Sheng Zhong

Title(s)Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Revealing protein-protein interactions and RNA-protein interactions at genome-scale in two weeks
    NIH R01GM138852Sep 18, 2020 - Aug 31, 2024
    Role: Principal Investigator
    Spatial in situ mapping of RNA-chromatin interactions at transcriptome-and-genome scale in human tissues
    NIH UG3CA256960Sep 11, 2020 - Aug 31, 2022
    Role: Principal Investigator
    Extremely high-throughput mapping of protein, RNA, and chromatin interactions in health and disease
    NIH DP1DK126138Jul 30, 2020 - Jun 30, 2025
    Role: Principal Investigator
    Mapping RNA interactomes by sequencing
    NIH DP1HD087990Sep 30, 2015 - Sep 30, 2020
    Role: Principal Investigator
    The second phase of NIH Common Fund 4D Nucleome Network Organizational Hub
    NIH U01CA200147Sep 1, 2015 - Aug 31, 2025
    Role: Principal Investigator
    Non-coding Variants Predisposing to Age-related Macular Degeneration
    NIH R01HG008135Aug 24, 2015 - Jun 30, 2019
    Role: Principal Investigator
    Evolutionary models for gene regulatory networks
    NIH DP2OD007417Sep 30, 2010 - Jun 30, 2015
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nat Commun. 2023 Oct 16; 14(1):6519. Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S. PMID: 37845234; PMCID: PMC10579264.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Alu transposable elements rewire enhancer-promoter network through RNA pairing. Mol Cell. 2023 09 21; 83(18):3234-3235. Wen X, Zhong S. PMID: 37738962.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    3. Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. bioRxiv. 2023 Jun 28. Luo Z, Wen X, Zhao W, Nguyen TC, Wan X, Richard JLC, Zhong S. PMID: 37425846; PMCID: PMC10326989.
      View in: PubMed   Mentions:
    4. PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. Cell Metab. 2022 05 03; 34(5):651-653. Chen X, Calandrelli R, Girardini J, Yan Z, Tan Z, Xu X, Hiniker A, Zhong S. PMID: 35508105; PMCID: PMC9531314.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    5. Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries. Nat Commun. 2021 08 19; 12(1):5031. Liu L, Limsakul P, Meng X, Huang Y, Harrison RES, Huang TS, Shi Y, Yu Y, Charupanit K, Zhong S, Lu S, Zhang J, Chien S, Sun J, Wang Y. PMID: 34413312; PMCID: PMC8376904.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    6. Revealing protein-protein interactions at the transcriptome scale by sequencing. Mol Cell. 2021 10 07; 81(19):4091-4103.e9. Johnson KL, Qi Z, Yan Z, Wen X, Nguyen TC, Zaleta-Rivera K, Chen CJ, Fan X, Sriram K, Wan X, Chen ZB, Zhong S. PMID: 34348091; PMCID: PMC8500946.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    7. Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Nat Commun. 2020 10 15; 11(1):5211. Calandrelli R, Xu L, Luo Y, Wu W, Fan X, Nguyen T, Chen CJ, Sriram K, Tang X, Burns AB, Natarajan R, Chen ZB, Zhong S. PMID: 33060583; PMCID: PMC7566596.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    8. Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction. Genome Biol. 2020 09 10; 21(1):225. Huang N, Fan X, Zaleta-Rivera K, Nguyen TC, Zhou J, Luo Y, Gao J, Fang RH, Yan Z, Chen ZB, Zhang L, Zhong S. PMID: 32907628; PMCID: PMC7488101.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    9. Presymptomatic Increase of an Extracellular RNA in Blood Plasma Associates with the Development of Alzheimer's Disease. Curr Biol. 2020 05 18; 30(10):1771-1782.e3. Yan Z, Zhou Z, Wu Q, Chen ZB, Koo EH, Zhong S. PMID: 32220323.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    10. Mapping RNA-chromatin interactions by sequencing with iMARGI. Nat Protoc. 2019 11; 14(11):3243-3272. Wu W, Yan Z, Nguyen TC, Bouman Chen Z, Chien S, Zhong S. PMID: 31619811; PMCID: PMC7314528.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    11. Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. Proc Natl Acad Sci U S A. 2019 09 17; 116(38):19200-19208. Zhou Z, Wu Q, Yan Z, Zheng H, Chen CJ, Liu Y, Qi Z, Calandrelli R, Chen Z, Chien S, Su HI, Zhong S. PMID: 31481608; PMCID: PMC6754586.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    12. EpiAlignment: alignment with both DNA sequence and epigenomic data. Nucleic Acids Res. 2019 07 02; 47(W1):W11-W19. Lu J, Cao X, Zhong S. PMID: 31114924; PMCID: PMC6602515.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    13. Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. Proc Natl Acad Sci U S A. 2019 02 19; 116(8):3328-3337. Yan Z, Huang N, Wu W, Chen W, Jiang Y, Chen J, Huang X, Wen X, Xu J, Jin Q, Zhang K, Chen Z, Chien S, Zhong S. PMID: 30718424; PMCID: PMC6386723.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    14. A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. PLoS Comput Biol. 2018 12; 14(12):e1006673. Lu J, Cao X, Zhong S. PMID: 30586383; PMCID: PMC6324829.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    15. GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Genomics Proteomics Bioinformatics. 2018 10; 16(5):365-372. Calandrelli R, Wu Q, Guan J, Zhong S. PMID: 30553884; PMCID: PMC6364044.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    16. RNA, Action through Interactions. Trends Genet. 2018 11; 34(11):867-882. Nguyen TC, Zaleta-Rivera K, Huang X, Dai X, Zhong S. PMID: 30177410; PMCID: PMC6195460.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    17. Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience. 2018 Sep 28; 7:16-29. Biase FH, Wu Q, Calandrelli R, Rivas-Astroza M, Zhou S, Chen Z, Zhong S. PMID: 30267678; PMCID: PMC6135740.
