Folding and finding RNA secondary structure.
暂无分享,去创建一个
[1] T. Steitz,et al. The roles of RNA in the synthesis of protein. , 2011, Cold Spring Harbor perspectives in biology.
[2] Eric Westhof,et al. Predicting and modeling RNA architecture. , 2011, Cold Spring Harbor perspectives in biology.
[3] E. Kierzek. Binding of short oligonucleotides to RNA: studies of the binding of common RNA structural motifs to isoenergetic microarrays. , 2009, Biochemistry.
[4] D. Mathews,et al. Improved RNA secondary structure prediction by maximizing expected pair accuracy. , 2009, RNA.
[5] Walter N. Moss,et al. Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. , 2009, Journal of molecular biology.
[6] Morgan C. Giddings,et al. Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. , 2009, RNA.
[7] D. Mathews,et al. Stochastic sampling of the RNA structural alignment space , 2009, Nucleic acids research.
[8] Kiyoshi Asai,et al. Prediction of RNA secondary structure using generalized centroid estimators , 2009, Bioinform..
[9] Kristin Reiche,et al. Structural profiles of human miRNA families from pairwise clustering , 2009, Bioinform..
[10] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[11] Sebastian Will,et al. RNAalifold: improved consensus structure prediction for RNA alignments , 2008, BMC Bioinformatics.
[12] D. Les,et al. Phylogenetic analysis of the internal transcribed spacer (ITS) region in Menyanthaceae using predicted secondary structure. , 2008, Molecular phylogenetics and evolution.
[13] Q. Cui,et al. An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.
[14] David H. Mathews,et al. NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon , 2008, Journal of the American Chemical Society.
[15] Chuan-Sheng Foo,et al. A max-margin model for efficient simultaneous alignment and folding of RNA sequences , 2008, ISMB.
[16] C. Feschotte. Transposable elements and the evolution of regulatory networks , 2008, Nature Reviews Genetics.
[17] Vegeir Knudsen,et al. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure , 2008, Nucleic Acids Res..
[18] Stefan L Ameres,et al. The impact of target site accessibility on the design of effective siRNAs , 2008, Nature Biotechnology.
[19] F. Major,et al. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.
[20] K. Morris,et al. RNA and transcriptional modulation of gene expression , 2008, Cell cycle.
[21] D. Mathews,et al. PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction , 2008, Nucleic acids research.
[22] D. Turner,et al. Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function , 2008, Nucleic acids research.
[23] David H. Mathews,et al. Efficient siRNA selection using hybridization thermodynamics , 2007, Nucleic acids research.
[24] Tobias Müller,et al. The ITS2 Database II: homology modelling RNA structure for molecular systematics , 2007, Nucleic Acids Res..
[25] Matthew D Disney,et al. A small molecule microarray platform to select RNA internal loop-ligand interactions. , 2007, ACS chemical biology.
[26] Chi Yu Chan,et al. Effect of target secondary structure on RNAi efficiency. , 2007, RNA.
[27] Kevin P. Murphy,et al. Efficient parameter estimation for RNA secondary structure prediction , 2007, ISMB/ECCB.
[28] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[29] I. K. Jordan,et al. Origin and Evolution of Human microRNAs From Transposable Elements , 2007, Genetics.
[30] Jessica L. Childs-Disney,et al. Using Selection to Identify and Chemical Microarray to Study the RNA Internal Loops Recognized by 6′‐N‐Acylated Kanamycin A , 2007, Chembiochem : a European journal of chemical biology.
[31] Dang D. Long,et al. Potent effect of target structure on microRNA function , 2007, Nature Structural &Molecular Biology.
[32] K. Weeks,et al. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. , 2007, Journal of the American Chemical Society.
[33] Jan Gorodkin,et al. Multiple structural alignment and clustering of RNA sequences , 2007, Bioinform..
[34] Rolf Backofen,et al. Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering , 2007, PLoS Comput. Biol..
[35] Kiyoshi Asai,et al. Robust prediction of consensus secondary structures using averaged base pairing probability matrices , 2007, Bioinform..
[36] Gustavo Caetano-Anollés,et al. Common evolutionary trends for SINE RNA structures. , 2007, Trends in genetics : TIG.
[37] G. Caetano-Anollés,et al. The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure , 2007, Journal of Molecular Evolution.
[38] Marcel Turcotte,et al. Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction? , 2007, BMC Bioinformatics.
[39] Gaurav Sharma,et al. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign , 2007, BMC Bioinformatics.
[40] T. Eickbush,et al. RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site , 2006, Proceedings of the National Academy of Sciences.
[41] Xiaoyu Zhang,et al. Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats , 2006, PLoS biology.
[42] Sean R. Eddy,et al. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints , 2006, BMC Bioinformatics.
[43] Serafim Batzoglou,et al. CONTRAfold: RNA secondary structure prediction without physics-based models , 2006, ISMB.
[44] J. Gorodkin,et al. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. , 2006, Genome research.
[45] Jan Krüger,et al. RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..
[46] Eugene Berezikov,et al. Approaches to microRNA discovery , 2006, Nature Genetics.
[47] Michael Zuker,et al. 22 Predicting RNA Secondary Structure , 2006 .
[48] David H. Mathews,et al. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change , 2006, BMC Bioinformatics.
[49] R. Giegerich,et al. Complete probabilistic analysis of RNA shapes , 2006, BMC Biology.
[50] D. Turner,et al. RNA challenges for computational chemists. , 2005, Biochemistry.
[51] Robert Giegerich,et al. Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction , 2005, Bioinform..
[52] C. Lawrence,et al. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. , 2005, RNA.
[53] Gary D. Stormo,et al. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% , 2005, Bioinform..
[54] P. Clote,et al. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. , 2005, RNA.
