Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo
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Nikolay V. Dokholyan | David Gotz | Alain Laederach | Benfeard Williams | Lela Lackey | D. Gotz | A. Laederach | N. Dokholyan | B. Williams | Lela Lackey | Chanin T. Woods | C. Woods | Benfeard Williams
[1] Claude E. Shannon,et al. Prediction and Entropy of Printed English , 1951 .
[2] W. Torgerson. Multidimensional scaling: I. Theory and method , 1952 .
[3] D. Defays,et al. An Efficient Algorithm for a Complete Link Method , 1977, Comput. J..
[4] J. Lawrence,et al. Intracellular localization of messenger RNAs for cytoskeletal proteins , 1986, Cell.
[5] W. Marzluff,et al. The stem-loop structure at the 3' end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability , 1987, Molecular and cellular biology.
[6] Bruce A. Shapiro,et al. An algorithm for comparing multiple RNA secondary structures , 1988, Comput. Appl. Biosci..
[7] D. Schümperli,et al. Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps , 1991, Molecular and cellular biology.
[8] W. Marzluff,et al. The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes. , 1992, Nucleic acids research.
[9] A. R. Srinivasan,et al. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.
[10] R. Singer,et al. Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype , 1994, The Journal of cell biology.
[11] M. Hentze,et al. Starting at the Beginning, Middle, and End: Translation Initiation in Eukaryotes , 1997, Cell.
[12] R. Singer,et al. Characterization of a beta-actin mRNA zipcode-binding protein , 1997, Molecular and cellular biology.
[13] H. Stanley,et al. Discrete molecular dynamics studies of the folding of a protein-like model. , 1998, Folding & design.
[14] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[15] T. Steitz,et al. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.
[16] C. Vonrhein,et al. Structure of the 30S ribosomal subunit , 2000, Nature.
[17] Elena Rivas,et al. Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.
[18] Frank Schluenzen,et al. High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium , 2001, Cell.
[19] X. Zhuang,et al. Exploring the folding landscape of a structured RNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[20] J. C. Wu,et al. RNA folding pathway functional intermediates: their prediction and analysis. , 2001, Journal of molecular biology.
[21] D. Ecker,et al. RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.
[22] D. Turner,et al. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. , 2002, Biochemistry.
[23] M. Chance,et al. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting". , 2002, Current opinion in structural biology.
[24] V. Ramakrishnan,et al. Ribosome Structure and the Mechanism of Translation , 2002, Cell.
[25] Rhiju Das,et al. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. , 2003, Journal of molecular biology.
[26] Robert Giegerich,et al. Abstract shapes of RNA. , 2004, Nucleic acids research.
[27] A. Serganov,et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.
[28] 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.
[29] Ye Ding,et al. Sfold web server for statistical folding and rational design of nucleic acids , 2004, Nucleic Acids Res..
[30] C. Lawrence,et al. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. , 2005, RNA.
[31] Harry F Noller,et al. RNA Structure: Reading the Ribosome , 2005, Science.
[32] 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.
[33] M. Buckle,et al. Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[34] Xiaowei Zhuang,et al. Single-molecule RNA folding. , 2005, Accounts of chemical research.
[35] D. Thirumalai,et al. RNA and protein folding: common themes and variations. , 2005, Biochemistry.
[36] J. Condeelis,et al. Spatial regulation of β-actin translation by Src-dependent phosphorylation of ZBP1 , 2005, Nature.
[37] D. Lilley,et al. Folding of the adenine riboswitch. , 2006, Chemistry & biology.
[38] K. Weeks,et al. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution , 2006, Nature Protocols.
[39] C. Lawrence,et al. Clustering of RNA secondary structures with application to messenger RNAs. , 2006, Journal of molecular biology.
[40] David H Mathews,et al. Revolutions in RNA secondary structure prediction. , 2006, Journal of molecular biology.
[41] Robert Giegerich,et al. RNAshapes: an integrated RNA analysis package based on abstract shapes. , 2006, Bioinformatics.
[42] M. Brenowitz,et al. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins , 2006, Nucleic acids research.
[43] Peter Clote,et al. Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model , 2007, J. Comput. Biol..
[44] John D. Hunter,et al. Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.
[45] D. Lafontaine,et al. Core requirements of the adenine riboswitch aptamer for ligand binding. , 2007, RNA.
[46] Y. Ponty. Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy , 2007, Journal of mathematical biology.
[47] A. Laederach,et al. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. , 2008, Current opinion in chemical biology.
[48] Seema Chauhan,et al. Tertiary interactions determine the accuracy of RNA folding. , 2008, Journal of the American Chemical Society.
[49] F. Ding,et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. , 2008, RNA.
[50] Morgan C. Giddings,et al. Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. , 2009, RNA.
