Rizi Ai

TitleAssistant Project Scientist
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0359
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. Ainsworth RI, Ai R, Ding B, Li N, Zhang K, Wang W. Bayesian Networks Predict Neuronal Transdifferentiation. G3 (Bethesda). 2018 May 30. PMID: 29848620.
      View in: PubMed
    2. Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, Ding B, Gulko PS, Wang W, Firestein GS. Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun. 2018 May 15; 9(1):1921. PMID: 29765031.
      View in: PubMed
    3. Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, Nguyen JD, Salathia N, Shallcross J, Souaiaia T, Spaethling JM, Walker CP, Wang J, Wang K, Wang W, Wildberg A, Zheng L, Chow RH, Eberwine J, Knowles JA, Zhang K, Kim J. Assessing characteristics of RNA amplification methods for single cell RNA sequencing. BMC Genomics. 2016 11 24; 17(1):966. PMID: 27881084.
      View in: PubMed
    4. Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016 Jun 24; 352(6293):1586-90. PMID: 27339989; PMCID: PMC5038589.
    5. Ai R, Hammaker D, Boyle DL, Morgan R, Walsh AM, Fan S, Firestein GS, Wang W. Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nat Commun. 2016 Jun 10; 7:11849. PMID: 27282753; PMCID: PMC4906396.
    6. Maeshima K, Stanford SM, Hammaker D, Sacchetti C, Zeng LF, Ai R, Zhang V, Boyle DL, Aleman Muench GR, Feng GS, Whitaker JW, Zhang ZY, Wang W, Bottini N, Firestein GS. Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation. JCI Insight. 2016 May 19; 1(7). PMID: 27275015.
      View in: PubMed
    7. Fan S, Huang K, Ai R, Wang M, Wang W. Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data. Genomics. 2016 Apr; 107(4):132-7. PMID: 26921858.
      View in: PubMed
    8. Fan S, Li C, Ai R, Wang M, Firestein GS, Wang W. Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. Bioinformatics. 2016 06 15; 32(12):1773-8. PMID: 26883487; PMCID: PMC4908326 [Available on 06/15/17].
    9. Ai R, Whitaker JW, Boyle DL, Tak PP, Gerlag DM, Wang W, Firestein GS. DNA Methylome Signature in Synoviocytes From Patients With Early Rheumatoid Arthritis Compared to Synoviocytes From Patients With Longstanding Rheumatoid Arthritis. Arthritis Rheumatol. 2015 Jul; 67(7):1978-80. PMID: 25808728; PMCID: PMC4485541.
    10. Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, Wildberg A, Wang W. Normalization and noise reduction for single cell RNA-seq experiments. Bioinformatics. 2015 Jul 01; 31(13):2225-7. PMID: 25717193; PMCID: PMC4481848.
    11. Yaghmaei S, Roberts C, Ai R, Mizwicki MT, Chang CE. Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications. In Silico Pharmacol. 2013; 1:2. PMID: 25505647; PMCID: PMC4215818.
    12. Ai R, Chang CE. Ligand-specific homology modeling of human cannabinoid (CB1) receptor. J Mol Graph Model. 2012 Sep; 38:155-64. PMID: 23079645.
      View in: PubMed
    13. Chang CE, Ai R, Gutierrez M, Marsella MJ. Homology modeling of cannabinoid receptors: discovery of cannabinoid analogues for therapeutic use. Methods Mol Biol. 2012; 819:595-613. PMID: 22183560.
      View in: PubMed
    14. Ai R, Qaiser Fatmi M, Chang CE. T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles. J Comput Aided Mol Des. 2010 Oct; 24(10):819-27. PMID: 20689979; PMCID: PMC2940022.
    15. Fatmi MQ, Ai R, Chang CE. Synergistic regulation and ligand-induced conformational changes of tryptophan synthase. Biochemistry. 2009 Oct 20; 48(41):9921-31. PMID: 19764814.
      View in: PubMed