[55] K. Gunsalus,et al. Combinatorial microRNA target predictions , 2005, Nature Genetics.
[56] Vivek Gowri-Shankar,et al. Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria. , 2005, Molecular biology and evolution.
[57] Tobias Müller,et al. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. , 2005, RNA.
[58] K. Weeks,et al. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). , 2005, Journal of the American Chemical Society.
[59] Peter F Stadler,et al. Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.
[60] Tobias Müller,et al. CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures , 2005, Silico Biol..
[61] Ian Holmes,et al. Stem Stem Stem Stem Loop Loop Loop LoopLoop Loop Loop Loop Loop Loop Loop , 2005 .
[62] R. Giegerich,et al. Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.
[63] Peter F. Stadler,et al. Alignment of RNA base pairing probability matrices , 2004, Bioinform..
[64] D. Mathews. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.
[65] Peter F. Stadler,et al. The Partition Function Variant of Sankoff's Algorithm , 2004, International Conference on Computational Science.
[66] Sean R. Eddy,et al. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction , 2004, BMC Bioinformatics.
[67] A. Hatzigeorgiou,et al. A combined computational-experimental approach predicts human microRNA targets. , 2004, Genes & development.
[68] 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.
[69] J. Mattick. RNA regulation: a new genetics? , 2004, Nature Reviews Genetics.
[70] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[71] Robert Giegerich,et al. Abstract shapes of RNA. , 2004, Nucleic acids research.
[72] Robert Giegerich,et al. Pure multiple RNA secondary structure alignments: a progressive profile approach , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[73] C. Lawrence,et al. A statistical sampling algorithm for RNA secondary structure prediction. , 2003, Nucleic acids research.
[74] J. Wendel,et al. Ribosomal ITS sequences and plant phylogenetic inference. , 2003, Molecular phylogenetics and evolution.
[75] John S Mattick,et al. Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences , 2003, Genome Biology.
[76] Robert K Jansen,et al. ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. , 2003, Molecular phylogenetics and evolution.
[77] Donald H. Burke,et al. Evolutionary Landscapes for the Acquisition of New Ligand Recognition by RNA Aptamers , 2003, Journal of Molecular Evolution.
[78] David A Case,et al. A novel method for finding tRNA genes. , 2003, RNA.
[79] C. Burge,et al. The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.
[80] C. Burge,et al. Vertebrate MicroRNA Genes , 2003, Science.
[81] W. Fontana. Modelling 'evo-devo' with RNA. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.
[82] Peter F. Stadler,et al. Networks in molecular evolution , 2002 .
[83] P. Stadler,et al. Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.
[84] R. Gutell,et al. The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.
[85] G. Caetano-Anollés. Tracing the evolution of RNA structure in ribosomes. , 2002, Nucleic acids research.
[86] Cédric Feschotte,et al. Plant transposable elements: where genetics meets genomics , 2002, Nature Reviews Genetics.
[87] E. Wagner,et al. Lead(II) as a probe for investigating RNA structure in vivo. , 2002, RNA.
[88] D. Turner,et al. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. , 2002, Journal of molecular biology.
[89] Akira Sakamaki,et al. using an , 2002 .
[90] D. Ecker,et al. RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.
[91] P Schuster,et al. Evolution in Silico and in Vitro: The RNA Model , 2001, Biological chemistry.
[92] P. Moore. 1 – A Spectroscopist’s View of RNA Conformation: RNA Structural Motifs , 2001 .
[93] D. Bartel,et al. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.
[94] Elena Rivas,et al. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs , 2000, Bioinform..
[95] A. Krogh,et al. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. , 1999, Nucleic acids research.
[96] R. Lück,et al. ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. , 1999, Nucleic acids research.
[97] R R Breaker,et al. Relationship between internucleotide linkage geometry and the stability of RNA. , 1999, RNA.
[98] Ronald R. Breaker,et al. Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group , 1999 .
[99] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[100] David W. Digby,et al. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. , 1999, Nucleic acids research.
[101] S. Eddy,et al. A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.
[102] P. Schuster,et al. Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.
[103] P. Moore. 6.02 – A Spectroscopist’s View of RNA Conformation: RNA Structural Motifs , 1999 .
[104] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[105] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[106] Gabriele Varani,et al. NMR investigation of RNA structure , 1996 .
[107] R. Lück,et al. Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. , 1996, Journal of molecular biology.
[108] 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.
[109] 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.
[110] R. Durbin,et al. RNA sequence analysis using covariance models. , 1994, Nucleic acids research.
[111] Carl R. Woese,et al. 4 Probing RNA Structure, Function, and History by Comparative Analysis , 1993 .
[112] R. Zwanzig,et al. Levinthal's paradox. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[113] C. Burks,et al. Identifying potential tRNA genes in genomic DNA sequences. , 1991, Journal of molecular biology.
[114] O. Kandler,et al. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[115] Bruce A. Shapiro,et al. A computational procedure for assessing the significance of RNA secondary structure , 1990, Comput. Appl. Biosci..
[116] 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.
[117] Jih-Hsiang Chen,et al. A program for predicting significant RNA secondary structures , 1988, Comput. Appl. Biosci..
[118] J. Ebel,et al. Probing the structure of RNAs in solution. , 1987, Nucleic acids research.
[119] Clive Richards,et al. The Blind Watchmaker , 1987, Bristol Medico-Chirurgical Journal.
[120] H. Noller,et al. Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. , 1986, Journal of molecular biology.
[121] D. Sankoff. Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .
[122] T. Cech,et al. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[123] Manolo Gouy,et al. An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules , 1984, Nucleic Acids Res..
[124] D. Sankoff,et al. RNA secondary structures and their prediction , 1984 .
[125] J. Ninio. Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs. , 1980, Biochimie.