Papers

Extracting information from RNA SHAPE data: Kalman filtering approach
S. Vaziri, P. Koehl*, and S. Aviran*
submitted

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

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

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

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements
K.E. Watters, K. Choudhary, S. Aviran, J.B. Lucks, K.L. Perry, and J.R. Thompson
Nucleic Acids Research, 46, 2573-2584, 2018
Software

PROBer provides a general toolkit for analyzing sequencing-based toeprinting assays
B. Li, A. Tambe, S. Aviran, and L. Pachter
Cell Systems, 4, 568-574.e7, 2017
Software

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

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

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

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

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

Excess false positive rates in methods for differential gene expression analysis using RNA-Seq data
D.M. Rocke, L. Ruan, Y. Zhang, J.J. Gossett, B. Durbin-Johnson, and S. Aviran
bioRxiv, 2015

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

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

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

See Commentary: RNA structure probing dash seq, PNAS, 108, 10933, 2011.

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

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

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

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

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

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

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

 

 

Peer-Reviewed Conference Papers

 

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

Optimal parsing trees for run-length coding of biased data
S. Aviran, P.H. Siegel, and J.K. Wolf,
Proceedings of the International Symposium on Information Theory (ISIT), 1495-1499, 2006.

Two-dimensional bit-stuffing schemes with multiple transformers
S. Aviran, P.H. Siegel, and J.K. Wolf,
Proceedings of the International Symposium on Information Theory (ISIT), 1478-1482, 2005.

Noise-predictive turbo equalization for partial-response channels
S. Aviran, P.H. Siegel, and J.K. Wolf,
Proceedings of the International Magnetics Conference (INTERMAG), 981-982, 2005.

An improvement to the bit stuffing algorithm
S. Aviran, P.H. Siegel, and J.K. Wolf,
Proceedings of the International Symposium on Information Theory (ISIT), 190, 2004.

Rate control for advanced wireless networks
O. Shaham, S. Aviran, E. Simony, and Y. Shapira,
Proceedings of the International Conference on 3rd Generation Wireless and Beyond, 444-449, 2001.

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