| Year |
Citation |
Score |
| 2023 |
Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nature Communications. 14: 6166. PMID 37789015 DOI: 10.1038/s41467-023-41799-1 |
0.316 |
|
| 2023 |
Zhang H, Li S, Dai N, Zhang L, Mathews DH, Huang L. LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules. Nucleic Acids Research. PMID 37650626 DOI: 10.1093/nar/gkad664 |
0.553 |
|
| 2023 |
Ali SE, Mittal A, Mathews DH. RNA Secondary Structure Analysis Using RNAstructure. Current Protocols. 3: e846. PMID 37487054 DOI: 10.1002/cpz1.846 |
0.475 |
|
| 2023 |
Zhou T, Dai N, Li S, Ward M, Mathews DH, Huang L. RNA design via structure-aware multifrontier ensemble optimization. Bioinformatics (Oxford, England). 39: i563-i571. PMID 37387188 DOI: 10.1093/bioinformatics/btad252 |
0.409 |
|
| 2023 |
Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and Molecular Life Sciences : Cmls. 80: 136. PMID 37131079 DOI: 10.1007/s00018-023-04764-1 |
0.757 |
|
| 2023 |
Zhang H, Zhang L, Liu K, Li S, Mathews DH, Huang L. Linear-Time Algorithms for RNA Structure Prediction. Methods in Molecular Biology (Clifton, N.J.). 2586: 15-34. PMID 36705896 DOI: 10.1007/978-1-0716-2768-6_2 |
0.558 |
|
| 2022 |
Zhang H, Li S, Zhang L, Mathews DH, Huang L. LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2. Nucleic Acids Research. PMID 36401871 DOI: 10.1093/nar/gkac1029 |
0.422 |
|
| 2022 |
Zhang L, Li S, Zhang H, Mathews DH, Huang L. LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. Arxiv. PMID 35795813 |
0.497 |
|
| 2022 |
Szikszai M, Wise M, Datta A, Ward M, Mathews DH. Deep learning models for RNA secondary structure prediction (probably) do not generalise across families. Bioinformatics (Oxford, England). PMID 35748706 DOI: 10.1093/bioinformatics/btac415 |
0.45 |
|
| 2022 |
Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks K, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in using endogenous pre-messenger RNA structure probing. Elife. 11. PMID 35695373 DOI: 10.7554/eLife.73888 |
0.456 |
|
| 2022 |
Szabat M, Prochota M, Kierzek R, Kierzek E, Mathews DH. A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N-Methyladenosine. Journal of Molecular Biology. 167632. PMID 35588868 DOI: 10.1016/j.jmb.2022.167632 |
0.511 |
|
| 2022 |
Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Research. PMID 35524574 DOI: 10.1093/nar/gkac261 |
0.424 |
|
| 2022 |
Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic Acids Research. PMID 35524551 DOI: 10.1093/nar/gkac287 |
0.48 |
|
| 2022 |
Kierzek E, Zhang X, Watson RM, Kennedy SD, Szabat M, Kierzek R, Mathews DH. Secondary structure prediction for RNA sequences including N-methyladenosine. Nature Communications. 13: 1271. PMID 35277476 DOI: 10.1038/s41467-022-28817-4 |
0.418 |
|
| 2022 |
Szutkowska B, Wieczorek K, Kierzek R, Zmora P, Peterson JM, Moss WN, Mathews DH, Kierzek E. Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment. International Journal of Molecular Sciences. 23. PMID 35269600 DOI: 10.3390/ijms23052452 |
0.725 |
|
| 2022 |
Schroeder GM, Cavender CE, Blau ME, Jenkins JL, Mathews DH, Wedekind JE. A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nature Communications. 13: 199. PMID 35017488 DOI: 10.1038/s41467-021-27790-8 |
0.454 |
|
| 2021 |
Li S, Zhang H, Zhang L, Liu K, Liu B, Mathews DH, Huang L. LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34887342 DOI: 10.1073/pnas.2116269118 |
0.551 |
|
| 2021 |
Li S, Zhang H, Zhang L, Liu K, Liu B, Mathews DH, Huang L. LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 34816262 DOI: 10.1101/2020.11.23.393488 |
0.549 |
|
| 2021 |
Kayedkhordeh M, Yamagami R, Bevilacqua PC, Mathews DH. Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots. Methods in Molecular Biology (Clifton, N.J.). 2167: 113-143. PMID 32712918 DOI: 10.1007/978-1-0716-0716-9_8 |
0.646 |
|
| 2020 |
Chavali SS, Cavender CE, Mathews DH, Wedekind JE. Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. Journal of the American Chemical Society. PMID 33170672 DOI: 10.1021/jacs.0c09689 |
0.53 |
