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Chongzhi Zang, Ph.D. - Publications

Affiliations: 
2011 Physics The George Washington University, Washington, DC, United States 
 2010-2016 Harvard University, Cambridge, MA, United States 
 2016- University of Virginia, Charlottesville, VA 
Area:
General Biophysics, Bioinformatics, Computational Biology
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58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zhao X, Hu W, Park SR, Zhu S, Hu SS, Zang C, Peng W, Shan Q, Xue HH. Publisher Correction: The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8T cell fates. Nature Immunology. PMID 38347084 DOI: 10.1038/s41590-024-01780-6  0.617
2024 Zhao X, Hu W, Park SR, Zhu S, Hu SS, Zang C, Peng W, Shan Q, Xue HH. The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8 T cell fates. Nature Immunology. PMID 38238608 DOI: 10.1038/s41590-023-01720-w  0.635
2022 Hu SS, Liu L, Li Q, Ma W, Guertin MJ, Meyer CA, Deng K, Zhang T, Zang C. Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Nature Communications. 13: 5533. PMID 36130957 DOI: 10.1038/s41467-022-33194-z  0.317
2022 Jiang Y, Harigaya Y, Zhang Z, Zhang H, Zang C, Zhang NR. Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions. Cell Systems. PMID 36055233 DOI: 10.1016/j.cels.2022.08.004  0.404
2022 Smith RJ, Zhang H, Hu SS, Yung T, Francis R, Lee L, Onaitis MW, Dirks PB, Zang C, Kim TH. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. Nature Communications. 13: 2965. PMID 35618699 DOI: 10.1038/s41467-022-30624-w  0.369
2022 Shan Q, Hu SS, Zhu S, Chen X, Badovinac VP, Peng W, Zang C, Xue HH. Publisher Correction: Tcf1 preprograms the mobilization of glycolysis in central memory CD8 T cells during recall responses. Nature Immunology. 23: 815. PMID 35414119 DOI: 10.1038/s41590-022-01202-5  0.593
2022 Shan Q, Hu SS, Zhu S, Chen X, Badovinac VP, Peng W, Zang C, Xue HH. Tcf1 preprograms the mobilization of glycolysis in central memory CD8 T cells during recall responses. Nature Immunology. PMID 35190717 DOI: 10.1038/s41590-022-01131-3  0.659
2021 Shi B, Li W, Song Y, Wang Z, Ju R, Ulman A, Hu J, Palomba F, Zhao Y, Le JP, Jarrard W, Dimoff D, Digman MA, Gratton E, Zang C, et al. UTX condensation underlies its tumour-suppressive activity. Nature. PMID 34526716 DOI: 10.1038/s41586-021-03903-7  0.423
2021 Ma W, Wang Z, Zhang Y, Magee NE, Feng Y, Shi R, Chen Y, Zang C. BARTweb: a web server for transcriptional regulator association analysis. Nar Genomics and Bioinformatics. 3: lqab022. PMID 33860225 DOI: 10.1093/nargab/lqab022  0.391
2021 Thomas ZV, Wang Z, Zang C. BART Cancer: a web resource for transcriptional regulators in cancer genomes. Nar Cancer. 3: zcab011. PMID 33778495 DOI: 10.1093/narcan/zcab011  0.326
2021 Wang Z, Zhang Y, Zang C. BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data. Bioinformatics (Oxford, England). PMID 33720325 DOI: 10.1093/bioinformatics/btab173  0.36
2020 Zang C, Wang Y, Peng W. RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data. Quantitative Biology (Beijing, China). 8: 359-368. PMID 34327037 DOI: 10.1007/s40484-020-0225-2  0.701
2020 Fang C, Wang Z, Han C, Safgren SL, Helmin KA, Adelman ER, Serafin V, Basso G, Eagen KP, Gaspar-Maia A, Figueroa ME, Singer BD, Ratan A, Ntziachristos P, Zang C. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. Genome Biology. 21: 247. PMID 32933554 DOI: 10.1186/S13059-020-02152-7  0.406
2020 Chen D, Chen QY, Wang Z, Zhu Y, Kluz T, Tan W, Li J, Wu F, Fang L, Zhang X, He R, Shen S, Sun H, Zang C, Jin C, et al. Polyadenylation of Histone H3.1 mRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements. Iscience. 23: 101518. PMID 32920490 DOI: 10.1016/J.Isci.2020.101518  0.38
2020 Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, ... ... Zang C, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/S41467-020-14743-W  0.432
2020 Shan Q, Hu S, Chen X, Danahy DB, Badovinac VP, Zang C, Xue HH. Ectopic Tcf1 expression instills a stem-like program in exhausted CD8 T cells to enhance viral and tumor immunity. Cellular & Molecular Immunology. PMID 32341523 DOI: 10.1038/S41423-020-0436-5  0.407
2020 Wang Z, Ma W, Zhang Y, Magee NE, Chen Y, Zang C. Abstract 3214: BART: An integrative bioinformatics toolkit and web server for functional transcription factor prediction Cancer Research. 80: 3214-3214. DOI: 10.1158/1538-7445.Am2020-3214  0.501