      View in: PubMed   Mentions: 4  
    18. GIVE: portable genome browsers for personal websites. Genome Biol. 2018 07 18; 19(1):92. Cao X, Yan Z, Wu Q, Zheng A, Zhong S. PMID: 30016975; PMCID: PMC6050681.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    19. RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. iScience. 2018 Jun 29; 4:204-215. Chen W, Yan Z, Li S, Huang N, Huang X, Zhang J, Zhong S. PMID: 30240742; PMCID: PMC6146591.
      View in: PubMed   Mentions: 21  
    20. Trends in Cannabis Use Disorder among Pregnant Women in the U.S., 1993-2014. J Gen Intern Med. 2018 03; 33(3):245-246. Shi Y, Zhong S. PMID: 29030807; PMCID: PMC5834953.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    21. Pattern-based Search of Epigenomic Data Using GeNemo. J Vis Exp. 2017 10 08; (128). Zheng A, Cao X, Zhong S. PMID: 29053670; PMCID: PMC5752390.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    22. SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Cell Rep. 2017 03 28; 18(13):3117-3128. Xiao S, Lu J, Sridhar B, Cao X, Yu P, Zhao T, Chen CC, McDee D, Sloofman L, Wang Y, Rivas-Astroza M, Telugu BPVL, Levasseur D, Zhang K, Liang H, Zhao JC, Tanaka TS, Stormo G, Zhong S. PMID: 28355564; PMCID: PMC5466819.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    23. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol. 2017 Feb 20; 27(4):602-609. Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S. PMID: 28132817; PMCID: PMC5319903.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimalsCells
    24. Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun. 2016 06 24; 7:12023. Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S. PMID: 27338251; PMCID: PMC4931010.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    25. GeNemo: a search engine for web-based functional genomic data. Nucleic Acids Res. 2016 07 08; 44(W1):W122-7. Zhang Y, Cao X, Zhong S. PMID: 27098038; PMCID: PMC4987887.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    26. P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell. 2015 Sep 17; 59(6):931-40. Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, Lin D, Wang W, Li G, Xu Y, Li O, Chung C, Yeh E, Jafari M, Ai M, Zhong Z, Shi W, Zheng L, Krawczyk M, Chen D, Shi C, Zin C, Zhu J, Mellon PL, Gao W, Abagyan R, Zhang L, Sun X, Zhong S, Zhuo Y, Rosenfeld MG, Liu Y, Zhang K. PMID: 26365380; PMCID: PMC4648709.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    27. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. PMID: 25409824; PMCID: PMC4266106.
      View in: PubMed   Mentions: 838     Fields:    Translation:HumansAnimalsCells
    28. Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res. 2014 Nov; 24(11):1787-96. Biase FH, Cao X, Zhong S. PMID: 25096407; PMCID: PMC4216920.
      View in: PubMed   Mentions: 94     Fields:    Translation:AnimalsCells
    29. Comparative epigenomics: defining and utilizing epigenomic variations across species, time-course, and individuals. Wiley Interdiscip Rev Syst Biol Med. 2014 Sep-Oct; 6(5):345-52. Xiao S, Cao X, Zhong S. PMID: 25044241; PMCID: PMC4851441.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    30. From genomes to societies: a holistic view of determinants of human health. Curr Opin Biotechnol. 2014 Aug; 28:134-42. Shi Y, Zhong S. PMID: 24686286; PMCID: PMC4111965.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    31. Enabling interspecies epigenomic comparison with CEpBrowser. Bioinformatics. 2013 May 01; 29(9):1223-5. Cao X, Zhong S. PMID: 23543396; PMCID: PMC3634190.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    32. Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Res. 2013 Feb; 23(2):352-64. Yu P, Xiao S, Xin X, Song CX, Huang W, McDee D, Tanaka T, Wang T, He C, Zhong S. PMID: 23033340; PMCID: PMC3561876.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
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