|
| 2020 |
Zhang H, Zhang L, Mathews DH, Huang L. LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities. Bioinformatics (Oxford, England). 36: i258-i267. PMID 32657379 DOI: 10.1093/Bioinformatics/Btaa460 |
0.6 |
|
| 2020 |
Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE. Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation. Nucleic Acids Research. PMID 32597951 DOI: 10.1093/Nar/Gkaa546 |
0.45 |
|
| 2020 |
Ermolenko DN, Mathews DH. Making ends meet: New functions of mRNA secondary structure. Wiley Interdisciplinary Reviews. Rna. e1611. PMID 32597020 DOI: 10.1002/Wrna.1611 |
0.583 |
|
| 2020 |
Cavender CE, Smith LG, Grossfield A, Mathews DH. Capturing the Influence of Solvent and Neighboring Residues in a Fixed-Charge Force Field for RNA Biophysical Journal. 118: 68a. DOI: 10.1016/J.Bpj.2019.11.547 |
0.456 |
|
| 2020 |
Smith LG, Kennedy SD, Turner DH, Grossfield A, Mathews DH. Can Simulations be Recycled to Benchmark RNA Force Fields Biophysical Journal. 118: 296a. DOI: 10.1016/J.Bpj.2019.11.1677 |
0.459 |
|
| 2019 |
Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinformatics (Oxford, England). 35: i295-i304. PMID 31510672 DOI: 10.1093/Bioinformatics/Btz375 |
0.545 |
|
| 2019 |
Zuber J, Mathews DH. Estimating Uncertainty in Predicted Folding Free Energy Changes of RNA Secondary Structure. Rna (New York, N.Y.). PMID 30952689 DOI: 10.1261/Rna.069203.118 |
0.561 |
|
| 2019 |
Mathews DH. How to Benchmark RNA Secondary Structure Prediction Accuracy. Methods (San Diego, Calif.). PMID 30951834 DOI: 10.1016/J.Ymeth.2019.04.003 |
0.605 |
|
| 2019 |
Ward M, Sun H, Datta A, Wise M, Mathews DH. Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change. Bioinformatics (Oxford, England). PMID 30923811 DOI: 10.1093/Bioinformatics/Btz222 |
0.536 |
|
| 2019 |
Wedekind JE, Dutta D, Cavender CE, DiCola AM, Schroeder GM, Mathews DH, Jenkins JL. Exploring low-energy pathways that interconvert the Apo and bound states of a metabolite-sensing gene-regulatory RNA switch Acta Crystallographica Section a Foundations and Advances. 75: a18-a18. DOI: 10.1107/S0108767319099811 |
0.435 |
|
| 2019 |
Smith LG, Cavender CE, Grossfield A, Mathews DH. Exploring Hydrogen Bond Geometry in RNA with F-SAPT Biophysical Journal. 116: 143a. DOI: 10.1016/J.Bpj.2018.11.791 |
0.403 |
|
| 2019 |
Cavender CE, Smith LG, Grossfield A, Mathews DH. Developing an Accurate All-Atom Fixed-Charge Force Field for RNA with Implicitly Polarized Charges Biophysical Journal. 116: 353a. DOI: 10.1016/J.Bpj.2018.11.1919 |
0.363 |
|
| 2018 |
Ghoneim DH, Zhang X, Brule CE, Mathews DH, Grayhack EJ. Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection. Nucleic Acids Research. PMID 30576464 DOI: 10.1093/Nar/Gky1262 |
0.317 |
|
| 2018 |
Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study. Nucleic Acids Research. PMID 30462314 DOI: 10.1093/Nar/Gky1118 |
0.729 |
|
| 2018 |
Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. Journal of Chemical Theory and Computation. PMID 30375860 DOI: 10.1021/Acs.Jctc.8B00633 |
0.45 |
|
| 2018 |
Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN. mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances. Nature Communications. 9: 4328. PMID 30337527 DOI: 10.1038/S41467-018-06792-Z |
0.551 |
|
| 2018 |
Braun J, Fischer S, Xu ZZ, Sun H, Ghoneim DH, Gimbel AT, Plessmann U, Urlaub H, Mathews DH, Weigand JE. Identification of new high affinity targets for Roquin based on structural conservation. Nucleic Acids Research. PMID 30295819 DOI: 10.1093/Nar/Gky908 |
0.464 |
|
| 2018 |
Zuber J, Cabral BJ, McFadyen I, Mauger DM, Mathews DH. Analysis of RNA Nearest Neighbor Parameters Reveals Interdependencies and Quantifies the Uncertainty in RNA Secondary Structure Prediction. Rna (New York, N.Y.). PMID 30104207 DOI: 10.1261/Rna.065102.117 |
0.573 |
|
| 2018 |
Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH. Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops. Rna (New York, N.Y.). PMID 30097542 DOI: 10.1261/Rna.066324.118 |
0.516 |
|
| 2018 |
Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucleic Acids Research. PMID 29961805 DOI: 10.1093/Nar/Gky529 |
0.482 |
|
| 2018 |
Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH. Improving RNA nearest neighbor parameters for helices by going beyond the two-state model. Nucleic Acids Research. PMID 29718397 DOI: 10.1093/Nar/Gky270 |
0.828 |
|
| 2018 |
Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH. Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. Biochemistry. PMID 29570276 DOI: 10.1021/Acs.Biochem.7B01306 |
0.587 |
|
| 2018 |
Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews D. Molecular Dynamics Correctly Models the Unusual Major Conformation of the GAGU RNA Internal Loop and with NMR Reveals an Unusual Minor Conformation. Rna (New York, N.Y.). PMID 29434035 DOI: 10.1261/Rna.064527.117 |
0.513 |
|
| 2018 |
Wedekind JE, Belashov IA, Crawford DW, Lavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR. Structure of HIV-1 TAR in complex with a lab-evolved protein provides insight into RNA recognition and synthesis of a constrained peptide that impairs transcription Acta Crystallographica Section a Foundations and Advances. 74: a345-a345. DOI: 10.1107/S0108767318096551 |
0.427 |
|
| 2018 |
Smith LG, Tan Z, Spasic A, Grossfield A, Mathews DH. Benchmarking RNA Force Fields using Hairpin Loop Folding Free Energy Change Biophysical Journal. 114: 435a. DOI: 10.1016/J.Bpj.2017.11.2408 |
0.514 |
|
| 2018 |
Cavender CE, Belashov IA, Wedekind JE, Mathews DH. Conformational Dynamics of the HIV-1 Trans-Activation Response Element RNA Hairpin Bound to a Lab-Evolved Peptide Biophysical Journal. 114: 337a. DOI: 10.1016/J.Bpj.2017.11.1886 |
0.41 |
|
| 2017 |
Payea MJ, Sloma MF, Kon Y, Young DL, Guy MP, Zhang X, De Zoysa T, Fields S, Mathews DH, Phizicky EM. Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. Rna (New York, N.Y.). PMID 29259051 DOI: 10.1261/Rna.064642.117 |
0.328 |
|
| 2017 |
Spasic A, Assmann SM, Bevilacqua PC, Mathews DH. Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Research. PMID 29177466 DOI: 10.1093/Nar/Gkx1057 |
0.764 |
|
| 2017 |
Sloma MF, Mathews DH. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. Plos Computational Biology. 13: e1005827. PMID 29107980 DOI: 10.1371/Journal.Pcbi.1005827 |
0.584 |
|
| 2017 |
Tan Z, Fu Y, Sharma G, Mathews DH. TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic Acids Research. PMID 29036420 DOI: 10.1093/Nar/Gkx815 |
0.526 |
|
| 2017 |
Smith LG, Zhao J, Mathews DH, Turner DH. Physics-based all-atom modeling of RNA energetics and structure. Wiley Interdisciplinary Reviews. Rna. 8. PMID 28815951 DOI: 10.1002/Wrna.1422 |
0.579 |
|
| 2017 |
Tan Z, Sharma G, Mathews DH. Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. Biophysical Journal. PMID 28735622 DOI: 10.1016/J.Bpj.2017.06.039 |
0.531 |
|
| 2017 |
Ward M, Datta A, Wise M, Mathews DH. Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic Acids Research. PMID 28586479 DOI: 10.1093/Nar/Gkx512 |
0.455 |
|
| 2017 |
Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses. 9. PMID 28445416 DOI: 10.3390/V9050093 |
0.603 |
|
| 2017 |
Zuber J, Sun H, Zhang X, McFadyen I, Mathews DH. A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction. Nucleic Acids Research. PMID 28334976 DOI: 10.1093/Nar/Gkx170 |
0.511 |
|
| 2017 |
Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH. Revised RNA dihedral parameters for the Amber force field improve RNA molecular dynamics. Journal of Chemical Theory and Computation. PMID 28048939 DOI: 10.1021/Acs.Jctc.6B00870 |
0.488 |
|
| 2016 |
Mathews DH, Turner DH, Watson RM. RNA Secondary Structure Prediction. Current Protocols in Nucleic Acid Chemistry. 67: 11.2.1-11.2.19. PMID 27911493 DOI: 10.1002/cpnc.19 |
0.563 |
|
| 2016 |
Sloma MF, Mathews DH. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. Rna (New York, N.Y.). 22: 1808-1818. PMID 27852924 DOI: 10.1261/Rna.053694.115 |
0.656 |
|
| 2016 |