2019 Jose CC, Wang Z, Tanwar VS, Zhang X, Zang C, Cuddapah S. Nickel-induced transcriptional changes persist  post exposure through epigenetic reprogramming. Epigenetics & Chromatin. 12: 75. PMID 31856895 DOI: 10.1186/S13072-019-0324-3  0.701
2019 Fei T, Li W, Peng J, Xiao T, Chen CH, Wu A, Huang J, Zang C, Liu XS, Brown M. Deciphering essential cistromes using genome-wide CRISPR screens. Proceedings of the National Academy of Sciences of the United States of America. PMID 31727847 DOI: 10.1073/Pnas.1908155116  0.459
2019 Cheng Q, Khoshdeli M, Ferguson BS, Jabbari K, Zang C, Parvin B. YY1 is a Cis-regulator in the organoid models of high mammographic density. Bioinformatics (Oxford, England). PMID 31688895 DOI: 10.1093/Bioinformatics/Btz812  0.33
2019 Shah KK, Whitaker RH, Busby T, Hu J, Shi B, Wang Z, Zang C, Placzek WJ, Jiang H. Specific inhibition of DPY30 activity by ASH2L-derived peptides suppresses blood cancer cell growth. Experimental Cell Research. PMID 31251903 DOI: 10.1016/J.Yexcr.2019.06.030  0.329
2019 Fang C, Wang Z, Martinez CA, Ntziachristos P, Zang C. Abstract 5181: Global alteration of CTCF binding in the cancer genome Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-5181  0.308
2018 Xiao T, Li W, Wang X, Xu H, Yang J, Wu Q, Huang Y, Geradts J, Jiang P, Fei T, Chi D, Zang C, Liao Q, Rennhack J, Andrechek E, et al. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987050 DOI: 10.1073/Pnas.1722617115  0.61
2018 Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinformatics (Oxford, England). PMID 29608647 DOI: 10.1093/Bioinformatics/Bty194  0.457
2018 Jose CC, Jagannathan L, Tanwar VS, Zhang X, Zang C, Cuddapah S. Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1. Molecular Carcinogenesis. PMID 29528143 DOI: 10.1002/Mc.22802  0.672
2017 Mei S, Meyer CA, Zheng R, Qin Q, Wu Q, Jiang P, Li B, Shi X, Wang B, Fan J, Shih C, Brown M, Zang C, Liu XS. Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer. Cancer Research. 77: e19-e22. PMID 29092931 DOI: 10.1158/0008-5472.Can-17-0327  0.641
2017 Severson E, Arnett KL, Wang H, Zang C, Taing L, Liu H, Pear WS, Shirley Liu X, Blacklow SC, Aster JC. Genome-wide identification and characterization of Notch transcription complex-binding sequence-paired sites in leukemia cells. Science Signaling. 10. PMID 28465412 DOI: 10.1126/Scisignal.Aag1598  0.467
2017 Xiao T, Li W, Wang X, Xu H, Wu Q, Jiang P, Yang J, Fei T, Zang C, Liao Q, Rennhack J, Andrechek E, Li N, Jeselsohn R, Liu SX, et al. Abstract PR06: CRISPR screens identified drivers of endocrine resistance and synthetic lethal vulnerabilities in breast cancer Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr06  0.476
2016 Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Research. PMID 27789702 DOI: 10.1093/Nar/Gkw983  0.664
2016 Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, et al. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. Bmc Bioinformatics. 17: 404. PMID 27716038 DOI: 10.1186/S12859-016-1274-4  0.659
2016 Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li XL, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Research. PMID 27466232 DOI: 10.1101/Gr.201574.115  0.692
2016 Zang C, Luyten A, Chen J, Liu XS, Shivdasani RA. NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes. Scientific Reports. 6: 30255. PMID 27457419 DOI: 10.1038/Srep30255  0.468
2016 Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nature Communications. 7: 11305. PMID 27072482 DOI: 10.1038/Ncomms11305  0.59
2016 Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. Abstract B24: High-dimensional genomic data integration and bias correction using MANCIE Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-B24  0.409
2015 Xu H, Xu K, He HH, Zang C, Chen CH, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu XS. Integrative analysis reveals the transcriptional collaboration between EZH2 and E2F1 in the regulation of cancer-related gene expression. Molecular Cancer Research : McR. PMID 26659825 DOI: 10.1158/1541-7786.Mcr-15-0313  0.737
2015 Jiang P, Wang H, Li W, Zang C, Li B, Wong YJ, Meyer C, Liu JS, Aster JC, Liu XS. Network analysis of gene essentiality in functional genomics experiments. Genome Biology. 16: 239. PMID 26518695 DOI: 10.1186/S13059-015-0808-9  0.656
