Chongzhi Zang, Ph.D.

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

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: https://zanglab.github.io/


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 40+ journal articles. A complete publication list can be found at my Google Scholar profile.
* indicates authors with equal contributions. # indicates co-corresponding authors. Underscored indicates lab members.

  1. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
    Celestia Fang*, Zhenjia Wang*, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, Maria E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos#, Chongzhi Zang#
    Genome Biology 21, 247 (2020)

  2. Polyadenylation of histone H3.1 mRNA promotes cell transformation by displacing H3.3 from gene regulatory elements
    Danqi Chen*, Qiao Yi Chen*, Zhenjia Wang*, Yusha Zhu, Thomas Kluz, Wuwei Tan, Jinquan Li, Feng Wu, Lei Fang, Xiaoru Zhang, Rongquan He, Steven Shen, Hong Sun, Chongzhi Zang#, Chunyuan Jin#, Max Costa#
    iScience 23, 101518 (2020)

  3. Expanded encyclopaedias of DNA elements in the human and mouse genomes
    The ENCODE Project Consortium, Jill E. Moore*, Michael J. Purcaro*, Henry E. Pratt*, Charles B. Epstein*, Noam Shoresh*, Jessika Adrian*, Trupti Kawli*, Carrie A. Davis*, Alexander Dobin*, Rajinder Kaul*, Jessica Halow*, Eric L. Van Nostrand*, Peter Freese*, David U. Gorkin*, Yin Shen*, Yupeng He*, Mark Mackiewicz*, Florencia Pauli-Behn*, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J. Farnham, J. Michael Cherry#, Richard M. Myers#, Bing Ren#, Brenton R. Graveley#, Mark B. Gerstein#, Len A. Pennacchio#, Michael P. Snyder#, Bradley E. Bernstein#, Barbara Wold#, Ross C. Hardison#, Thomas R. Gingeras#, John A. Stamatoyannopoulos#, Zhiping Weng#
    Nature 583, 699–710 (2020)

  4. Perspectives on ENCODE
    The ENCODE Project Consortium, Michael P. Snyder#, Thomas R. Gingeras, Jill E. Moore, Zhiping Weng, Mark B. Gerstein, Bing Ren, Ross C. Hardison, John A. Stamatoyannopoulos, Brenton R. Graveley, Elise A. Feingold, Michael J. Pazin, Michael Pagan, Daniel A. Gilchrist, Benjamin C. Hitz, J. Michael Cherry, Bradley E. Bernstein, Eric M. Mendenhall, Daniel R. Zerbino, Adam Frankish, Paul Flicek, Richard M. Myers
    Nature 583, 693–698 (2020)

  5. An integrative ENCODE resource for cancer genomics
    Jing Zhang*, Donghoon Lee*, Vineet Dhiman*, Peng Jiang*, Jie Xu*, Patrick McGillivray*, Hongbo Yang*, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T. Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J. Klein, Michael Snyder, David M. Gilbert, Kevin Yip, Chao Cheng, Feng Yue#, X. Shirley Liu#, Kevin P. White#, Mark Gerstein#
    Nature Communications 11, 3696 (2020)

  6. Ectopic Tcf1 expression instills a stem-like program in exhausted CD8+ T cells to enhance viral and tumor immunity
    Qiang Shan*, Sheng’en Hu*, Xia Chen, Derek B. Danahy, Vladimir P. Badovinac, Chongzhi Zang#, Hai-Hui Xue#
    Cellular & Molecular Immunology, doi:10.1038/s41423-020-0436-5 (2020)

  7. Nickel induced transcriptional changes persist post exposure through epigenetic reprograming
    Cynthia C Jose*, Zhenjia Wang*, Vinay Singh Tanwar, Xiaoru Zhang, Chongzhi Zang#, Suresh Cuddapah#
    Epigenetics & Chromatin 12, 75 (2019)

  8. Deciphering essential cistromes using genome-wide CRISPR screens
    Teng Fei*, Wei Li*, Jingyu Peng*, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Jialiang Huang, Chongzhi Zang, X. Shirley Liu#, Myles Brown#
    Proceedings of the National Academy of Sciences USA 116, 25186–25195 (2019)

  9. YY1 is a cis-regulator in the organoid models of high mammographic density
    Qingsu Cheng, Mina Khoshdeli, Bradley S. Ferguson, Kosar Jabbari, Chongzhi Zang#, Bahram Parvin#
    Bioinformatics 36, 1663–1667 (2019)

  10. 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)

  11. 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)

  12. 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#, X. Shirley Liu#
    Cancer Research 77, e19–e22 (2017)

  13. 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)

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. 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)

  21. 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)

  22. 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)

  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. 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)

  25. 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)

  26. 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)

  27. 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)

  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. 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)

  30. 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)

  31. 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: September 20, 2020