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LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH.

Bioinformatics. 2019 Jul 15;35(14):i295-i304. doi: 10.1093/bioinformatics/btz375.


CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation.

Tuladhar R, Yeu Y, Tyler Piazza J, Tan Z, Rene Clemenceau J, Wu X, Barrett Q, Herbert J, Mathews DH, Kim J, Hyun Hwang T, Lum L.

Nat Commun. 2019 Sep 6;10(1):4056. doi: 10.1038/s41467-019-12028-5.


Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.

Zuber J, Mathews DH.

RNA. 2019 Jun;25(6):747-754. doi: 10.1261/rna.069203.118. Epub 2019 Apr 5.


How to benchmark RNA secondary structure prediction accuracy.

Mathews DH.

Methods. 2019 Jun 1;162-163:60-67. doi: 10.1016/j.ymeth.2019.04.003. Epub 2019 Apr 2. Review.


Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change.

Ward M, Sun H, Datta A, Wise M, Mathews DH.

Bioinformatics. 2019 Mar 28. pii: btz222. doi: 10.1093/bioinformatics/btz222. [Epub ahead of print]


Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection.

Ghoneim DH, Zhang X, Brule CE, Mathews DH, Grayhack EJ.

Nucleic Acids Res. 2019 Feb 20;47(3):1164-1177. doi: 10.1093/nar/gky1262.


Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC.

Nucleic Acids Res. 2019 Jan 10;47(1):29-42. doi: 10.1093/nar/gky1118.


Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.

Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH.

J Chem Theory Comput. 2018 Dec 11;14(12):6598-6612. doi: 10.1021/acs.jctc.8b00633. Epub 2018 Nov 27.


mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN.

Nat Commun. 2018 Oct 18;9(1):4328. doi: 10.1038/s41467-018-06792-z.


Identification of new high affinity targets for Roquin based on structural conservation.

Braun J, Fischer S, Xu ZZ, Sun H, Ghoneim DH, Gimbel AT, Plessmann U, Urlaub H, Mathews DH, Weigand JE.

Nucleic Acids Res. 2018 Dec 14;46(22):12109-12125. doi: 10.1093/nar/gky908.


Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.

Zuber J, Cabral BJ, McFadyen I, Mauger DM, Mathews DH.

RNA. 2018 Nov;24(11):1568-1582. doi: 10.1261/rna.065102.117. Epub 2018 Aug 13.


Accelerated RNA secondary structure design using preselected sequences for helices and loops.

Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH.

RNA. 2018 Nov;24(11):1555-1567. doi: 10.1261/rna.066324.118. Epub 2018 Aug 10.


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.

Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE.

Nucleic Acids Res. 2018 Jul 27;46(13):6401-6415. doi: 10.1093/nar/gky529.


Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH.

Nucleic Acids Res. 2018 Jun 1;46(10):4883-4892. doi: 10.1093/nar/gky270.


Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH.

Biochemistry. 2018 Apr 10;57(14):2121-2131. doi: 10.1021/acs.biochem.7b01306. Epub 2018 Mar 23.


Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews DH.

RNA. 2018 May;24(5):656-672. doi: 10.1261/rna.064527.117. Epub 2018 Feb 6.


Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.

Payea MJ, Sloma MF, Kon Y, Young DL, Guy MP, Zhang X, De Zoysa T, Fields S, Mathews DH, Phizicky EM.

RNA. 2018 Mar;24(3):410-422. doi: 10.1261/rna.064642.117. Epub 2017 Dec 19.


Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH.

Nucleic Acids Res. 2018 Jan 9;46(1):314-323. doi: 10.1093/nar/gkx1057.


Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

Sloma MF, Mathews DH.

PLoS Comput Biol. 2017 Nov 6;13(11):e1005827. doi: 10.1371/journal.pcbi.1005827. eCollection 2017 Nov.


TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.

Tan Z, Fu Y, Sharma G, Mathews DH.

Nucleic Acids Res. 2017 Nov 16;45(20):11570-11581. doi: 10.1093/nar/gkx815.


Physics-based all-atom modeling of RNA energetics and structure.

Smith LG, Zhao J, Mathews DH, Turner DH.

Wiley Interdiscip Rev RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1422. Review.


Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.

Tan Z, Sharma G, Mathews DH.

Biophys J. 2017 Jul 25;113(2):330-338. doi: 10.1016/j.bpj.2017.06.039. Epub 2017 Jul 20.


Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.

Ward M, Datta A, Wise M, Mathews DH.

Nucleic Acids Res. 2017 Aug 21;45(14):8541-8550. doi: 10.1093/nar/gkx512.


Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ.

