Mathews lab

Computational Biology of RNA

• Home
• Research
• Publications
• RNAstructure Software
• RNAstructure Web Servers
• Group

Publications:

• 170. Malik, A., Zhang, L., Gautam, M., Dai, N., Li, S., Zhang, H., Mathews, D.H., & Huang, L. (2024). LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. Journal of Molecular Biology. In Press.
• 169. Zuber, J., & Mathews, D.H. (2024). Estimating RNA Secondary Structure Folding Free Energy Changes with efn2. Methods in Molecular Biology. 2726:1-13.
• 168. Mittal, A., Turner, D.H., & Mathews, D.H. (2024). NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures. Journal of Molecular Biology. In Press.
• 167. Zhang, H., Li, S., Dai, N., Zhang, L., Mathews, D. H., & Huang, L. (2023). LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules. Nucleic Acids Research. 51: e94.
• 166. Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Jiang, H., Chen, C., Shen, H., Li, H., Mathews, D. H., Zhang, Y., & Huang, L. (2023). Algorithm for optimized mRNA design improves stability and immunogenicity. Nature. 621: 396-403. arXiv.
• 165. Pham, T.M., Miffin, T., Sun, H., Sharp, K.K., Wang, X., Zhu, M., Hoshika, S., Peterson, R.J., Benner, S.A., Kahn, J.D., & Mathews, D.H. (2023). DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. ACS Synthetic Biology. 12: 2750-2763. bioRxiv.
• 164. Hedaya, O.M., Subbaiah, K.C.V., Jiang, F., Xie, L.H., Wu, J., Khor, E., Zhu, M., Mathews, D.H., Proschel, C., Yao, P. (2023). Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nature Communications. 14: 6166. bioRxiv.
• 163. Li, S., Dai, N., Zhang, H., Malik, A., Mathews, D.H., & Huang, L. (2023). LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs. arXiv:2307.09580.
• 162. Courtney, E., Datta, A., Mathews, D.H., & Ward, M. (2023). memerna: Sparse RNA Folding Including Coaxial Stacking. bioRxiv. 2023.08.04.551958.
• 161. Mathews, D.H., Casadio, R., & Sternberg, M.J.E. (2023). Computational Resources for Molecular Biology 2023. Journal of Molecular Biology. 435: 168160.
• 160. Zhou, T., Dai, N., Li, S., Ward, M., Mathews, D.H., & Huang L. (2023). RNA design via structure-aware multifrontier ensemble optimization. Bioinformatics. 39: i563-i571.
• 159. Zhou, T., Gilliam, N.J., Li, S., Spaudau, S., Osborn, R.M., Anderson, C.S., Mariani, T.J., Thakar, J., Dewhurst, S., Mathews, D.H., Huang, L., & Sun, Y. (2023). Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection. mBio. 14: e0025023. bioRxiv.
• 158. Zuber, J., Sah, S.K., Mathews, D.H., & Rustchenko, E. (2023). Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants. Microorganisms. 11: 1870.
• 157. Ali, S.E., Mittal, A., & Mathews, D.H. (2023) RNA Secondary Structure Analysis Using RNAstructure. Current Protocols. 3:e846.
• 156. Schroeder, G.M., Akinyemi, O., Malik, J., Focht, C.M., Pritchett, E.M., Baker, C.D., McSally, J.P., Jenkins, J.L., Mathews, D.H., & Wedekind, J.E. (2023). A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic Acids Research. 51:2464-2484.
• 155. Zhang, H., Li, S., Zhang, L., Mathews, D.H., & Huang, L. (2023). LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2. Nucleic Acids Research. 51:e7
• 154. Zhang, H., Zhang, L., Liu, K., Li, S., Mathews, D.H., & Huang, L. (2023). Linear-Time Algorithms for RNA Structure Prediction. Methods in Molecular Biology. 2586:15-34
• 153. Cavender, C.E., Schroeder, G.M., Mathews, D.H., & Wedekind, J.E. (2023). Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model. Methods in Molecular Biology. 2568: 53-73.
• 152. Mirska, B., Woźniak, T., Lorent, D., Ruszkowska, A., Peterson, J.M., Moss, W.N., Mathews, D.H., Kierzek, R., & Kierzek, E. (2023). In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and Molecular Life Sciences. 80: 136.
• 151. Zhang, L., Li, S., Zhang, H., Mathews, D.H., & Huang, L. (2022). LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. ArXiv. arXiv:2206.14794v1
• 150. Lai, W.C., Zhu, M., Belinite, M., Ballard, G., Mathews, D.H., & Ermolenko, D. (2022). Intrinsically unstructured sequences in the mRNA 3’ UTR reduce the ability of poly(A) tail to enhance translation. Journal of Molecular Biology. 434: 167877.
• 149. Szikszai, M., Wise, M., Datta, A., Ward, M., & Mathews, D. H. (2022). Deep learning models for RNA secondary structure prediction (probably) do not generalise across families. Bioinformatics. 38: 3892-3899. bioRxiv.