Xu ZZ, Mathews DH. Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods in Molecular Biology (Clifton, N.J.). 1490: 163-176. PMID 27665598 DOI: 10.1007/978-1-4939-6433-8_10 |
0.566 |
|
| 2016 |
DiChiacchio L, Mathews DH. Predicting RNA-RNA Interactions Using RNAstructure. Methods in Molecular Biology (Clifton, N.J.). 1490: 51-62. PMID 27665592 DOI: 10.1007/978-1-4939-6433-8_4 |
0.815 |
|
| 2016 |
Xu ZZ, Mathews DH. Prediction of Secondary Structures Conserved in Multiple RNA Sequences. Methods in Molecular Biology (Clifton, N.J.). 1490: 35-50. PMID 27665591 DOI: 10.1007/978-1-4939-6433-8_3 |
0.612 |
|
| 2016 |
Xu ZZ, Mathews DH. Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods in Molecular Biology (Clifton, N.J.). 1490: 15-34. PMID 27665590 DOI: 10.1007/978-1-4939-6433-8_2 |
0.532 |
|
| 2016 |
Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC. Bridging the gap between in vitro and in vivo RNA folding. Quarterly Reviews of Biophysics. 49: e10. PMID 27658939 DOI: 10.1017/S003358351600007X |
0.748 |
|
| 2015 |
DiChiacchio L, Sloma MF, Mathews DH. AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure. Bioinformatics (Oxford, England). PMID 26589271 DOI: 10.1093/Bioinformatics/Btv682 |
0.815 |
|
| 2015 |
Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. NMR-assisted prediction of secondary structure for RNA: Incorporation of direction-dependent chemical shift constraints. Biochemistry. PMID 26451676 DOI: 10.1021/Acs.Biochem.5B00833 |
0.814 |
|
| 2015 |
Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. Rna (New York, N.Y.). 21: 1898-907. PMID 26370581 DOI: 10.1261/Rna.051367.115 |
0.42 |
|
| 2015 |
Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic Acids Research. PMID 26170232 DOI: 10.1093/Nar/Gkv706 |
0.586 |
|
| 2015 |
Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 26106162 DOI: 10.1073/Pnas.1503955112 |
0.437 |
|
| 2015 |
Aytenfisu AH, Spasic A, Grossfield A, Stern H, Mathews DH. 99 Improving the amber RNA force field. Journal of Biomolecular Structure & Dynamics. 33: 63. PMID 26103311 DOI: 10.1080/07391102.2015.1032661 |
0.472 |
|
| 2015 |
Spasic A, Needham L, Mathews DH. 100 Examining the unusual conformation of GAGU internal loop using molecular dynamics. Journal of Biomolecular Structure & Dynamics. 33: 63-4. PMID 26103310 DOI: 10.1080/07391102.2015.1032662 |
0.327 |
|
| 2015 |
Sloma MF, Mathews DH. 97 Exact probability calculation of RNA loop formation identifies folding motifs in secondary structures. Journal of Biomolecular Structure & Dynamics. 33: 62. PMID 26103308 DOI: 10.1080/07391102.2015.1032714 |
0.612 |
|
| 2015 |
Tan Z, Spasic A, Mathews DH. 96 Benchmark of Amber ff12SB force field by comparison of estimated hairpin loop folding stabilities to experiments. Journal of Biomolecular Structure & Dynamics. 33: 61-2. PMID 26103307 DOI: 10.1080/07391102.2015.1032713 |
0.303 |
|
| 2015 |
Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. Plos One. 10: e0130200. PMID 26075601 DOI: 10.1371/Journal.Pone.0130200 |
0.434 |
|
| 2015 |
Sloma MF, Mathews DH. Improving RNA secondary structure prediction with structure mapping data. Methods in Enzymology. 553: 91-114. PMID 25726462 DOI: 10.1016/Bs.Mie.2014.10.053 |
0.609 |
|
| 2015 |
Wang X, Sharp KK, Hoshika S, Bellaousov S, Zhang X, Mathews DH, Benner SA, Peterson RJ, Kahn JD. Structure and Thermodynamics of Aegis Nucleotides P and Z in DNA Biophysical Journal. 108: 395a. DOI: 10.1016/J.Bpj.2014.11.2165 |
0.41 |
|
| 2014 |
Fu Y, Sharma G, Mathews DH. Dynalign II: common secondary structure prediction for RNA homologs with domain insertions. Nucleic Acids Research. 42: 13939-48. PMID 25416799 DOI: 10.1093/Nar/Gku1172 |
0.594 |
|
| 2014 |
Zhang X, Walker RC, Phizicky EM, Mathews DH. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. Journal of Chemical Theory and Computation. 10: 3473-3483. PMID 25136272 DOI: 10.1021/Ct500107Y |
0.442 |
|
| 2014 |
Guy MP, Young DL, Payea MJ, Zhang X, Kon Y, Dean KM, Grayhack EJ, Mathews DH, Fields S, Phizicky EM. Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes & Development. 28: 1721-32. PMID 25085423 DOI: 10.1101/Gad.245936.114 |
