaun M. Purcell, Steven A. McCarroll, Mark Daly, Bogdan Pasaniuc, Patrick F. Sullivan, Benjamin M. Neale, Naomi R. Wray, Soumya Raychaudhuri, Alkes L. Price
    The American Journal of Human Genetics 95, 535–552 (2014)

  16. Discovery of biomarkers predictive of GSI response in triple negative breast cancer and adenoid cystic carcinoma
    Alexander Stoeck, Serguei Lejnine, Andrew Truong, Li Pan, Hongfang Wang, Chongzhi Zang, Jing Yuan, Chris Ware, John MacLean, Philip W. Garrett-Engele, Michael Kluk, Jason Laskey, Brian B. Haines, Christopher Moskaluk, Leigh Zawel, Stephen Fawell, D. Gary Gilliland, Theresa Zhang, Brandon Kremer, Birgit Knoechel, Bradley E. Bernstein, Warren S. Pear, X. Shirley Liu, Jon C. Aster, Sriram Sathyanarayanan
    Cancer Discovery 4(10), 1154–1167 (2014)

  17. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia
    Yumi Yashiro-Ohtani, Hongfang Wang, Chongzhi Zang, Kelly L. Arnett, Will Bailis, Yugong Ho, Birgit Knoechel, Claudia Lanauze, Lumena Louis, Katherine S. Forsyth, Sujun Chen, Yoonjie Chung, Jonathan Schug, Gerd A. Blobel, Stephen A. Liebhaber, Bradley E. Bernstein, Stephen C. Blacklow, X. Shirley Liu, Jon C. Aster, Warren S. Pear
    Proceedings of the National Academy of Sciences USA 111(46), E4946–E4953 (2014)

  18. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
    Xiaoqi Zheng, Qian Zhao, Huajun Wu, Wei Li, Haiyun Wang, Clifford A. Meyer, Qian Alvin Qin, Han Xu, Chongzhi Zang, Peng Jiang, Fuqiang Li, Yong Hou, Jianxing He, Jun Wang, Jun Wang, Peng Zhang, Yong Zhang, X. Shirley Liu
    Genome Biology 15, 419 (2014)

  19. Targets analysis by integration of transcripome and ChIP-seq data with BETA
    Su Wang, Hanfei Sun, Jian Ma, Chongzhi Zang, Chenfei Wang, Juan Wang, Qianzi Tang, Clifford A. Meyer, Yong Zhang, X. Shirley Liu
    Nature Protocols 8, 2502–2515 (2013)

  20. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis
    Hong Hao, Douglas S. Kim, Bernward Klocke, Kory R. Johnson, Kairong Cui, Norimoto Gotoh, Chongzhi Zang, Janina Gregorski, Linn Gieser, Weiqun Peng, Yang Fann, Martin Seifert, Keji Zhao, Anand Swaroop
    PLoS Genetics 8(4), e1002649 (2012)

  21. PTIP promotes chromatin changes critical for immunoglobulin switch recombination
    Jeremy A. Daniel, Margarida A. Santos*, Zhibin Wang*, Chongzhi Zang*, Mila Jankovic, Anna Gazumyan, Kristopher R. Schwab, Arito Yamane, Darius Filsuf, Young-Wook Cho, Kai Ge, Weiqun Peng, Michel C. Nussenzweig, Rafael Casellas, Gregory R. Dressler, Keji Zhao, André Nussenzweig
    Science 329, 917–923 (2010)

  22. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation
    Lai Wei, Golnaz Vahedi, Hong-Wei Sun, Wendy T. Watford, Hiroaki Takatori, Haydee L. Ramos, Hayato Takahashi, Jonathan Liang, Gustavo Gutierrez-Cruz, Chongzhi Zang, Weiqun Peng, John J. O'Shea, Yuka Kanno
    Immunity 32, 840–851 (2010)

  23. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, Weiqun Peng
    Bioinformatics 25, 1952–1958 (2009)

  24. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
    Zhibin Wang*, Chongzhi Zang*, Kairong Cui*, Dustin E. Schones, Artem Barski, Weiqun Peng, Keji Zhao
    Cell 138, 1019–1031 (2009)

  25. H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions
    Chunyuan Jin*, Chongzhi Zang*, Gang Wei, Kairong Cui, Weiqun Peng, Keji Zhao, Gary Felsenfeld
    Nature Genetics 41, 941–945 (2009)

  26. Chromatin signatures in multipotent hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    Kairong Cui*, Chongzhi Zang*, Tae-Young Roh, Dustin E. Schones, Richard W. Childs, Weiqun Peng, Keji Zhao
    Cell Stem Cell 4, 80–93 (2009)

  27. Genome-wide analysis of histone methylations reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells
    Yasuto Araki, Zhibin Wang, Chongzhi Zang, William H. Wood, Dustin Schones, Kairong Cui, Tae-Young Roh, Brad Lhotsky, Robert P. Wersto, Weiqun Peng, Kevin G. Becker, Keji Zhao, Nan-ping Weng
    Immunity 30, 912–925 (2009)

  28. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells
    Gang Wei, Lai Wei, Jinfang Zhu, Chongzhi Zang, Jane Hu-Li, Zhengju Yao, Kairong Cui, Yuka Kanno, Tae-Young Roh, Wendy Watford, Dustin E. Schones, Weiqun Peng, Hong-wei Sun, William E. Paul, John J. O’Shea, Keji Zhao
    Immunity 30, 155–167 (2009)

  29. Combinatorial patterns of histone acetylations and methylations in the human genome
    Zhibin Wang*, Chongzhi Zang*, Jeffrey A. Rosenfeld*, Dustin E. Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q. Zhang, Keji Zhao
    Nature Genetics 40, 897–903 (2008)


Last modified: April 25, 2017