2015 Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K, Ripke S, Day FR, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature Genetics. PMID 26414678 DOI: 10.1038/Ng.3404  0.502
2015 Wang H, Zang C, Liu XS, Aster JC. The role of Notch receptors in transcriptional regulation. Journal of Cellular Physiology. 230: 982-8. PMID 25418913 DOI: 10.1002/Jcp.24872  0.622
2014 Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E, Kähler AK, Hultman CM, Purcell SM, et al. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. American Journal of Human Genetics. 95: 535-52. PMID 25439723 DOI: 10.1016/J.Ajhg.2014.10.004  0.466
2014 Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, et al. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proceedings of the National Academy of Sciences of the United States of America. 111: E4946-53. PMID 25369933 DOI: 10.1073/Pnas.1407079111  0.641
2014 Luyten A, Zang C, Liu XS, Shivdasani RA. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells. Genes & Development. 28: 1827-39. PMID 25128499 DOI: 10.1101/Gad.240101.114  0.647
2014 Stoeck A, Lejnine S, Truong A, Pan L, Wang H, Zang C, Yuan J, Ware C, MacLean J, Garrett-Engele PW, Kluk M, Laskey J, Haines BB, Moskaluk C, Zawel L, et al. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discovery. 4: 1154-67. PMID 25104330 DOI: 10.1158/2159-8290.CD-13-0830  0.487
2014 Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology. 15: 419. PMID 25103624 DOI: 10.1186/S13059-014-0419-X  0.634
2014 Wang H, Zang C, Taing L, Arnett KL, Wong YJ, Pear WS, Blacklow SC, Liu XS, Aster JC. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proceedings of the National Academy of Sciences of the United States of America. 111: 705-10. PMID 24374627 DOI: 10.1073/pnas.1315023111  0.592
2014 He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods. 11: 73-8. PMID 24317252 DOI: 10.1038/Nmeth.2762  0.649
2014 Wang H, Yashiro-Ohtani Y, Zang C, Wong YJ, Bailis W, Knoechel B, Bernstein B, Blacklow S, Liu XS, Pear WS, Aster JC. Alternative Super-Enhancer States Determine MYC Sensitivity to Notch and Brd4 Inhibitors in T Lymphoblastic Leukemia/Lymphoma Blood. 124: 863-863. DOI: 10.1182/Blood.V124.21.863.863  0.485
2013 Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature Protocols. 8: 2502-15. PMID 24263090 DOI: 10.1038/Nprot.2013.150  0.591
2012 Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. Plos Genetics. 8: e1002649. PMID 22511886 DOI: 10.1371/Journal.Pgen.1002649  0.764
2012 Wang H, Zang C, Taing L, Wong H, Yashiro-Ohtani Y, Blacklow S, Pear WS, Liu XS, Aster JC. Genome-Wide Analysis of NOTCH1, ETS Family Factors, and RUNX1 Binding in Human T Lymphoblastic Leukemia Cells Reveals Distinct Regulatory Elements Blood. 120: 1277-1277. DOI: 10.1182/Blood.V120.21.1277.1277  0.404
2010 Daniel JA, Santos MA, Wang Z, Zang C, Schwab KR, Jankovic M, Filsuf D, Chen HT, Gazumyan A, Yamane A, Cho YW, Sun HW, Ge K, Peng W, Nussenzweig MC, et al. PTIP promotes chromatin changes critical for immunoglobulin class switch recombination Science. 329: 917-923. PMID 20671152 DOI: 10.1126/Science.1187942  0.767
2010 Wei L, Vahedi G, Sun HW, Watford WT, Takatori H, Ramos HL, Takahashi H, Liang J, Gutierrez-Cruz G, Zang C, Peng W, O'Shea JJ, Kanno Y. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity. 32: 840-51. PMID 20620946 DOI: 10.1016/J.Immuni.2010.06.003  0.738
2009 Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 138: 1019-31. PMID 19698979 DOI: 10.1016/J.Cell.2009.06.049  0.801
2009 Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nature Genetics. 41: 941-5. PMID 19633671 DOI: 10.1038/Ng.409  0.768
2009 Araki Y, Wang Z, Zang C, Wood WH, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity. 30: 912-25. PMID 19523850 DOI: 10.1016/J.Immuni.2009.05.006  0.802
2009 Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (Oxford, England). 25: 1952-8. PMID 19505939 DOI: 10.1093/Bioinformatics/Btp340  0.805
2009 Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity. 30: 155-67. PMID 19144320 DOI: 10.1016/J.Immuni.2008.12.009  0.775
2009 Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 4: 80-93. PMID 19128795 DOI: 10.1016/J.Stem.2008.11.011  0.792
2008 Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154  0.769
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