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Sheng Zhong

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentBioengineering
Address9500 Gilman Drive #0412
La Jolla CA 92093
Phone858-246-1118
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    Collapse Research 
    Collapse Research Activities and Funding
    Mapping RNA interactomes by sequencing
    NIH/NICHD DP1HD087990Sep 30, 2015 - Jul 31, 2020
    Role: Principal Investigator
    The Organizational Hub and Web Portal for the 4D Nucleome Network
    NIH/NCI U01CA200147Sep 1, 2015 - Aug 31, 2020
    Role: Principal Investigator
    Non-coding Variants Predisposing to Age-related Macular Degeneration
    NIH/NHGRI R01HG008135Aug 24, 2015 - Jun 30, 2018
    Role: Principal Investigator
    Evolutionary models for gene regulatory networks
    NIH DP2OD007417Sep 30, 2010 - Aug 31, 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.
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    1. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. Corrigendum: The 4D nucleome project. Nature. 2017 12 14; 552(7684):278. PMID: 29168505.
      View in: PubMed
    2. Shi Y, Zhong S. Trends in Cannabis Use Disorder among Pregnant Women in the U.S., 1993-2014. J Gen Intern Med. 2017 Oct 13. PMID: 29030807.
      View in: PubMed
    3. Zheng A, Cao X, Zhong S. Pattern-based Search of Epigenomic Data Using GeNemo. J Vis Exp. 2017 10 08; (128). PMID: 29053670.
      View in: PubMed
    4. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226. PMID: 28905911.
      View in: PubMed
    5. 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. SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Cell Rep. 2017 03 28; 18(13):3117-3128. PMID: 28355564.
      View in: PubMed
    6. Maier JA, Rivas-Astroza M, Deng J, Dowling A, Oboikovitz P, Cao X, Behringer RR, Cretekos CJ, Rasweiler JJ, Zhong S, Sears KE. Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC Evol Biol. 2017 03 23; 17(1):86. PMID: 28335721.
      View in: PubMed
    7. Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol. 2017 02 20; 27(4):610-612. PMID: 28222283.
      View in: PubMed
    8. Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol. 2017 Feb 20; 27(4):602-609. PMID: 28132817.
      View in: PubMed
    9. Zhang H, Fei R, Xue B, Yu S, Zhang Z, Zhong S, Gao Y, Zhou X. Pnserpin: A Novel Serine Protease Inhibitor from Extremophile Pyrobaculum neutrophilum. Int J Mol Sci. 2017 Jan 07; 18(1). PMID: 28067849.
      View in: PubMed
    10. Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S. Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun. 2016 Jun 24; 7:12023. PMID: 27338251; PMCID: PMC4931010.
    11. Zhang Y, Cao X, Zhong S. GeNemo: a search engine for web-based functional genomic data. Nucleic Acids Res. 2016 07 08; 44(W1):W122-7. PMID: 27098038.
      View in: PubMed
    12. 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. P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell. 2015 Sep 17; 59(6):931-40. PMID: 26365380; PMCID: PMC4648709.
    13. Sears KE, Maier JA, Rivas-Astroza M, Poe R, Zhong S, Kosog K, Marcot JD, Behringer RR, Cretekos CJ, Rasweiler JJ, Rapti Z. The Relationship between Gene Network Structure and Expression Variation among Individuals and Species. PLoS Genet. 2015 Aug; 11(8):e1005398. PMID: 26317994; PMCID: PMC4552942.
    14. 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. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. PMID: 25409824.
      View in: PubMed
    15. Huang W, Cao X, Biase FH, Yu P, Zhong S. Time-variant clustering model for understanding cell fate decisions. Proc Natl Acad Sci U S A. 2014 Nov 04; 111(44):E4797-806. PMID: 25339442; PMCID: PMC4226122.
    16. Biase FH, Cao X, Zhong S. 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. PMID: 25096407; PMCID: PMC4216920.
    17. Xiao S, Cao X, Zhong S. 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. PMID: 25044241; PMCID: PMC4851441.
    18. Shi Y, Zhong S. From genomes to societies: a holistic view of determinants of human health. Curr Opin Biotechnol. 2014 Aug; 28:134-42. PMID: 24686286; PMCID: PMC4111965.
    19. Chen CC, Xiao S, Xie D, Cao X, Song CX, Wang T, He C, Zhong S. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput Biol. 2013; 9(12):e1003367. PMID: 24339764; PMCID: PMC3854512.
    20. Cingolani P, Cao X, Khetani RS, Chen CC, Coon M, Sammak A, Bollig-Fischer A, Land S, Huang Y, Hudson ME, Garfinkel MD, Zhong S, Robinson GE, Ruden DM. Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. BMC Genomics. 2013 Sep 30; 14:666. PMID: 24079845; PMCID: PMC3850688.
    21. Cao X, Zhong S. Enabling interspecies epigenomic comparison with CEpBrowser. Bioinformatics. 2013 May 01; 29(9):1223-5. PMID: 23543396; PMCID: PMC3634190.
    22. Yu P, Xiao S, Xin X, Song CX, Huang W, McDee D, Tanaka T, Wang T, He C, Zhong S. Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Res. 2013 Feb; 23(2):352-64. PMID: 23033340; PMCID: PMC3561876.