[51] D. Lafontaine,et al. Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches. , 2009, Methods in molecular biology.
[52] Kiyoshi Asai,et al. Prediction of RNA secondary structure using generalized centroid estimators , 2009, Bioinform..
[53] Sean R Eddy,et al. A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.
[54] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[55] A. Yonath. Hibernating Bears , Antibiotics , and the Evolving Ribosome ( Nobel Lecture ) * * , 2010 .
[56] A. Laederach,et al. Evaluation of the information content of RNA structure mapping data for secondary structure prediction. , 2010, RNA.
[57] Daniel Herschlag,et al. Multiple Native States Reveal Persistent Ruggedness of an RNA Folding Landscape , 2010, Nature.
[58] A. Yonath. Polar bears, antibiotics, and the evolving ribosome (Nobel Lecture). , 2010, Angewandte Chemie.
[59] Alain Laederach,et al. Disease-Associated Mutations That Alter the RNA Structural Ensemble , 2010, PLoS genetics.
[60] S. Almo,et al. ZBP1 recognition of beta-actin zipcode induces RNA looping. , 2010, Genes & development.
[61] T. Irving,et al. Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering. , 2010, Journal of the American Chemical Society.
[62] Patricia Bouchard,et al. Riboswitch structure: an internal residue mimicking the purine ligand , 2009, Nucleic acids research.
[63] Russ B Altman,et al. RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. , 2011, RNA.
[64] Rhiju Das,et al. A two-dimensional mutate-and-map strategy for non-coding RNA structure. , 2011, Nature chemistry.
[65] Rick Russell,et al. The Azoarcus Group I Intron Ribozyme Misfolds and Is Accelerated for Refolding by ATP-dependent RNA Chaperone Proteins* , 2011, The Journal of Biological Chemistry.
[66] Francesca Fanelli,et al. Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces , 2010, J. Comput. Chem..
[67] F. Ding,et al. Discrete molecular dynamics , 2012 .
[68] É. Massé,et al. Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms , 2011, PLoS genetics.
[69] Rhiju Das,et al. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. , 2011, RNA.
[70] K. Weeks,et al. The mechanisms of RNA SHAPE chemistry. , 2012, Journal of the American Chemical Society.
[71] Feng Ding,et al. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. , 2012, The journal of physical chemistry. B.
[72] Julius B. Lucks,et al. An RNA Mapping DataBase for curating RNA structure mapping experiments , 2012, Bioinform..
[73] F. Ding,et al. DMD: An Efficient And Versatile Simulation Method For Fine Protein Characterization , 2012 .
[74] S. Almo,et al. Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. , 2012, Genes & development.
[75] Alain Laederach,et al. Structural effects of linkage disequilibrium on the transcriptome. , 2012, RNA.
[76] Alain Laederach,et al. Evaluating our ability to predict the structural disruption of RNA by SNPs , 2012, BMC Genomics.
[77] Jiasheng Wang,et al. ACTB in cancer. , 2013, Clinica chimica acta; international journal of clinical chemistry.
[78] Michael C. Hout,et al. Multidimensional Scaling , 2003, Encyclopedic Dictionary of Archaeology.
[79] Joshua S. Martin,et al. Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation , 2013, PLoS Comput. Biol..
[80] Howard Y. Chang,et al. RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.
[81] Steven Busan,et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.
[82] John D. Westbrook,et al. The Nucleic Acid Database: new features and capabilities , 2013, Nucleic Acids Res..
[83] K. Weeks,et al. Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR , 2015, RNA.
[84] A. Ferré-D’Amaré,et al. Synthesis and applications of RNAs with position-selective labeling and mosaic composition , 2015, Nature.
[85] Rhiju Das,et al. Consistent global structures of complex RNA states through multidimensional chemical mapping , 2015, eLife.
[86] Alain Laederach,et al. The potential of the riboSNitch in personalized medicine , 2015, Wiley interdisciplinary reviews. RNA.
[87] Christopher A. Lavender,et al. In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state , 2015, Proceedings of the National Academy of Sciences.
[88] D. Herschlag,et al. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. , 2015, Current opinion in structural biology.
[89] K. Weeks,et al. Detection of RNA-Protein Interactions in Living Cells with SHAPE. , 2015, Biochemistry.
[90] Pablo Cordero,et al. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis , 2015, PLoS Comput. Biol..
[91] N. Perrone-Bizzozero,et al. Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1 , 2015, Nucleic acids research.
[92] Kaoru Inoue,et al. SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells , 2016, Proceedings of the National Academy of Sciences.
[93] D. Herschlag,et al. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. , 2016, Journal of molecular biology.
[94] A. Laederach,et al. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution , 2016, Wiley interdisciplinary reviews. RNA.