0.365 |
|
| 2014 |
Mathews DH. RNA Secondary Structure Analysis Using RNAstructure. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 46: 12.6.1-25. PMID 24939127 DOI: 10.1002/0471250953.bi1206s46 |
0.439 |
|
| 2014 |
Mathews DH. Using the RNAstructure Software Package to Predict Conserved RNA Structures. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 46: 12.4.1-22. PMID 24939126 DOI: 10.1002/0471250953.Bi1204S46 |
0.573 |
|
| 2014 |
Aytenfisu AH, Spasic A, Seetin MG, Serafini J, Mathews DH. Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA. Journal of Chemical Theory and Computation. 10: 1292-1301. PMID 24803859 DOI: 10.1021/Ct400861G |
0.825 |
|
| 2014 |
Andronescu M, Condon A, Turner DH, Mathews DH. The determination of RNA folding nearest neighbor parameters. Methods in Molecular Biology (Clifton, N.J.). 1097: 45-70. PMID 24639154 DOI: 10.1007/978-1-62703-709-9_3 |
0.567 |
|
| 2013 |
Stern HA, Mathews DH. Accelerating calculations of RNA secondary structure partition functions using GPUs. Algorithms For Molecular Biology : Amb. 8: 29. PMID 24180434 DOI: 10.1186/1748-7188-8-29 |
0.657 |
|
| 2013 |
Bellaousov S, Reuter JS, Seetin MG, Mathews DH. RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic Acids Research. 41: W471-4. PMID 23620284 DOI: 10.1093/Nar/Gkt290 |
0.852 |
|
| 2013 |
Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proceedings of the National Academy of Sciences of the United States of America. 110: 5498-503. PMID 23503844 DOI: 10.1073/Pnas.1219988110 |
0.679 |
|
| 2013 |
Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S. Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Research. 41: 3819-32. PMID 23393189 DOI: 10.1093/Nar/Gkt063 |
0.571 |
|
| 2013 |
Leonard CW, Hajdin CE, Karabiber F, Mathews DH, Favorov OV, Dokholyan NV, Weeks KM. Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry. 52: 588-95. PMID 23316814 DOI: 10.1021/Bi300755U |
0.659 |
|
| 2013 |
Fu Y, Xu Z, Lu ZJ, Zhao S, Mathews DH. 31 Discovery of novel ncRNA by scanning multiple genome alignments Journal of Biomolecular Structure and Dynamics. 31: 19-19. DOI: 10.1080/07391102.2013.786463 |
0.446 |
|
| 2013 |
Mathews DH, Aytenfisu AH. 39 Simulation of RNA tandem GA base pairs provides insights about the forces behind conformational preference Journal of Biomolecular Structure and Dynamics. 31: 18-18. DOI: 10.1080/07391102.2013.786462 |
0.565 |
|
| 2013 |
Bellaousov S, Mathews DH. 29 Accelerating nucleic acid design using pre-selected sequences Journal of Biomolecular Structure and Dynamics. 31: 18-18. DOI: 10.1080/07391102.2013.786461 |
0.474 |
|
| 2013 |
Zhang X, Walker R, Mathews DH. 28 The study of tRNA modifications by molecular dynamics Journal of Biomolecular Structure and Dynamics. 31: 17-17. DOI: 10.1080/07391102.2013.786460 |
0.437 |
|
| 2012 |
Spasic A, Serafini J, Mathews DH. The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. Journal of Chemical Theory and Computation. 8: 2497-2505. PMID 23112748 DOI: 10.1021/Ct300240K |
0.527 |
|
| 2012 |
Schmidt K, Xu Z, Mathews DH, Butler JS. Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. Rna (New York, N.Y.). 18: 1934-45. PMID 22923767 DOI: 10.1261/Rna.033431.112 |
0.557 |
|
| 2012 |
Seetin MG, Mathews DH. RNA structure prediction: an overview of methods. Methods in Molecular Biology (Clifton, N.J.). 905: 99-122. PMID 22736001 DOI: 10.1007/978-1-61779-949-5_8 |
0.856 |
|
| 2012 |
Seetin MG, Mathews DH. TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics (Oxford, England). 28: 792-8. PMID 22285566 DOI: 10.1093/Bioinformatics/Bts044 |
0.856 |
|
| 2012 |
Xu Z, Almudevar A, Mathews DH. Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research. 40: e26. PMID 22139940 DOI: 10.1093/Nar/Gkr1081 |
0.574 |
|
| 2011 |
Van Nostrand KP, Kennedy SD, Turner DH, Mathews DH. Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change. Journal of Chemical Theory and Computation. 7: 3779-3792. PMID 22116780 DOI: 10.1021/Ct200223Q |
0.795 |
|
| 2011 |
Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/Rna.2753211 |
0.356 |
|
| 2011 |
Noble E, Mathews DH, Chen JL, Turner DH, Takimoto T, Kim B. Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. The Journal of Biological Chemistry. 286: 22965-70. PMID 21555520 DOI: 10.1074/Jbc.M111.239509 |
0.578 |
|
| 2011 |
Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. Rna Biology. 8: 468-77. PMID 21521948 DOI: 10.4161/rna.8.3.14421 |
0.41 |
|
| 2011 |
Seetin MG, Mathews DH. Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. Journal of Computational Chemistry. 32: 2232-44. PMID 21509787 DOI: 10.1002/Jcc.21806 |
0.854 |
|
| 2011 |
Harmanci AO, Sharma G, Mathews DH. TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences. Bmc Bioinformatics. 12: 108. PMID 21507242 DOI: 10.1186/1471-2105-12-108 |
0.624 |
|
| 2011 |
Xu Z, Mathews DH. Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics (Oxford, England). 27: 626-32. PMID 21193521 DOI: 10.1093/Bioinformatics/Btq726 |
0.616 |
|
| 2011 |
Liu B, Diamond JM, Mathews DH, Turner DH. Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters. Biochemistry. 50: 640-53. PMID 21133351 DOI: 10.1021/Bi101470N |
0.573 |
|
| 2011 |
Nasrallah CA, Mathews DH, Huelsenbeck JP. Quantifying the impact of dependent evolution among sites in phylogenetic inference. Systematic Biology. 60: 60-73. PMID 21081481 DOI: 10.1093/Sysbio/Syq074 |
0.526 |
|
| 2011 |
Sharma G, Harmanci AO, Mathews DH. Iterative estimation of structures of multiple RNA homologs: Turbofold Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 529-532. DOI: 10.1109/ICASSP.2011.5946457 |
0.482 |
|
| 2010 |
Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 6: 910-29. PMID 26613316 DOI: 10.1021/Ct900440T |
0.799 |
|
| 2010 |
Réblová K, St?elcová Z, Kulhánek P, Beššeová I, Mathews DH, Nostrand KV, Yildirim I, Turner DH, Sponer J. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. Journal of Chemical Theory and Computation. 2010: 910-929. PMID 21132104 |
0.489 |
|
| 2010 |
Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods. 7: 995-1001. PMID 21057495 DOI: 10.1038/Nmeth.1529 |
0.617 |
|
| 2010 |
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Computational approaches for RNA energy parameter estimation. Rna (New York, N.Y.). 16: 2304-18. PMID 20940338 DOI: 10.1261/Rna.1950510 |
0.625 |
|
| 2010 |
Bellaousov S, Mathews DH. ProbKnot: fast prediction of RNA secondary structure including pseudoknots. Rna (New York, N.Y.). 16: 1870-80. PMID 20699301 DOI: 10.1261/Rna.2125310 |
0.619 |
|
| 2010 |
Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harbor Perspectives in Biology. 2: a003665. PMID 20685845 DOI: 10.1101/Cshperspect.A003665 |
0.803 |
|
| 2010 |
Liu B, Mathews DH, Turner DH. RNA pseudoknots: folding and finding. F1000 Biology Reports. 2: 8. PMID 20495679 DOI: 10.3410/B2-8 |
0.596 |
|
| 2010 |
Mathews DH. Using OligoWalk to identify efficient siRNA sequences. Methods in Molecular Biology (Clifton, N.J.). 629: 109-21. PMID 20387146 DOI: 10.1007/978-1-60761-657-3_8 |
0.541 |
|
| 2010 |
Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. Bmc Bioinformatics. 11: 129. PMID 20230624 DOI: 10.1186/1471-2105-11-129 |
0.656 |
|
| 2010 |
Piekna-Przybylska D, DiChiacchio L, Mathews DH, Bambara RA. A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer. Nature Structural & Molecular Biology. 17: 83-9. PMID 19966801 DOI: 10.1038/Nsmb.1687 |
0.748 |
|
| 2010 |
Turner DH, Mathews DH. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Research. 38: D280-2. PMID 19880381 DOI: 10.1093/Nar/Gkp892 |
0.513 |
|
| 2009 |
Rigby ST, Van Nostrand KP, Rose AE, Gorelick RJ, Mathews DH, Bambara RA. Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site. Journal of Molecular Biology. 394: 694-707. PMID 19853618 DOI: 10.1016/J.Jmb.2009.10.036 |
0.754 |
|
| 2009 |
Lu ZJ, Gloor JW, Mathews DH. Improved RNA secondary structure prediction by maximizing expected pair accuracy. Rna (New York, N.Y.). 15: 1805-13. PMID 19703939 DOI: 10.1261/Rna.1643609 |
0.6 |
|
| 2009 |