• 148. Kumar, J., Lackey, L., Waldern, J. M., Dey, A., Mathews, D. H., & Laederach, A. (2022). Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing. Elife. 11:e73888. bioRxiv.
• 147.Szabat, M., Prochota, M., Kierzek, R., Kierzek, E., & Mathews, D.H. (2022). A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine. Journal of Molecular Biology. 434: 167632.
• 146. Casadio, R., Mathews, D.H., & Sternberg, M.J.E. (2022). Computational Resources for Molecular Biology 2022. Journal of Molecular Biology. 434:167625.
• 145. Zuber, J., Schroeder, S. J., Sun, H., Turner, D. H., & Mathews, D. H. (2022). Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Research. 50: 5251-5262. bioRxiv. 2021.10.16.464667
• 144. Szutkowska, B., Wieczorek, K., Kierzek, R., Zmora, P., Peterson, J. M., Moss, W. N., Mathews, D. H., & Kierzek, E. (2022). Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment. International Journal of Molecular Sciences. 23:2452.
• 143. Kierzek, E., Zhang, X., Watson, R. M., Kierzek, R., & Mathews, D. H. (2022). Secondary Structure Prediction for RNA Sequences Including N⁶-methyladenosine. Nature Communications. 13: 1271. bioRxiv.
• 142. Schroeder, G. M., Cavender, C. E., Blau, M. E., Jenkins, J. L., Mathews, D. H., & Wedekind, J. E. (2022). A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nature Communications. 13: 199.
• 141. Bao, C., Zhu, M., Nykonchuk, I., Wakabayashi, H., Mathews, D. H. & Ermolenko, D. (2022). Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation. Nature Communications. 13: 988.2021.08.16.456581. bioRxiv.
• 140. Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A. M. K., Cavender, C. E., Tebaldi, T., Pulvino, M. J., Jenkins, J. L., Mathews, D. H., Halene, S., & Kielkopf, C. L. (2022). Pre-mRNA Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the pre-mRNA Splice Site Signal. Nucleic Acids Research. 50: 5299-5312. bioRxiv. 2021.09.27.462007.
• 139. Ermolenko, D. N., & Mathews, D. H. (2021).  Making ends meet: New functions of mRNA secondary structure.  WIREs RNA. e1611.
• 138. Kayedkhordeh, M., Yamagami, R., Bevilacqua, P. C., & Mathews, D. H. (2021).  Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots. Methods in Molecular Biology. 2167: 113-143.
• 137. Li, S., Zhang, H., Zhang, L., Liu, K., Liu, B., Mathews, D.H., & Huang, L. (2021). LinearTurboFold: Linear-Time RNA Structural Alignment and Conserved Structure Prediction with Applications to Coronaviruses. Proceedings of the National Academy of Sciences, USA. 118: e2116269118. bioRxiv 2020.11.23.393488.
• 136. Chavali, S. S., Cavender, C. E., Mathews, D. H., & Wedekind, J.E. (2020). Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. Journal of the American Chemical Society. 142:19835-19839.
• 135. Schroeder, G. M., Dutta, D., Cavender, C. E., Jenkins, J. L., Pritchett, E. M., Baker, C. D., Ashton, J. M., Mathews, D. H., & Wedekind, J. E. (2020).  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.  48: 8146-8164.
• 134. Zhang, L., Zhang, H., Mathews, D. H., & Huang, L. (2020). ThreshKnot: Thresholded ProbKnot for Improved RNA Secondary Structure Prediction. arXiv. 912.12796v2.
• 133. Zhang, H., Zhang, L., Mathews, D. H., & Huang, L. (2020). LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities. Bioinformatics. 36:i258-i267. arxiv.
• 132. Sloma, M. F., Zuker, M., & Mathews, D. H. (2020). Predictive methods using RNA sequences. In Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins, 4th edition (Baxevanis, A. D., Bader, G. D. & Wishart, D. S., eds.), John Wiley & Sons, Inc.
• 131. Ward, M., Sun, H., Datta, A., Wise, M., & Mathews, D. H. (2019). Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change. Bioinformatics. 35: 4298-4306.
• 130. Huang, L., Zhang, H., Deng, D., Zhao, K., Liu, K., Hendrix, D. A., & Mathews, D. H. (2019). LinearFold: Linear-Time Prediction of RNA Secondary Structures. Bioinformatics. 35: i295-i304. BioRxiv.
• 129. Zuber, J., & Mathews, D. H. (2019). Estimating Uncertainty in Predicted Folding Free Energy Changes of RNA Secondary Structures. RNA. 25: 747-754.
• 128. Tuladhar, R., Yeu, Y., Piazza, J. T., Tan, Z., Clemenceau, J. R.,Wu, X., Barrett, Q., Herbert, J., Mathews, D. H., Kim, J., Hwang, T. H., & Lum, L. (2019). CRISPR/Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nature Communications. 10: 4056. BioRxiv.
