Computational Multiomics LabTHE ZHENG LAB
PUBLICATIONS
Google Scholar
    # co-first authors, * co-correspondence
  • Zhang Y#, Zheng R#, Tsuji T, Wang CH, Liu X, Xing YH, Darcy J, Lynes M, Lundh M, Arianti R, Dong R, Rivera M, Kristóf E, Kahn CR, Chen K*, Tseng YH*, A conserved hormonal signalling–H2A.Z axis rapidly reorganizes 3D chromatin interactions in adipocyte thermogenesis, Nature Metabolism. https://www.nature.com/articles/s42255-026-01510-2
  • Zhu Z#, Zheng R#*, Yu Y, Zhang L, Chen K*. Human single-cell atlas analysis reveals heterogeneous endothelial signaling. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1093/gpbjnl/qzag025.
  • Zheng R#, Zhang Y#, Tsuji T, Gao X, Wagner A, Yosef N, Chen H, Zhang L, Tseng YH, Chen K. MEBOCOST: Metabolite-mediated Cell Communication Modeling by Single Cell Transcriptome. Nucleic Acids Res. https://academic.oup.com/nar/article/53/12/gkaf569/8174779
  • Li Y#, Wu X#, Sheng C#, Liu H#, Liu H#, Tang Y#, Liu C#, Ding Q#, Xie B#, Xiao X#, Zheng R#, Yu Q#, Guo Z, Ma J, Wang J, Gao J, Tian M, Wang W, Zhou J, Jiang L, Gu M, Shi S, Paull M, Yang G, Yang W, Landau S, Bao X, Hu X*, Liu XS*, Xiao T*. IGSF8 is an innate immune checkpoint and cancer immunotherapy target. Cell. 2024 May 23;187(11):2703-2716.e23.
  • Xian G#, Zheng R#, Lv J, Zhu S, Chen M, Gao X, Yuan S, Chen Z, Youker K, Cooke JP, Chen K$, Zhang L$, Transcription Factor 4 Maintains Endothelial Cell Identity by Inhibiting Endothelial to Mesenchymal Transition, Nucleic Acids Res. 2025. doi: 10.1093/nar/gkaf931
  • Shamsi F#, Zheng R#, Ho LL, Chen K*, Tseng YH*. Comprehensive analysis of intercellular communication in the thermogenic adipose niche. Commun Biol. 2023 Jul 21;6(1):761. doi: 10.1038/s42003-023-05140-2. PMID: 37479789; PMCID: PMC10361964.
  • Lv J, Meng S, Gu Q, Zheng R, Gao X, Kim JD, Chen M, Xia B, Zuo Y, Zhu S, Zhao D, Li Y, Wang G, Wang X, Meng Q, Cao Q, Cooke JP, Fang L, Chen K, Zhang L. Epigenetic landscape reveals MECOM as an endothelial lineage regulator. Nat Commun. 2023 Apr 25;14(1):2390. doi: 10.1038/s41467-023-38002-w. PMID: 37185814; PMCID: PMC10130150.
  • Wang Y, Zong H, Yang F, Tong Y, Xie Y, Zhang Z, Huang H, Zheng R, Wang S, Huang D, Tan F, Cheng S, Crabbe MJC, Zhang X. A knowledge empowered explainable gene ontology fingerprint approach to improve gene functional explication and prediction. iScience. 2023 Mar 7;26(4):106356. doi: 10.1016/j.isci.2023.106356. PMID: 37091235; PMCID: PMC10119605.
  • Han T, Wang X, Shi S, Zhang W, Wang J, Wu Q, Li Z, Fu J, Zheng R, Zhang J, Tang Q, Zhang P, Wang C. Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity. Cancer Immunol Res. 2023 Mar 1;11(3):381-398. doi: 10.1158/2326-6066.CIR-22-0056. PMID: 36629846.
  • Cui K, Gao X, Wang B, Wu H, Arulsamy K, Dong Y, Xiao Y, Jiang X, Malovichko MV, Li K, Peng Q, Lu YW, Zhu B, Zheng R, Wong S, Cowan DB, Linton M, Srivastava S, Shi J, Chen K, Chen H. Epsin Nanotherapy Regulates Cholesterol Transport to Fortify Atheroma Regression. Circ Res. 2023 Jan 6;132(1):e22-e42. doi: 10.1161/CIRCRESAHA.122.321723. Epub 2022 Nov 29. PMID: 36444722; PMCID: PMC9822875.
