Xiaoyi Cao

TitleAssistant Project Scientist
InstitutionUniversity of California San Diego
Address9500 Gilman Drive #0412
La Jolla CA 92093
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    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. Cao X, Yan Z, Wu Q, Zheng A, Zhong S. GIVE: portable genome browsers for personal websites. Genome Biol. 2018 Jul 18; 19(1):92. PMID: 30016975.
      View in: PubMed
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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.
    7. 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
    8. 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
    9. 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.
    10. 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.
    11. 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.
    12. 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.
    13. 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.
    14. Cao X, Zhong S. Enabling interspecies epigenomic comparison with CEpBrowser. Bioinformatics. 2013 May 01; 29(9):1223-5. PMID: 23543396; PMCID: PMC3634190.
    15. 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.
    16. 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
    17. 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.
    18. 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.
    19. 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.
    20. 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.
    21. 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.
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