Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data
O. Mizrahi, M. Corley, O. Feldman, T. Fröhlking, L. Sun, A. Ziesel, M. Antczak, M. Bernetti, S.I. Elhajjajy, W. Huang, G.G. Nguyen, S.S. Park, R.I. Perez Martell, L. Trinity, K. Xu, T. Zok, G. Bussi, H. Jabbari, Y. Orenstein, S. Aviran*, M.M. Meyer*, and G.W. Yeo*
submitted
Designer artificial environments for membrane protein synthesis
C. Meyer, A. Arizzi, T. Henson, S. Aviran, M. Longo, and C. Tan
submitted
Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer
J. Wang, B.Z. Fite, A.J. Kare, B. Wu, M. Raie, S.K. Tumbale, N. Zhang, R.R. Davis, C.G. Tepper, S. Aviran, A.M. Newman, D.A. King, and K.W. Ferrara
Theranostics, 12, 7884-7902, 2022
Computational approaches to RNA structure ensemble deconvolution from structure probing data
S. Aviran and D. Incarnato
Journal of Molecular Biology, 434, 167635, 2022
Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites
P. Radecki, R. Uppuluri, K. Deshpande, and S. Aviran
RNA Biology, 18, 521-536, 2021
Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets
P. Radecki, R. Uppuluri, and S. Aviran
Nucleic Acids Research Genomics and Bioinformatics, 3, lqab073, 2021
Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP
P.D. Garcia, R.W. Leach, G.M. Wadsworth, K. Choudhary, H. Li, S. Aviran, H.D. Kim, and V.A. Zakian
Nature Communications, 11, 2173, 2020
Genome-wide discovery of DEAD-box RNA helicase targets reveals RNA structural remodeling in transcription termination
Y. Lai, K. Choudhary, S. Cloutier, Z. Xing, S. Aviran*, and E.J. Tran*
Genetics, 212, 153-174, 2019
dStruct: identifying differentially reactive regions from RNA structurome profiling data
K. Choudhary, Y. Lai, E.J. Tran, and S. Aviran
Genome Biology, 20, 40, 2019
Software
Extracting information from RNA SHAPE data: Kalman filtering approach
S. Vaziri, P. Koehl*, and S. Aviran*
PLoS ONE, 13, e0207029, 2018
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, 020784, 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: K.M. Weeks, 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.