The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.
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[1] L. Pachter,et al. Rational experiment design for sequencing-based RNA structure mapping , 2014, RNA.
[2] S. Oliviero,et al. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome , 2014, Genome Biology.
[3] Kyle E. Watters,et al. SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing , 2014, Nucleic acids research.
[4] Nikolay V. Dokholyan,et al. Single-molecule correlated chemical probing of RNA , 2014, Proceedings of the National Academy of Sciences.
[5] Stuart Aitken,et al. Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution , 2014, Nucleic acids research.
[6] Sharon R Grossman,et al. RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites , 2014, Cell.
[7] Howard Y. Chang,et al. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification , 2014, Nature Biotechnology.
[8] Steven Busan,et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.
[9] Sean R Eddy,et al. Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. , 2014, Annual review of biophysics.
[10] Kevin M Weeks,et al. RNA secondary structure modeling at consistent high accuracy using differential SHAPE , 2014, RNA.
[11] J. Doudna,et al. Insights into RNA structure and function from genome-wide studies , 2014, Nature Reviews Genetics.
[12] K. Weeks,et al. Ribosome RNA assembly intermediates visualized in living cells. , 2014, Biochemistry.
[13] J. Woolford,et al. Mod-seq: high-throughput sequencing for chemical probing of RNA structure , 2014, RNA.
[14] Lukasz Jan Kielpinski,et al. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility , 2014, Nucleic acids research.
[15] Christopher R. Sibley,et al. iCLIP: Protein–RNA interactions at nucleotide resolution , 2014, Methods.
[16] Qiangfeng Cliff Zhang,et al. Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.
[17] Yiliang Ding,et al. Determination of in vivo RNA structure in low-abundance transcripts , 2013, Nature Communications.
[18] K. Weeks,et al. The cellular environment stabilizes adenine riboswitch RNA structure. , 2013, Biochemistry.
[19] Manolis Kellis,et al. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.
[20] Y. Zhang,et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.
[21] D. Tollervey,et al. Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.
[22] Yiliang Ding,et al. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. , 2013, Analytical biochemistry.
[23] Howard Y. Chang,et al. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing , 2013, Nature Protocols.
[24] Rhiju Das,et al. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. , 2013, Methods in molecular biology.
[25] D. Mathews,et al. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots , 2013, Proceedings of the National Academy of Sciences.
[26] M. Meyer,et al. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA , 2013, Nature Protocols.
[27] Michael P Snyder,et al. SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data , 2013, Genome research.
[28] B. Gregory,et al. PRMD: an integrated database for plant RNA modifications , 2012, Plant Cell.
[29] Robert Tibshirani,et al. Genome-wide measurement of RNA folding energies. , 2012, Molecular cell.
[30] Peter Clote,et al. Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction , 2012, PloS one.
[31] Rhiju Das,et al. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. , 2012, Biochemistry.
[32] Peter F. Stadler,et al. RNA Folding Algorithms with G-Quadruplexes , 2012, BSB.
[33] K. Weeks,et al. Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. , 2012, Journal of the American Chemical Society.
[34] Anna M. McGeachy,et al. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments , 2012, Nature Protocols.
[35] Li-San Wang,et al. SAVoR: a server for sequencing annotation and visualization of RNA structures , 2012, Nucleic Acids Res..
[36] Manolis Kellis,et al. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction , 2012, Nucleic acids research.
[37] Paul Ryvkin,et al. Global analysis of RNA secondary structure in two metazoans. , 2012, Cell reports.
[38] R. Sachidanandam,et al. Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing , 2011, Nucleic acids research.
[39] Howard Y. Chang,et al. Understanding the transcriptome through RNA structure , 2011, Nature Reviews Genetics.
[40] Cole Trapnell,et al. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) , 2011, Proceedings of the National Academy of Sciences.
[41] Cole Trapnell,et al. Modeling and automation of sequencing-based characterization of RNA structure , 2011, Proceedings of the National Academy of Sciences.
[42] Gaurav Sharma,et al. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences , 2011, BMC Bioinformatics.
[43] David H. Mathews,et al. Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences , 2011, Bioinform..
[44] Eric Westhof,et al. The RNA structurome: high-throughput probing , 2010, Nature Methods.
[45] D. Haussler,et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.
[46] K. Weeks,et al. SHAPE-directed RNA secondary structure prediction. , 2010, Methods.
[47] Howard Y. Chang,et al. Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.
[48] P. Ryvkin,et al. Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis , 2010, PLoS genetics.
[49] K. Weeks. Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.
[50] A. Laederach,et al. Evaluation of the information content of RNA structure mapping data for secondary structure prediction. , 2010, RNA.
[51] David H. Mathews,et al. RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.
[52] David H. Mathews,et al. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..
[53] Phillip A Sharp,et al. The Centrality of RNA , 2009, Cell.
[54] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[55] Morgan C. Giddings,et al. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. , 2008, RNA.
[56] M. Jennings,et al. Chloride Homeostasis in Saccharomyces cerevisiae: High Affinity Influx, V-ATPase-dependent Sequestration, and Identification of a Candidate Cl− Sensor , 2008, The Journal of general physiology.
[57] A. Serganov,et al. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins , 2007, Nature Reviews Genetics.
[58] K. Weeks,et al. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution , 2006, Nature Protocols.
[59] Aleksey Y. Ogurtsov,et al. A periodic pattern of mRNA secondary structure created by the genetic code , 2006, Nucleic acids research.
[60] James W. Brown,et al. The RNA Ontology Consortium: an open invitation to the RNA community. , 2006, RNA.
[61] O. Uhlenbeck,et al. The structure-function dilemma of the hammerhead ribozyme. , 2005, Annual review of biophysics and biomolecular structure.
[62] K. Aultman,et al. Partial P1 nuclease digestion as a probe of tRNA structure. , 2005, European journal of biochemistry.
[63] D. Mathews. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.
[64] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[65] R. Gutell,et al. The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.
[66] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[67] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[68] D. Crothers,et al. In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. , 1995, RNA.
[69] T. Cech,et al. Analysis of the structure of Tetrahymena nuclear RNAs in vivo: telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. , 1995, RNA.
[70] R. Gutell,et al. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. , 1994, Microbiological reviews.
[71] R. Gutell,et al. Comparative studies of RNA: inferring higher-order structure from patterns of sequence variation , 1993 .
[72] D. Turner,et al. Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[73] J. Ebel,et al. Probing the structure of RNAs in solution. , 1987, Nucleic acids research.
[74] D. Turner,et al. Improved free-energy parameters for predictions of RNA duplex stability. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[75] S. Altman,et al. Structure in solution of M1 RNA, the catalytic subunit of ribonuclease P from Escherichia coli. , 1984, Biochemistry.
[76] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[77] R. Gutell,et al. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. , 1980, Nucleic acids research.
[78] O. Uhlenbeck,et al. Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. , 1978, Biochemistry.
[79] Howard Y. Chang,et al. RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.
[80] T. Adilakshmi,et al. Structural analysis of RNA in living cells by in vivo synchrotron X-ray footprinting. , 2009, Methods in enzymology.
[81] R. Kierzek,et al. A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme. , 2007, Chemistry & biology.
[82] M. Ares,et al. Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.
[83] O. Uhlenbeck,et al. T4-induced RNA ligase joins single-stranded oligoribonucleotides. , 1975, Proceedings of the National Academy of Sciences of the United States of America.