Harmanci AO, Sharma G, Mathews DH. Stochastic sampling of the RNA structural alignment space. Nucleic Acids Research. 37: 4063-75. PMID 19429694 DOI: 10.1093/Nar/Gkp276 |
0.473 |
|
| 2009 |
Deigan KE, Li TW, Mathews DH, Weeks KM. Accurate SHAPE-directed RNA structure determination. Proceedings of the National Academy of Sciences of the United States of America. 106: 97-102. PMID 19109441 DOI: 10.1073/Pnas.0806929106 |
0.68 |
|
| 2008 |
Hart JM, Kennedy SD, Mathews DH, Turner DH. NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. Journal of the American Chemical Society. 130: 10233-9. PMID 18613678 DOI: 10.1021/Ja8026696 |
0.621 |
|
| 2008 |
Lu ZJ, Mathews DH. OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research. 36: W104-8. PMID 18490376 DOI: 10.1093/Nar/Gkn250 |
0.536 |
|
| 2008 |
Lu ZJ, Mathews DH. Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research. 36: 3738-45. PMID 18483081 DOI: 10.1093/Nar/Gkn266 |
0.412 |
|
| 2008 |
Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. Plos Biology. 6: e96. PMID 18447581 DOI: 10.1371/Journal.Pbio.0060096 |
0.542 |
|
| 2008 |
Harmanci AO, Sharma G, Mathews DH. PARTS: probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Research. 36: 2406-17. PMID 18304945 DOI: 10.1093/Nar/Gkn043 |
0.6 |
|
| 2008 |
Lu ZJ, Mathews DH. Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research. 36: 640-7. PMID 18073195 DOI: 10.1093/Nar/Gkm920 |
0.499 |
|
| 2008 |
Harmanci AO, Sharma G, Mathews DH. Probabilistic structural alignment of RNA sequences Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 645-648. DOI: 10.1109/ICASSP.2008.4517692 |
0.477 |
|
| 2007 |
Mathews DH, Turner DH, Zuker M. RNA secondary structure prediction. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.2. PMID 18428968 DOI: 10.1002/0471142700.Nc1102S28 |
0.632 |
|
| 2007 |
Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH. NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA. Biochemistry. 46: 12665-78. PMID 17929882 DOI: 10.1021/Bi700802S |
0.681 |
|
| 2007 |
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics (Oxford, England). 23: i19-28. PMID 17646296 DOI: 10.1093/bioinformatics/btm223 |
0.404 |
|
| 2007 |
Tyagi R, Mathews DH. Predicting helical coaxial stacking in RNA multibranch loops. Rna (New York, N.Y.). 13: 939-51. PMID 17507661 DOI: 10.1261/Rna.305307 |
0.713 |
|
| 2007 |
Harmanci AO, Sharma G, Mathews DH. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. Bmc Bioinformatics. 8: 130. PMID 17445273 DOI: 10.1186/1471-2105-8-130 |
0.598 |
|
| 2007 |
Harmanci AO, Sharma G, Mathews DH. Toward turbo decoding of RNA secondary structure Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 1. DOI: 10.1109/ICASSP.2007.366692 |
0.534 |
|
| 2007 |
Sharma G, Harmanci AO, Mathews DH. Probabilistic methods for improving efficiency of RNA secondary structure prediction across multiple sequences Conference Record - Asilomar Conference On Signals, Systems and Computers. 34-38. DOI: 10.1109/ACSSC.2007.4487159 |
0.432 |
|
| 2006 |
Mathews DH. RNA secondary structure analysis using RNAstructure. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 12.6. PMID 18428759 DOI: 10.1002/0471250953.Bi1206S13 |
0.65 |
|
| 2006 |
Lu ZJ, Turner DH, Mathews DH. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research. 34: 4912-24. PMID 16982646 DOI: 10.1093/Nar/Gkl472 |
0.562 |
|
| 2006 |
Duan S, Mathews DH, Turner DH. Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA. Biochemistry. 45: 9819-32. PMID 16893182 DOI: 10.1021/Bi052618X |
0.768 |
|
| 2006 |
Kierzek E, Mathews DH, Ciesielska A, Turner DH, Kierzek R. Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides. Nucleic Acids Research. 34: 3609-14. PMID 16870722 DOI: 10.1093/Nar/Gkl232 |
0.598 |
|
| 2006 |
Mathews DH, Turner DH. Prediction of RNA secondary structure by free energy minimization. Current Opinion in Structural Biology. 16: 270-8. PMID 16713706 DOI: 10.1016/J.Sbi.2006.05.010 |
0.577 |
|
| 2006 |
