Sharon Aviran

Title(s)Associate Professor, Biomedical Engineering
SchoolEngineering
Phone530-752-6978
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    Methods for RNA structural analysis using computation and structure mapping exper
    NIH R00HG006860Jul 23, 2012 - Dec 31, 2017
    Role: Principal Investigator
    Methods for RNA structural analysis using computation and structure mapping exper
    NIH K99HG006860Jul 23, 2012 - Dec 30, 2013
    Role: Principal Investigator

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    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. Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer. Theranostics. 2022; 12(18):7884-7902. Wang J, Fite BZ, Kare AJ, Wu B, Raie M, Tumbale SK, Zhang N, Davis RR, Tepper CG, Aviran S, Newman AM, King DA, Ferrara KW. PMID: 36451859; PMCID: PMC9706583.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    2. Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data. J Mol Biol. 2022 09 30; 434(18):167635. Aviran S, Incarnato D. PMID: 35595163.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    3. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. RNA Biol. 2021 10 15; 18(sup1):521-536. Radecki P, Uppuluri R, Deshpande K, Aviran S. PMID: 34606413; PMCID: PMC8677038.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    4. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. NAR Genom Bioinform. 2021 Sep; 3(3):lqab073. Radecki P, Uppuluri R, Aviran S. PMID: 34447931; PMCID: PMC8384053.
      View in: PubMed   Mentions: 1  
    5. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020 05 01; 11(1):2173. Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA. PMID: 32358529; PMCID: PMC7195438.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    6. Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics. 2019 05; 212(1):153-174. Lai YH, Choudhary K, Cloutier SC, Xing Z, Aviran S, Tran EJ. PMID: 30902808; PMCID: PMC6499532.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    7. dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome Biol. 2019 02 21; 20(1):40. Choudhary K, Lai YH, Tran EJ, Aviran S. PMID: 30791935; PMCID: PMC6385470.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    8. Extracting information from RNA SHAPE data: Kalman filtering approach. PLoS One. 2018; 13(11):e0207029. Vaziri S, Koehl P, Aviran S. PMID: 30462682; PMCID: PMC6248965.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    9. Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures. Genes (Basel). 2018 Jun 14; 9(6). Radecki P, Ledda M, Aviran S. PMID: 29904019; PMCID: PMC6027059.
      View in: PubMed   Mentions: 6     Fields:    
    10. 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. Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR. PMID: 29294088; PMCID: PMC5861449.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    11. Publisher Correction: Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun. 2018 03 13; 9(1):1110. Li H, Aviran S. PMID: 29535318; PMCID: PMC5849728.
      View in: PubMed   Mentions:    Fields:    
    12. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biol. 2018 03 01; 19(1):28. Ledda M, Aviran S. PMID: 29495968; PMCID: PMC5833111.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    13. Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun. 2018 02 09; 9(1):606. Li H, Aviran S. PMID: 29426922; PMCID: PMC5807309.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    14. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst. 2017 05 24; 4(5):568-574.e7. Li B, Tambe A, Aviran S, Pachter L. PMID: 28501650; PMCID: PMC5758053.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    15. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. Quant Biol. 2017 Mar; 5(1):3-24. Choudhary K, Deng F, Aviran S. PMID: 28717530; PMCID: PMC5510538.
      View in: PubMed   Mentions: 21  
    16. SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. Bioinformatics. 2017 02 01; 33(3):441-443. Choudhary K, Ruan L, Deng F, Shih N, Aviran S. PMID: 28172632; PMCID: PMC6075182.
      View in: PubMed   Mentions: 5     Fields:    
    17. FoldAtlas: a repository for genome-wide RNA structure probing data. Bioinformatics. 2017 01 15; 33(2):306-308. Norris M, Kwok CK, Cheema J, Hartley M, Morris RJ, Aviran S, Ding Y. PMID: 27663500; PMCID: PMC5254078.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    18. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics. 2016 12 01; 32(23):3575-3583. Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. PMID: 27497441; PMCID: PMC5181532.
      View in: PubMed   Mentions: 11     Fields:    
    19. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA. 2016 08; 22(8):1109-19. Deng F, Ledda M, Vaziri S, Aviran S. PMID: 27251549; PMCID: PMC4931104.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    20. Rational experiment design for sequencing-based RNA structure mapping. RNA. 2014 Dec; 20(12):1864-77. Aviran S, Pachter L. PMID: 25332375; PMCID: PMC4238353.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    21. SHAPE-Seq: High-Throughput RNA Structure Analysis. Curr Protoc Chem Biol. 2012 Dec 01; 4(4):275-97. Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. PMID: 23788555.
      View in: PubMed   Mentions: 42     Fields:    
    22. RNA structure characterization from chemical mapping experiments. . 2011 Sep 1; 1743-1750. Aviran AS, Lucks LJ, Pachter PL. .
      View in: Publisher Site   Mentions:
    23. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11069-74. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. PMID: 21642536; PMCID: PMC3131376.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    24. 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. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. PMID: 21642531; PMCID: PMC3131332.
      View in: PubMed   Mentions: 206     Fields:    Translation:Cells
    25. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol. 2010 Aug 12; 6(8). Aviran S, Shah PS, Schaffer DV, Arkin AP. PMID: 20711350; PMCID: PMC2920833.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    26. Optimal Parsing Trees for Run-Length Coding of Biased Data. IEEE Transactions on Information Theory. 2008 Feb 1; 54(2):841-849. Aviran AS, Siegel SP, Wolf WJ. .
      View in: Publisher Site   Mentions:
    27. Optimal Parsing Trees for Run-Length Coding of Biased Data. . 2006 Jul 1; 1495-1499. Aviran AS, Siegel SP, Wolf WJ. .
      View in: Publisher Site   Mentions:
    28. Noise-Predictive Turbo Equalization for Partial-Response Channels. IEEE Transactions on Magnetics. 2005 Oct 1; 41(10):2959-2961. Aviran AS, Siegel SP, Wolf WJ. .
      View in: Publisher Site   Mentions:
    29. An Improvement to the Bit Stuffing Algorithm. IEEE Transactions on Information Theory. 2005 Aug 1; 51(8):2885-2891. Aviran AS, Siegel SP, Wolf WJ. .
      View in: Publisher Site   Mentions:
    30. Two-Dimensional Bit-Stuffing Schemes with Multiple Transformers. . 2005 Jan 1; 1478-1482. Aviran AS, Siegel SP, Wolf WJ. .
      View in: Publisher Site   Mentions:
    31. Vertex characterization of partition polytopes of bipartitions and of planar point sets. Discrete Applied Mathematics. 2002 Dec 1; 124(1-3):1-15. Aviran AS, Lev-Tov LN, Onn OS, Rothblum RU. .
      View in: Publisher Site   Mentions:
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