Sharon Aviran

image of Sharon Aviran

Assistant Professor


UC Davis Genome Center
Biomedical Engineering (Grad)

Offices and Labs

Genome and Biomedical Sciences Facility, 2319


2006 PhD Electrical Engineering UCSD

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. 


NHGRI Pathway to Independence Award (K99/R00)

Department and Center Affiliations

Genome Center


RNA Society

CBS Grad Group Affiliations

Integrated Genetics and Genomics

Specialties / Focus

Integrated Genetics and Genomics
  • Computational Biology

Graduate Groups not Housed in CBS

Applied Mathematics
Biomedical Engineering
Computer Science
Designated Emphasis in Biotechnology


Computational RNA Genomics website

Teaching Interests

Bioinformatics, Big Data Analysis, Genomics, Probability and Random Processes, Signal Processing


1/12/2018 10:29:32 PM
  • 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, gkx1273, 2017

  • 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