Uzilov AV, Keegan JM, Mathews DH. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. Bmc Bioinformatics. 7: 173. PMID 16566836 DOI: 10.1186/1471-2105-7-173 |
0.473 |
|
| 2006 |
Mathews DH. Revolutions in RNA secondary structure prediction. Journal of Molecular Biology. 359: 526-32. PMID 16500677 DOI: 10.1016/J.Jmb.2006.01.067 |
0.59 |
|
| 2006 |
Mathews DH, Case DA. Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair. Journal of Molecular Biology. 357: 1683-93. PMID 16487974 DOI: 10.1016/J.Jmb.2006.01.054 |
0.445 |
|
| 2006 |
Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/Rna.2343206 |
0.606 |
|
| 2006 |
Mathews DH, Schroeder SJ, Turner DH, Zuker M. 22 Predicting RNA Secondary Structure Cold Spring Harbor Monograph Archive. 43: 631-657. DOI: 10.1101/087969739.43.631 |
0.572 |
|
| 2006 |
Mathews DH. Predicting RNA secondary structure by free energy minimization Theoretical Chemistry Accounts. 116: 160-168. DOI: 10.1007/S00214-005-0027-7 |
0.664 |
|
| 2005 |
Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH, Kierzek R. The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Research. 33: 5082-93. PMID 16155181 DOI: 10.1093/Nar/Gki789 |
0.535 |
|
| 2005 |
Mathews DH. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics (Oxford, England). 21: 2246-53. PMID 15731207 DOI: 10.1093/Bioinformatics/Bti349 |
0.652 |
|
| 2004 |
Mathews D. Predicting the secondary structure common to two RNA sequences with Dynalign Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 18428718 DOI: 10.1002/0471250953.Bi1204S08 |
0.596 |
|
| 2004 |
Mathews DH. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. Rna (New York, N.Y.). 10: 1178-90. PMID 15272118 DOI: 10.1261/Rna.7650904 |
0.6 |
|
| 2004 |
Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH. Secondary structure models of the 3' untranslated regions of diverse R2 RNAs. Rna (New York, N.Y.). 10: 978-87. PMID 15146081 DOI: 10.1261/Rna.5216204 |
0.538 |
|
| 2004 |
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 101: 7287-92. PMID 15123812 DOI: 10.1073/Pnas.0401799101 |
0.721 |
|
| 2003 |
Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM. Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Research. 31: 4989-94. PMID 12930948 DOI: 10.1093/Nar/Gkg710 |
0.426 |
|
| 2002 |
Mathews DH, Turner DH. Use of chemical modification to elucidate RNA folding pathways. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.9. PMID 18428887 DOI: 10.1002/0471142700.Nc1109S09 |
0.592 |
|
| 2002 |
Mathews DH, Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology. 317: 191-203. PMID 11902836 DOI: 10.1006/Jmbi.2001.5351 |
0.547 |
|
| 2002 |
Mathews DH, Turner DH. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry. 41: 869-80. PMID 11790109 DOI: 10.1021/Bi011441D |
0.582 |
|
| 2001 |
Diamond JM, Turner DH, Mathews DH. Thermodynamics of three-way multibranch loops in RNA. Biochemistry. 40: 6971-81. PMID 11389613 DOI: 10.1021/Bi0029548 |
0.664 |
|
| 2001 |
Xia T, Mathews DH, Turner DH. 2 – Thermodynamics of RNA Secondary Structure Formation Rna. 21-48. DOI: 10.1016/B978-008043408-7/50023-X |
0.742 |
|
| 1999 |
Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. Predicting oligonucleotide affinity to nucleic acid targets. Rna (New York, N.Y.). 5: 1458-69. PMID 10580474 DOI: 10.1017/S1355838299991148 |
0.704 |
|
| 1999 |
Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology. 288: 911-40. PMID 10329189 DOI: 10.1006/Jmbi.1999.2700 |
0.563 |
|
| 1998 |
Mathews DH, Andre TC, Kim J, Turner DH, Zuker M. An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Thermodynamic Parameters Acs Symposium Series. 682: 246-257. |
0.487 |
|
| 1997 |
Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. Rna (New York, N.Y.). 3: 1-16. PMID 8990394 |
0.388 |
|
| 1995 |
Li Y, Bevilacqua PC, Mathews D, Turner DH. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry. 34: 14394-9. PMID 7578043 DOI: 10.1021/Bi00044A016 |
0.581 |
|
| 1994 |
Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 91: 9218-22. PMID 7524072 DOI: 10.1073/Pnas.91.20.9218 |
0.555 |
|
| Show low-probability matches. |