Sharon Aviran
Sharon Aviran
Associate Professor at UC Davis
Verified email at - Homepage
Cited by
Cited by
Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
JB Lucks, SA Mortimer, C Trapnell, S Luo, S Aviran, GP Schroth, ...
Proceedings of the National Academy of Sciences 108 (27), 11063-11068, 2011
Modeling and automation of sequencing-based characterization of RNA structure
S Aviran, C Trapnell, JB Lucks, SA Mortimer, S Luo, GP Schroth, ...
Proceedings of the National Academy of Sciences 108 (27), 11069-11074, 2011
SHAPE–Seq: high‐throughput RNA structure analysis
SA Mortimer, C Trapnell, S Aviran, L Pachter, JB Lucks
Current protocols in chemical biology 4 (4), 275-297, 2012
RNA structure characterization from chemical mapping experiments
S Aviran, JB Lucks, L Pachter
2011 49th Annual Allerton Conference on Communication, Control, and …, 2011
Data-directed RNA secondary structure prediction using probabilistic modeling
F Deng, M Ledda, S Vaziri, S Aviran
RNA 22 (8), 1109-1119, 2016
Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes
H Li, S Aviran
Nature communications 9 (1), 1-13, 2018
Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions
K Choudhary, F Deng, S Aviran
Quantitative Biology 5 (1), 3-24, 2017
Rational experiment design for sequencing-based RNA structure mapping
S Aviran, L Pachter
RNA 20 (12), 1864-1877, 2014
Optimal parsing trees for run-length coding of biased data
S Aviran, PH Siegel, JK Wolf
IEEE transactions on information theory 54 (2), 841-849, 2008
Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements
KE Watters, K Choudhary, S Aviran, JB Lucks, KL Perry, JR Thompson
Nucleic acids research 46 (5), 2573-2584, 2018
Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles
S Aviran, PS Shah, DV Schaffer, AP Arkin
PLoS computational biology 6 (8), e1000883, 2010
PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures
M Ledda, S Aviran
Genome biology 19 (1), 1-18, 2018
FoldAtlas: a repository for genome-wide RNA structure probing data
M Norris, CK Kwok, J Cheema, M Hartley, RJ Morris, S Aviran, Y Ding
Bioinformatics 33 (2), 306-308, 2017
Controlling false positive rates in methods for differential gene expression analysis using rna-seq data
DM Rocke, L Ruan, JJ Gossett, B Durbin-Johnson, S Aviran
Biorxiv, 018739, 2015
Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP
PD Garcia, RW Leach, GM Wadsworth, K Choudhary, H Li, S Aviran, ...
Nature communications 11 (1), 1-19, 2020
An improvement to the bit stuffing algorithm
S Aviran, PH Siegel, JK Wolf
IEEE transactions on information theory 51 (8), 2885-2891, 2005
System and a method for accelerating communication of TCP/IP based content
S Aviran
US Patent App. 10/486,393, 2004
Metrics for rapid quality control in RNA structure probing experiments
K Choudhary, NP Shih, F Deng, M Ledda, B Li, S Aviran
Bioinformatics 32 (23), 3575-3583, 2016
PROBer provides a general toolkit for analyzing sequencing-based toeprinting assays
B Li, A Tambe, S Aviran, L Pachter
Cell systems 4 (5), 568-574. e7, 2017
dStruct: identifying differentially reactive regions from RNA structurome profiling data
K Choudhary, YH Lai, EJ Tran, S Aviran
Genome biology 20 (1), 1-26, 2019
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