Sharon Aviran

Sharon Aviran

Position Title
Associate Professor

Biomedical Engineering, College of Engineering
Genome Center

Genome and Biomedical Sciences Facility, 2319

Research Interests

Computational Genomics, RNA Structure


My group develops computational methods for analysis of new and emerging genome-wide sequencing-based assays that measure structure and abundance of RNA transcripts. We also develop methods to integrate these experimental data into structure prediction algorithms to improve their accuracy and to better predict RNA-protein interactions. 

Grad Group Affiliations

  • Applied Mathematics
  • Biomedical Engineering
  • Biophysics
  • Computer Science
  • Designated Emphasis in Biotechnology

Specialties / Focus

  • Computational Biology


Honors and Awards

  • NHGRI Pathway to Independence Award (K99/R00)

    Professional Societies

    • RNA Society


    • 2006 PhD Electrical Engineering UCSD


    Y. Lai, K. Choudhary, S. Cloutier, Z. Xing, S. Aviran, and E.J. Tran, Genome-wide discovery of DEAD-box RNA helicase targets reveals structural remodeling in transcription termination, Genetics, 212, 153-174, 2019

    K. Choudhary, Y. Lai, E.J. Tran, and S. Aviran, dStruct: identifying differentially reactive regions from structurome profiling data, Genome Biology, 20, 40, 2019

    S. Vaziri, P. Koehl, and S. Aviran, PLoS One, 13, e0207029, 2018

    P. Radecki, M. Ledda, and S. Aviran, Automated  recognition of RNA structure motifs by their SHAPE data signatures, Genes, 9, 300, 2018

    H. Li and S. Aviran, Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes, Nature Communications, 9, 606, 2018

    M. Ledda and S. Aviran, patteRNA: transcriptome-wide search for functional RNA elements via structural data signatures, Genome Biology, 19, 28, 2018 

    K. Watters, K. Choudhary, S. Aviran, J.B. Lucks, K.L. Perry, and J.R. Thompson, Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elementsNucleic Acids Research, 46, 2573-84, 2018

    B. Li, A. Tambe, S. Aviran, and L. Pachter, PROBer provides a general toolkit for analyzing sequencing-based toeprinting assays, Cell Systems, 4, 568-574.e72017

    K. Choudhary*, F. Deng*, and S. Aviran, Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions, Quantitative Biology, 5, 3-24, 2017

    K. Choudhary, L. Ruan, F. Deng, N.P. Shih, and S. Aviran, SEQualyzer: Interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data, Bioinformatics, 33, 441-443, 2017

    M. Norris, C.K. Kwok, J. Cheema, M. Hartley, R.J. Morris, S. Aviran, and Y. Ding, FoldAtlas: a repository for genome-wide RNA structure probing data, Bioinformatics, 33, 306-308, 2017

    K. Choudhary, N.P. Shih, F. Deng, M. Ledda, B. Li, and S. Aviran, Metrics for rapid quality control in RNA structure probing experiments, Bioinformatics, 32, 3575-3583, 2016

    F. Deng*, M. Ledda*, S. Vaziri, and S. Aviran, Data-directed RNA secondary structure prediction using probabilistic modeling, RNA, 22, 1109-1119, 2016

    S. Aviran and L. Pachter, Rational experiment design for sequencing-based RNA structure mapping, RNA, 20, 1864-1877, 2014

    S.A. Mortimer, C. Trapnell*, S. Aviran*, L. Pachter, and J.B. Lucks, SHAPE-Seq: high throughput RNA structure analysis, Current Protocols in Chemical Biology, 4, 275-299, 2012

    S. Aviran, J.B. Lucks, and L. Pachter, RNA structure characterization from chemical mapping experiments, Proceedings of the 49th Allerton Conference on Communication, Control, and Computing, 1743-1750, 2011

    S. Aviran, C. Trapnell, J.B. Lucks, S.A. Mortimer, S. Luo, G.P. Schroth, J.A. Doudna, A.P. Arkin, and L. Pachter, Modeling and automation of sequencing-based characterization of RNA structure, Proceedings of the National Academy of Sciences (PNAS), 108, 11069-11074, 2011

    J.B. Lucks, S.A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G.P. Schroth, L. Pachter, J.A. Doudna, and A.P. Arkin, Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), Proceedings of the National Academy of Sciences (PNAS), 108, 11063-11068, 2011

    S. Aviran, P.S. Shah, D.V. Schaffer, and A.P. Arkin, Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles, PLoS Computational Biology, 6, e1000883, 2010

    S. Aviran, P.H. Siegel, and J.K. Wolf, Optimal parsing trees for run-length coding of biased data, IEEE Transactions on Information Theory, 54, 841-849, 2008

    S. Aviran, P.H. Siegel, and J.K. Wolf, Noise-predictive turbo equalization for partial-response channels, IEEE Transactions on Magnetics, 41, 2959-2961, 2005

    S. Aviran, P.H. Siegel, and J.K. Wolf, An improvement to the bit stuffing algorithm, IEEE Transactions on Information Theory, 51, 2885-2891, 2005

    S. Aviran, N. Lev-Tov, S. Onn, and U.G. Rothblum, Vertex characterization of partition polytopes of bipartitions and of planar point sets, Discrete Applied Mathematics, 124, 1-15, 2002

    S. Aviran and S. Onn, Momentopes, the complexity of vector partitioning, and Davenport-Schinzel sequences, Discrete & Computational Geometry, 27, 409-417, 2002