David H. Mathews, Ph.D. - Publications

Affiliations: 
2001 University of Rochester, Rochester, NY 
Area:
Biochemistry

114 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.6
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  0.6
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  0.48
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  0.52
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  0.52
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  0.72
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  0.72
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  0.68
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  0.6
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  0.68
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  0.72
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  0.52
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  0.48
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  0.72
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  0.68
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  1
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  0.6
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.48
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  0.48
2015 Kayedkhordeh M, Bellaousov S, Mathews DH. 98 Improving nucleic acid design using biased sequence initialization. Journal of Biomolecular Structure & Dynamics. 33: 62-3. PMID 26103309 DOI: 10.1080/07391102.2015.1032715  0.52
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  0.68
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  0.48
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.72
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.72
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  0.88
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  0.88
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  0.88
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  0.88
2010 Liu B, Mathews DH, Turner DH. RNA pseudoknots: folding and finding. F1000 Biology Reports. 2: 8. PMID 20495679 DOI: 10.3410/B2-8  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
2008 Lu ZJ, Mathews DH. Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research. 36: 640-7. PMID 18073195 DOI: 10.1093/nar/gkm920  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
2006 Mathews DH. Predicting RNA secondary structure by free energy minimization Theoretical Chemistry Accounts. 116: 160-168. DOI: 10.1007/s00214-005-0027-7  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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.  0.88
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  0.88
1995 Herrick DM, Wolfs FLH, Bryan DC, Freeman CG, Kurz KL, Mathews DH, Perera PAA, Zanni MT. Elastic scattering and quasielastic transfer for S32+96,100Mo at Elab=180 MeV Physical Review C. 52: 744-754. DOI: 10.1103/PhysRevC.52.744  0.88
1995 Freeman CG, Herrick DM, Bryan DC, Kurz KL, Mathews DH, Perera PAA, Wolfs FLH, Zanni MT. New focal plane detector system for the rochester recoil mass spectrometer Nuclear Inst. and Methods in Physics Research, A. 357: 450-457. DOI: 10.1016/0168-9002(94)01742-5  0.88
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  0.88
1994 Wolfs FLH, White CA, Bryan DC, Freeman CG, Herrick DM, Kurz KL, Mathews DH, Perera PAA, Zanni MT. Breakup of 87 MeV B11 Physical Review C. 49: 2538-2548. DOI: 10.1103/PhysRevC.49.2538  0.88
Show low-probability matches.