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Sharon Aviran

Title(s)Assistant Professor, Biomedical Engineering
SchoolUniversity of California, Davis
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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. Lai YH, Choudhary K, Cloutier SC, Xing Z, Aviran S, Tran EJ. Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics. 2019 05; 212(1):153-174. PMID: 30902808.
      View in: PubMed
    2. Choudhary K, Lai YH, Tran EJ, Aviran S. dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome Biol. 2019 02 21; 20(1):40. PMID: 30791935.
      View in: PubMed
    3. Vaziri S, Koehl P, Aviran S. Extracting information from RNA SHAPE data: Kalman filtering approach. PLoS One. 2018; 13(11):e0207029. PMID: 30462682.
      View in: PubMed
    4. Radecki P, Ledda M, Aviran S. Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures. Genes (Basel). 2018 Jun 14; 9(6). PMID: 29904019.
      View in: PubMed
    5. Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. Nucleic Acids Res. 2018 03 16; 46(5):2573-2584. PMID: 29294088.
      View in: PubMed
    6. Li H, Aviran S. Publisher Correction: Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun. 2018 03 13; 9(1):1110. PMID: 29535318.
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    7. Ledda M, Aviran S. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biol. 2018 03 01; 19(1):28. PMID: 29495968.
      View in: PubMed
    8. Li H, Aviran S. Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun. 2018 02 09; 9(1):606. PMID: 29426922.
      View in: PubMed
    9. Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst. 2017 05 24; 4(5):568-574.e7. PMID: 28501650.
      View in: PubMed
    10. Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. Quant Biol. 2017 Mar; 5(1):3-24. PMID: 28717530.
      View in: PubMed
    11. Choudhary K, Ruan L, Deng F, Shih N, Aviran S. SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. Bioinformatics. 2017 02 01; 33(3):441-443. PMID: 28172632.
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    12. Norris M, Kwok CK, Cheema J, Hartley M, Morris RJ, Aviran S, Ding Y. FoldAtlas: a repository for genome-wide RNA structure probing data. Bioinformatics. 2017 01 15; 33(2):306-308. PMID: 27663500.
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    13. Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics. 2016 12 01; 32(23):3575-3583. PMID: 27497441.
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    14. Deng F, Ledda M, Vaziri S, Aviran S. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA. 2016 08; 22(8):1109-19. PMID: 27251549.
      View in: PubMed
    15. Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. RNA. 2014 Dec; 20(12):1864-77. PMID: 25332375.
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    16. Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Curr Protoc Chem Biol. 2012 Dec 01; 4(4):275-97. PMID: 23788555.
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    17. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11063-8. PMID: 21642531.
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    18. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11069-74. PMID: 21642536.
      View in: PubMed
    19. Aviran S, Shah PS, Schaffer DV, Arkin AP. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol. 2010 Aug 12; 6(8). PMID: 20711350.
      View in: PubMed