Chongzhi Zang Lab  

Publications


Google Scholar profile


Recent Preprints

* indicates authors with equal contributions. # indicates co-corresponding authors. Underscored are lab members.
  1. BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
    Zhenjia Wang, Yifan Zhang, Chongzhi Zang
    bioRxiv 2020.08.19.258095 (2020)

  2. BARTweb: a web server for transcription factor association analysis
    Wenjing Ma*, Zhenjia Wang*, Yifan Zhang*, Neal E Magee, Yang Chen, Chongzhi Zang
    bioRxiv 2020.01.17.952838 (2020)


Selected Publications

  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. An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding
    Luke T. Oostdyk, Zhenjia Wang, Chongzhi Zang, Hui Li, Michael J. McConnell, Bryce M. Paschal
    Scientific Reports 10, 4844 (2020)

  8. 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)

  9. 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)

  10. 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)

  11. Specific inhibition of DPY30 activity by ASH2L-derived peptides suppressesblood cancer cell growth
    Kushani K. Shah, Robert H. Whitaker, Theodore Busby, Jing Hu, Bi Shi, Zhenjia Wang, Chongzhi Zang, William J.Placzek, Hao Jiang
    Experimental Cell Research 382, 111485 (2019)

  12. 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)

  13. 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 115, 7869–7878 (2018)

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. Prior to joining UVA

  19. 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)

  20. 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)

  21. 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)

  22. 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)

  23. 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)

  24. 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)

  25. 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)

  26. 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)

  27. 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)

  28. 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)

  29. 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)

  30. 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)

  31. 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)

  32. 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)

  33. 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)

  34. 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)

  35. 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)

  36. 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)

  37. 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)

  38. 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)

  39. 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)

  40. 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)

  41. 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)

  42. 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)

  43. 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)

  44. 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)

  45. 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: September 15, 2020