Chongzhi Zang, Ph.D.

Assistant Professor of Public Health Sciences
Assistant Professor of Biomedical Engineering
Assistant Professor of Biochemistry and Molecular Genetics

Center for Public Health Genomics
University of Virginia School of Medicine
P. O. Box 800717, Charlottesville, VA 22908

Office: West Complex (MSB) 6131C
Phone: 434-243-5397
Email: zang@virginia.edu

CV: download
Lab website: faculty.virginia.edu/zanglab


Education and Training

B.S., Physics, Peking University, 2005

Ph.D., Physics, The George Washington University, 2010

Postdoc, Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard University, 2010–2016


Research Interests

Bioinformatics methodology development; Epigenetics and chromatin biology; Transcriptional regulation; Cancer genomics and epigenomics; Statistical methods for biomedical data integration; Theoretical and computational biophysics


Research Description

The research in my lab focuses on developing computational methodologies and integrative genomics approaches to study epigenetics and transcriptional regulation of gene expression in a variety of mammalian cell systems and human diseases such as cancer.

How gene expression is regulated in chromatin is a fundamental question in molecular biology. High-throughput technologies such as next-generation sequencing (NGS) have become powerful tools for studying gene regulation at the genomic scale. We conduct computational research that leverages these genomics technologies. Some research directions include:

1. Next-generation sequencing bioinformatics

We are interested in developing statistical methods and novel algorithms for analyzing massive data from next-generation sequencing (NGS) coupled with various assays for studying genomic chromatin profiles, such as ChIP-seq for transcription factor and histone mark profiling, ATAC-seq and DNase-seq for chromatin accessibility profiling, etc. As a pioneer in ChIP-seq bioinformatics, we developed SICER (Bioinformatics 2009), one of the most widely used methods for ChIP-seq data analysis with exceptional performance for board histone modification marks. We are developing novel statistical models and computational methods for analyzing DNase/ATAC-seq data and for studying chromatin dynamics.

2. Chromatin, epigenetics, and transcriptional regulation

Our ultimate goal is to understand the fundamental mechanisms in transcriptional regulation and the functions of chromatin. We characterized dozens of histone modifications and histone modifying enzymes at the genomic scale (Nat Genet 2008, Nat Genet 2009, Cell 2009, Cell Stem Cell 2009). Leveraging the large amount of publicly available ChIP-seq data, we developed MARGE (Genome Res 2016), a computational method to predict cis-regulatory profiles from differential expression gene sets using integrative learning approaches. We are specifically interested in studying functional enhancer regulation of gene expression in cancers.

3. Genomic data integration for chromatin dynamics and regulatory networks

High-dimensional genomic data analysis is challenging because of noises and biases in high-throughput experiments. We developed MANCIE (Nat Commun 2016), a method for bias correction and data integration of cross-platform genomic profiles on the same samples, using a Bayesian-supported principal component analysis (PCA)-based approach. We are interested in using statistical modeling and machine-learning approaches to integrate public genomic data for characterizing physical properties of mammalian epigenomes and dynamic interactions between chromatin and DNA in human cell systems.


Selected Publications

Selected from 30+ journal articles. A complete publication list can be found at my Google Scholar profile.
* indicates authors with equal contributions.

  1. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles
    Zhenjia Wang, Mete Civelek, Clint L. Miller, Nathan C. Sheffield, Michael J. Guertin, Chongzhi Zang
    Bioinformatics 34, 2867–2869 (2018)

  2. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy
    Tengfei Xiao, Wei Li, Xiaoqing Wang, Han Xu, Jixin Yang, Qiu Wu, Ying Huang, Joseph Geradts, Peng Jiang, Teng Fei, David Chi, Chongzhi Zang, Qi Liao, Jonathan Rennhack, Eran Andrechek, Nanlin Li, Simone Detre, Mitchell Dowsett, Rinath M. Jeselsohn, X. Shirley Liu, Myles Brown
    Proceedings of the National Academy of Sciences USA, doi:10.1073/pnas.1722617115 (2018)

  3. Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1
    Cynthia C Jose, Lakshmanan Jagannathan, Vinay Singh Tanwar, Xiaoru Zhang, Chongzhi Zang, Suresh Cuddapah
    Molecular Carcinogenesis 57, 794–806 (2018)

  4. Cistrome Cancer: a web resource for integrative gene regulation modeling in cancer
    Shenglin Mei, Clifford A. Meyer, Rongbin Zheng, Qian Qin, Qiu Wu, Peng Jiang, Bo Li, Xiaohui Shi, Binbin Wang, Jingyu Fan, Celina Shih, Myles Brown, Chongzhi Zang§(co-corresponding author), X. Shirley Liu§
    Cancer Research 77, e19–e22 (2017)

  5. Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions
    André L. Martins, Ninad M. Walavalkar, Warren D. Anderson, Chongzhi Zang, Michael J. Guertin
    Nucleic Acids Research 46 (2), e9 (2018)

  6. Genome-wide identification and characterization of Notch transcription complex-binding sequence-paired sites in leukemia cells
    Eric Severson*, Kelly L. Arnett*, Hongfang Wang*, Chongzhi Zang*, Len Taing, Hudan Liu, Warren S. Pear, X. Shirley Liu, Stephen C. Blacklow, Jon C. Aster
    Science Signaling 10, 477, eaag1598 (2017)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. 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)

  13. 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)

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. 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)

  21. 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)

  22. 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)

  23. 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)

  24. 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)

  25. 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)

  26. 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)

  27. 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)

  28. 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)

  29. 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)

  30. 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)

  31. 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)

  32. 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)

  33. 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)

  34. Fluorescence measurement and acoustic diagnostics of plasma channels in air
    Zuo-Qiang Hao, Jie Zhang, Jin Yu, Zhe Zhang, Jia-Yong Zhong, Chong-Zhi Zang, Zhan Jin, Zhao-Hua Wang, Zhi-Yi Wei
    Acta Physica Sinica 55, 299–303 (2006)


Software


Honors and Awards


Recruiting

My lab is recruiting motivated young students and scholars to work on a variety of topics in computational biology in a collaborative research team. Postdocs, graduate students, and undergraduate students are all welcome. Please contact me for any questions.

Prospective postdocs can find the job details and submit applications here.




"While the art of printing is left to us science can never be retrograde; what is once acquired of real knowledge can never be lost."

—Thomas Jefferson, 1799



Last modified: August 30, 2018