Year |
Citation |
Score |
2022 |
Aviran S, Incarnato D. Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data. Journal of Molecular Biology. 167635. PMID 35595163 DOI: 10.1016/j.jmb.2022.167635 |
0.422 |
|
2021 |
Radecki P, Uppuluri R, Deshpande K, Aviran S. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. Rna Biology. 1-16. PMID 34606413 DOI: 10.1080/15476286.2021.1971382 |
0.413 |
|
2021 |
Radecki P, Uppuluri R, Aviran S. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. Nar Genomics and Bioinformatics. 3: lqab073. PMID 34447931 DOI: 10.1093/nargab/lqab073 |
0.412 |
|
2020 |
Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nature Communications. 11: 2173. PMID 32358529 DOI: 10.1038/S41467-020-15875-9 |
0.343 |
|
2019 |
Lai YH, Choudhary K, Cloutier SC, Xing Z, Aviran S, Tran EJ. Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics. PMID 30902808 DOI: 10.1534/Genetics.119.302058 |
0.476 |
|
2019 |
Choudhary K, Lai YH, Tran EJ, Aviran S. dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome Biology. 20: 40. PMID 30791935 DOI: 10.1186/S13059-019-1641-3 |
0.437 |
|
2018 |
Vaziri S, Koehl P, Aviran S. Extracting information from RNA SHAPE data: Kalman filtering approach. Plos One. 13: e0207029. PMID 30462682 DOI: 10.1371/Journal.Pone.0207029 |
0.419 |
|
2018 |
Radecki P, Ledda M, Aviran S. Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures. Genes. 9. PMID 29904019 DOI: 10.3390/Genes9060300 |
0.482 |
|
2018 |
Li H, Aviran S. Publisher Correction: Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nature Communications. 9: 1110. PMID 29535318 DOI: 10.1038/S41467-018-03519-Y |
0.372 |
|
2018 |
Ledda M, Aviran S. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biology. 19: 28. PMID 29495968 DOI: 10.1186/S13059-018-1399-Z |
0.504 |
|
2018 |
Li H, Aviran S. Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nature Communications. 9: 606. PMID 29426922 DOI: 10.1038/S41467-018-02923-8 |
0.442 |
|
2017 |
Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. Nucleic Acids Research. PMID 29294088 DOI: 10.1093/Nar/Gkx1273 |
0.449 |
|
2017 |
Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. Quantitative Biology (Beijing, China). 5: 3-24. PMID 28717530 DOI: 10.1007/s40484-017-0093-6 |
0.436 |
|
2017 |
Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems. PMID 28501650 DOI: 10.1016/J.Cels.2017.04.007 |
0.46 |
|
2017 |
Choudhary K, Ruan L, Deng F, Shih N, Aviran S. SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. Bioinformatics (Oxford, England). 33: 441-443. PMID 28172632 DOI: 10.1093/Bioinformatics/Btw627 |
0.474 |
|
2016 |
Choudhary K, Ruan L, Deng F, Shih N, Aviran S. SEQualyzer: Interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. Bioinformatics (Oxford, England). PMID 27694194 DOI: 10.1093/bioinformatics/btw627 |
0.408 |
|
2016 |
Norris M, Cheema J, Kwok CK, Hartley M, Morris RJ, Aviran S, Ding Y. FoldAtlas: a repository for genome-wide RNA structure probing data. Bioinformatics (Oxford, England). PMID 27663500 DOI: 10.1093/Bioinformatics/Btw611 |
0.501 |
|
2016 |
Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics (Oxford, England). PMID 27497441 DOI: 10.1093/Bioinformatics/Btw501 |
0.464 |
|
2016 |
Deng F, Ledda M, Vaziri S, Aviran S. Data-directed RNA secondary structure prediction using probabilistic modeling. Rna (New York, N.Y.). PMID 27251549 DOI: 10.1261/Rna.055756.115 |
0.484 |
|
2014 |
Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. Rna (New York, N.Y.). 20: 1864-77. PMID 25332375 DOI: 10.1261/Rna.043844.113 |
0.405 |
|
2012 |
Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4: 275-97. PMID 23788555 DOI: 10.1002/9780470559277.Ch120019 |
0.502 |
|
2011 |
Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108 |
0.501 |
|
2011 |
Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America. 108: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108 |
0.516 |
|
2011 |
Aviran S, Lucks JB, Pachter L. RNA structure characterization from chemical mapping experiments 2011 49th Annual Allerton Conference On Communication, Control, and Computing, Allerton 2011. 1743-1750. DOI: 10.1109/Allerton.2011.6120379 |
0.326 |
|
2008 |
Aviran S, Siegel PH, Wolf JK. Optimal parsing trees for run-length coding of biased data Ieee Transactions On Information Theory. 54: 841-849. DOI: 10.1109/Tit.2007.913570 |
0.515 |
|
2005 |
Aviran S, Siegel PH, Wolf JK. An improvement to the bit stuffing algorithm Ieee Transactions On Information Theory. 51: 2885-2891. DOI: 10.1109/Tit.2005.851764 |
0.506 |
|
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