  • Gupta K, Wang G, Zhang S, Gao X, Zheng R, Zhang Y, Meng Q, Zhang L, Cao Q, Chen K. StripeDiff: Model-based algorithm for differential analysis of chromatin stripe. Sci Adv. 2022 Dec 9;8(49):eabk2246. doi: 10.1126/sciadv.abk2246. Epub 2022 Dec 7. PMID: 36475785; PMCID: PMC9728969.
  • Ding D, Zheng R, Tian Y, Jimenez R, Hou X, Weroha SJ, Wang L, Shi L, Huang H. Retinoblastoma protein as an intrinsic BRD4 inhibitor modulates small molecule BET inhibitor sensitivity in cancer. Nat Commun. 2022 Oct 23;13(1):6311. doi: 10.1038/s41467-022-34024-y. PMID: 36274096; PMCID: PMC9588789.
  • Wang Y, Tong Y, Zhang Z, Zheng R, Huang D, Yang J, Zong H, Tan F, Xie Y, Huang H, Zhang X. ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. Nucleic Acids Res. 2022 Jan 7;50(D1):D918-D927. doi: 10.1093/nar/gkab779. PMID: 34500462; PMCID: PMC8728280.
  • Sun D, Wang J, Han Y, Dong X, Ge J, Zheng R, Shi X, Wang B, Li Z, Ren P, Sun L, Yan Y, Zhang P, Zhang F, Li T, Wang C. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acids Res. 2021 Jan 8;49(D1):D1420-D1430. doi: 10.1093/nar/gkaa1020. PMID: 33179754; PMCID: PMC7778907.
  • Zheng R#, Dong X#, Shi X, Zhang X*, Meyer CA*, Cistrome Data Browser and Toolkit: Analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data. Quantitative Biology, 8, no. 3 (2020): 267-276.
  • Li W, Zhang N, Jin C, Long MD, Rajabi H, Yasumizu Y, Fushimi A, Yamashita N, Hagiwara M, Zheng R, Wang J, Kui L, Singh H, Kharbanda S, Hu Q, Liu S, Kufe D. MUC1-C drives stemness in progression of colitis to colorectal cancer. JCI Insight. 2020 Jun 18;5(12):e137112. doi: 10.1172/jci.insight.137112. PMID: 32427590; PMCID: PMC7406273.
  • Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XS. Determinants of transcription factor regulatory range. Nat Commun. 2020 May 18;11(1):2472. doi: 10.1038/s41467-020-16106-x. PMID: 32424124; PMCID: PMC7235260.
  • Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XS. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol. 2020 Feb 7;21(1):32. doi: 10.1186/s13059-020-1934-6. PMID: 32033573; PMCID: PMC7007693.
  • Li S, Wan C, Zheng R, Fan J, Dong X, Meyer CA, Liu XS. Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. Nucleic Acids Res. 2019 Jul 2;47(W1):W206-W211. doi: 10.1093/nar/gkz332. PMID: 31053864; PMCID: PMC6602521.
  • Zheng R#, Wan C#, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X*, Meyer CA*, Liu XS*. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 2019 Jan 8;47(D1):D729-D735. doi: 10.1093/nar/gky1094. PMID: 30462313; PMCID: PMC6324081.
  • Wang Y, Wang Y, Wang S, Tong Y, Jin L, Zong H, Zheng R, Yang J, Zhang Z, Ouyang E, Zhou M, Zhang X. GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer. Database (Oxford). 2019 Jan 1;2019:baz051. doi: 10.1093/database/baz051. PMID: 31089686; PMCID: PMC6517830.
  • 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 Res. 2017 Nov 1;77(21):e19-e22. doi: 10.1158/0008-5472.CAN-17-0327. PMID: 29092931; PMCID: PMC5826647.
  • 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 Res. 2017 Jan 4;45(D1):D658-D662. doi: 10.1093/nar/gkw983. Epub 2016 Oct 26. PMID: 27789702; PMCID: PMC5210658.
  • Liu S, Jiang L, Zhong T, Kong S, Zheng R, Kong F, Zhang C, Zhang L, An L. Effect of Acrylamide on Oocyte Nuclear Maturation and Cumulus Cells Apoptosis in Mouse In Vitro. PLoS One. 2015 Aug 14;10(8):e0135818. doi: 10.1371/journal.pone.0135818. PMID: 26275143; PMCID: PMC4537141.
  • Liu S*, Yu C, Cheng D, Han X, Jiang L, Zheng R, Meng X, Zhang T, Huo L. Aroclor 1254 impairs the development of ovarian follicles by inducing the apoptosis of granulosa cells. Toxicology Research. 2015;4(2):302-10.