Viruses. 2017 Apr 26;9(5). pii: E93. doi: 10.3390/v9050093.


Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH.

J Chem Theory Comput. 2017 Feb 14;13(2):900-915. doi: 10.1021/acs.jctc.6b00870. Epub 2017 Jan 24.


RNA Secondary Structure Prediction.

Mathews DH, Turner DH, Watson RM.

Curr Protoc Nucleic Acid Chem. 2016 Dec 1;67:11.2.1-11.2.19. doi: 10.1002/cpnc.19.


Experiment-Assisted Secondary Structure Prediction with RNAstructure.

Xu ZZ, Mathews DH.

Methods Mol Biol. 2016;1490:163-76. doi: 10.1007/978-1-4939-6433-8_10.


Predicting RNA-RNA Interactions Using RNAstructure.

DiChiacchio L, Mathews DH.

Methods Mol Biol. 2016;1490:51-62. doi: 10.1007/978-1-4939-6433-8_4.


Prediction of Secondary Structures Conserved in Multiple RNA Sequences.

Xu ZZ, Mathews DH.

Methods Mol Biol. 2016;1490:35-50. doi: 10.1007/978-1-4939-6433-8_3.


Secondary Structure Prediction of Single Sequences Using RNAstructure.

Xu ZZ, Mathews DH.

Methods Mol Biol. 2016;1490:15-34. doi: 10.1007/978-1-4939-6433-8_2.


Bridging the gap between in vitro and in vivo RNA folding.

Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC.

Q Rev Biophys. 2016 Jan;49:e10. Epub 2016 Jun 24.


AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.

DiChiacchio L, Sloma MF, Mathews DH.

Bioinformatics. 2016 Apr 1;32(7):1033-9. doi: 10.1093/bioinformatics/btv682. Epub 2015 Nov 20.


Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH.

Biochemistry. 2015 Nov 17;54(45):6769-82. doi: 10.1021/acs.biochem.5b00833. Epub 2015 Nov 3.


Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.

Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH.

RNA. 2015 Nov;21(11):1898-907. doi: 10.1261/rna.051367.115. Epub 2015 Sep 14.


Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ.

Nucleic Acids Res. 2015 Sep 3;43(15):7247-59. doi: 10.1093/nar/gkv706. Epub 2015 Jul 13.


Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.

Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3485-94. doi: 10.1073/pnas.1503955112. Epub 2015 Jun 23.


Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH.

PLoS One. 2015 Jun 15;10(6):e0130200. doi: 10.1371/journal.pone.0130200. eCollection 2015.


Improving RNA secondary structure prediction with structure mapping data.

Sloma MF, Mathews DH.

Methods Enzymol. 2015;553:91-114. doi: 10.1016/bs.mie.2014.10.053. Epub 2015 Feb 3.


Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.

Fu Y, Sharma G, Mathews DH.

Nucleic Acids Res. 2014 Dec 16;42(22):13939-48.


Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.

Zhang X, Walker RC, Phizicky EM, Mathews DH.

J Chem Theory Comput. 2014 Aug 12;10(8):3473-3483. Epub 2014 May 28.


Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.

Guy MP, Young DL, Payea MJ, Zhang X, Kon Y, Dean KM, Grayhack EJ, Mathews DH, Fields S, Phizicky EM.

Genes Dev. 2014 Aug 1;28(15):1721-32. doi: 10.1101/gad.245936.114.


RNA Secondary Structure Analysis Using RNAstructure.

Mathews DH.

Curr Protoc Bioinformatics. 2014 Jun 17;46:12.6.1-25. doi: 10.1002/0471250953.bi1206s46.


Using the RNAstructure Software Package to Predict Conserved RNA Structures.

Mathews DH.

Curr Protoc Bioinformatics. 2014 Jun 17;46:12.4.1-22. doi: 10.1002/0471250953.bi1204s46.


Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

Aytenfisu AH, Spasic A, Seetin MG, Serafini J, Mathews DH.

J Chem Theory Comput. 2014 Mar 11;10(3):1292-1301. Epub 2014 Jan 22.


The determination of RNA folding nearest neighbor parameters.

Andronescu M, Condon A, Turner DH, Mathews DH.

Methods Mol Biol. 2014;1097:45-70. doi: 10.1007/978-1-62703-709-9_3. Review.


Accelerating calculations of RNA secondary structure partition functions using GPUs.

Stern HA, Mathews DH.

Algorithms Mol Biol. 2013 Nov 1;8(1):29. doi: 10.1186/1748-7188-8-29.


RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W471-4. doi: 10.1093/nar/gkt290. Epub 2013 Apr 24.


Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503. doi: 10.1073/pnas.1219988110. Epub 2013 Mar 15.

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