Zang, Chongzhi, Ph.D.

Associate Professor
Center for Public Health Genomics
P. O. Box 800717
Charlottesville, VA 22908-0717
Phone: 1-434-243-5397
Fax: 1-434-982-1815
Email: zang@virginia.edu
Health System West Complex, Room 6131C

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

Other Appointments

• Associate Professor of Biochemistry and Molecular Genetics
• Associate Professor of Biomedical Engineering

Research Interests

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

Selected Recent Publications

* indicates co-first authors. ^# indicates co-senior authors. Underscored are Zang Lab members.

1. Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA
   Shengen Shawn Hu, Lin Liu, Qi Li, Wenjing Ma, Michael J. Guertin, Clifford A. Meyer, Ke Deng, Tingting Zhang, Chongzhi Zang
   Nature Communications 13, 5533 (2022)
2. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions
   Ryan J. Smith*, Hongpan Zhang*, Shengen Shawn Hu*, Theodora Yung, Roshane Francis, Lilian Lee, Mark W. Onaitis, Peter B. Dirks, Chongzhi Zang^#, Tae-Hee Kim^#
   Nature Communications 13, 2965 (2022)
3. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk
   Adam W. Turner*, Shengen Shawn Hu*, Jose Verdezoto Mosquera, Wei Feng Ma, Chani J. Hodonsky, Doris Wong, Gaëlle Auguste, Yipei Song, Katia Sol-Church, Emily Farber, Soumya Kundu, Anshul Kundaje, Nicolas G. Lopez, Lijiang Ma, Saikat Kumar B. Ghosh, Suna Onengut-Gumuscu, Euan A. Ashley, Thomas Quertermous, Aloke V. Finn, Nicholas J. Leeper, Jason C. Kovacic, Johan L.M. Björkgren, Chongzhi Zang^#, Clint L. Miller^#
   Nature Genetics, doi: 10.1038/s41588-022-01069-0 (2022)
4. Tcf1 preprograms the mobilization of glycolysis in central memory CD8⁺ T cells during recall responses
   Qiang Shan*, Shengen Shawn Hu*, Shaoqi Zhu, Xia Chen, Vladimir P. Badovinac, Weiqun Peng, Chongzhi Zang^#, Hai-Hui Xue^#
   Nature Immunology 23, 386-398 (2022)
5. UTX condensation underlies its tumour-suppressive activity
   Bi Shi*, Wei Li*, Yansu Song*, Zhenjia Wang*, Rui Ju, Aleksandra Ulman, Jing Hu, Francesco Palomba, Yanfang Zhao, John Philip Le, William Jarrard, David Dimoff, Michelle A. Digman, Enrico Gratton, Chongzhi Zang, Hao Jiang
   Nature 597, 726–731 (2021)
6. BARTweb: a web server for transcriptional regulator association analysis
   Wenjing Ma*, Zhenjia Wang*, Yifan Zhang, Neal E Magee, Yayi Feng, Ruoyao Shi, Yang Chen, Chongzhi Zang
   NAR Genomics and Bioinformatics 3(2), lqab022 (2021)
7. BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
   Zhenjia Wang, Yifan Zhang, Chongzhi Zang
   Bioinformatics 37, 3075–3078 (2021)
8. BART Cancer: a web resource for transcriptional regulators in cancer genomes
   Zachary V. Thomas, Zhenjia Wang, Chongzhi Zang
   NAR Cancer 3, zcab011 (2021)
9. RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data
   Chongzhi Zang^#, Yiren Wang, Weiqun Peng^#
   Quantitative Biology 8, 359–368 (2020)
10. 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)
11. 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)
12. Expanded encyclopaedias of DNA elements in the human and mouse genomes
    The ENCODE Project Consortium (including Chongzhi Zang), 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)
13. 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)
14. 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)
15. 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)
16. 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)
17. 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)

See complete list of publications at Google Scholar.

Recruitment

The Zang 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 Dr. Zang for any questions.