    23. Zelin E, Zhang Y, Toogun OA, Zhong S, Freeman BC. The p23 molecular chaperone and GCN5 acetylase jointly modulate protein-DNA dynamics and open chromatin status. Mol Cell. 2012 Nov 09; 48(3):459-70. PMID: 23022381; PMCID: PMC3496002.
    24. Xiao S, Xie D, Cao X, Yu P, Xing X, Chen CC, Musselman M, Xie M, West FD, Lewin HA, Wang T, Zhong S. Comparative epigenomic annotation of regulatory DNA. Cell. 2012 Jun 08; 149(6):1381-92. PMID: 22682255; PMCID: PMC3372872.
    25. Sears KE, Patel A, Hübler M, Cao X, Vandeberg JL, Zhong S. Disparate Igf1 expression and growth in the fore- and hind limbs of a marsupial mammal (Monodelphis domestica). J Exp Zool B Mol Dev Evol. 2012 Jun; 318(4):279-93. PMID: 22821864.
      View in: PubMed
    26. Lee J, Seok S, Yu P, Kim K, Smith Z, Rivas-Astroza M, Zhong S, Kemper JK. Genomic analysis of hepatic farnesoid X receptor binding sites reveals altered binding in obesity and direct gene repression by farnesoid X receptor in mice. Hepatology. 2012 Jul; 56(1):108-17. PMID: 22278336; PMCID: PMC3343176.
    27. Ament SA, Wang Y, Chen CC, Blatti CA, Hong F, Liang ZS, Negre N, White KP, Rodriguez-Zas SL, Mizzen CA, Sinha S, Zhong S, Robinson GE. The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression. PLoS Genet. 2012; 8(3):e1002596. PMID: 22479195; PMCID: PMC3315457.
    28. Rivas-Astroza M, Xie D, Cao X, Zhong S. Mapping personal functional data to personal genomes. Bioinformatics. 2011 Dec 15; 27(24):3427-9. PMID: 22006915; PMCID: PMC3232370.
    29. Xie D, Chen CC, He X, Cao X, Zhong S. Towards an evolutionary model of transcription networks. PLoS Comput Biol. 2011 Jun; 7(6):e1002064. PMID: 21695281; PMCID: PMC3111474.
    30. Huang W, Cao X, Zhong S. Network-based comparison of temporal gene expression patterns. Bioinformatics. 2010 Dec 01; 26(23):2944-51. PMID: 20889495; PMCID: PMC2982154.
    31. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug; 28(8):827-38. PMID: 20676074.
      View in: PubMed
    32. Cai J, Xie D, Fan Z, Chipperfield H, Marden J, Wong WH, Zhong S. Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells. PLoS Comput Biol. 2010 Mar 12; 6(3):e1000707. PMID: 20300647; PMCID: PMC2837392.
    33. Xie D, Chen CC, Ptaszek LM, Xiao S, Cao X, Fang F, Ng HH, Lewin HA, Cowan C, Zhong S. Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res. 2010 Jun; 20(6):804-15. PMID: 20219939; PMCID: PMC2877577.
    34. Hong F, Fang F, He X, Cao X, Chipperfield H, Xie D, Wong WH, Ng HH, Zhong S. Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells. PLoS Comput Biol. 2009 Dec; 5(12):e1000607. PMID: 20019792; PMCID: PMC2784941.
    35. He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PLoS One. 2009 Dec 01; 4(12):e8155. PMID: 19956545; PMCID: PMC2780727.
    36. Chen CC, Zhong S. Inferring gene regulatory networks by thermodynamic modeling. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S19. PMID: 18831784; PMCID: PMC2559883.
    37. Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics. 2008 Aug 12; 9 Suppl 9:S10. PMID: 18793455; PMCID: PMC2537561.
    38. Xie D, Cai J, Chia NY, Ng HH, Zhong S. Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Res. 2008 Aug; 18(8):1325-35. PMID: 18490265; PMCID: PMC2493426.
    39. Jiang J, Chan YS, Loh YH, Cai J, Tong GQ, Lim CA, Robson P, Zhong S, Ng HH. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol. 2008 Mar; 10(3):353-60. PMID: 18264089.
      View in: PubMed
    40. Chen CC, Zhu XG, Zhong S. Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells. BMC Genomics. 2008; 9 Suppl 1:S18. PMID: 18366607; PMCID: PMC2386060.
    41. Zhong S, Xie D. Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework. Artif Intell Med. 2007 Oct; 41(2):105-15. PMID: 17913480.
      View in: PubMed
    42. Lu Y, He X, Zhong S. Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W105-14. PMID: 17545194; PMCID: PMC1933158.
    43. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep; 24(9):1151-61. PMID: 16964229.
      View in: PubMed
    44. Ai L, Tao Q, Zhong S, Fields CR, Kim WJ, Lee MW, Cui Y, Brown KD, Robertson KD. Inactivation of Wnt inhibitory factor-1 (WIF1) expression by epigenetic silencing is a common event in breast cancer. Carcinogenesis. 2006 Jul; 27(7):1341-8. PMID: 16501252.
      View in: PubMed
    45. Zhong S, Li C, Wong WH. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. 2003 Jul 01; 31(13):3483-6. PMID: 12824349; PMCID: PMC169004.
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