• 127. Mathews, D. H. (2019). How to Benchmark RNA Secondary Structure Prediction Accuracy. Methods. 162-163: 60-67.
• 126. Ghoneim, D.H., Zhang, X., Brule, C.E., Mathews, D.H., & Grayhack, E.J. (2019). Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection. Nucleic Acids Research. 47: 1164-1177.
• 125. Yamagami, R., Kayedkhordeh, M., Mathews, D.H., & Bevilacqua, P.C. (2019). Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study. Nucleic Acids Research. 47: 29-42.
• 124. Braun, J., Fischer, S., Xu, Z. Z., Sun, H., Ghoneim, D. H., Gimbel, A. T., Plessmann, U., Urlaub, H., Mathews, D. H., & Weigand, J. E. (2018). Identification of New High Affinity Targets for Roquin Based on Structural Conservation. Nucleic Acids Research. 46: 12109-12125.
• 123. Zuber, J., Cabral, B. J., McFadyen, I., Mauger, D. M., & Mathews, D. H. (2018). Analysis of RNA Nearest Neighbor Parameters Reveals Interdependencies and Quantifies the Uncertainty in RNA Secondary Structure Prediction. RNA. 24: 1568-1582. sequence_and_structure_dataset, interactive_Figure_3, interactive_Figure_4
• 122. Bellaousov, S., Kayedkhordeh, M., Peterson, R. J. & Mathews, D. H. (2018). Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops. RNA. 24: 1555-1567.
• 121. Belashov, I. A., Crawford, D.W., Cavender, C.E., Dai, P., Beardslee, P.C., Mathews, D.H., Pentelute, B.L., McNaughton, B.R., & Wedekind, J. E. (2018). 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. 46: 6401-6415.
• 120. Smith, L. G., Tan, Z., Spasic, A., Dutta, D., Salas-Estrada, L. A., Grossfield, A., & Mathews, D. H. (2018). Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. Journal of Chemical Theory and Computation. 14:6598-6612. BioRxiv.
• 119. Lai, W. C., Kayedkhordeh, M., Cornell, E. V., Farah, E., Bellaousov, S., Rietmeijer, R., Mathews, D. H., & Ermolenko, D. N. (2018). mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances. Nature Communications. 9: 4328. BioRxiv.
• 118. Spasic, A., Berger, K. D., Chen, J. L., Seetin, M. G., Turner, D. H., & Mathews, D. H. (2018). Improving RNA Nearest Neighbor Parameters for Helices by Going Beyond the Two-State Model. Nucleic Acids Research. 46: 4883-4892.
• 117. Berger, K. D., Kennedy, S. D., Schroeder, S. J., Znosko, B. M., Sun, H., Mathews, D. H., & Turner, D. H. (2018). Surprising Sequence Effects on GU Closure of RNA Internal Loops. Biochemistry. 57: 2121-2131.
• 116. Spasic, A., Kennedy, S. D., Needham, L., Manoharan, M., Kierzek, R., Turner, D. H., & Mathews, D. H. (2018). Molecular Dynamics Correctly Models the Unusual Major Conformation of the GAGU RNA Internal Loop and with NMR Reveals an Unusual Minor Conformation. RNA. 24: 656-672.
• 115. Payea, M. J., Sloma, M. F., Kon, Y., Young, D. L., Guy, M. P., Zhang, X., De Zoysa, T., Fields, S., Mathews, D. H., & Phizicky, E. M. (2018). Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. RNA. 24: 410-422.
• 114. Spasic, A., Assmann, S. M., Bevilacqua, P. C., & Mathews, D. H. (2018). Modeling RNA Secondary Structure Folding Ensembles Using SHAPE Mapping Data. Nucleic Acids Research. 46: 314-323.
• 113. Sloma, M. F. & Mathews, D. H. (2017). Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Computational Biology. 13, e1005827.
• 112. Tan, Z., Fu, Y., Sharma, G., & Mathews, D. H. (2017). TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic Acids Research. 45: 11570-11581. RNAStralign Database of structures and alignments.
• 111. Smith, L. G., Zhao, J., Mathews, D. H., & Turner D. H. (2017). Physics-based all-atom modeling of RNA energetics and structure. Wiley Interdisciplinary Reviews RNA. 8, 1422.
• 110. Tan, Z., Sharma, G., & Mathews, D. H. (2017). Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. Biophysical Journal. 113, 330-338.
• 109. Ward, M., Datta, A., Wise, M., & Mathews, D. H. (2017). Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic Acids Research. 45, 8541-8550.
• 108. Gamache, E. R. , Doh, J. H., Ritz, J., Laederach, A., Bellaousov, S., Mathews,D. H., & Curcio, M. J. (2017). Structure-function model for kissing loop interactions that initiate dimerization of Ty1 RNA. Viruses. 9, E93.
• 107. Zuber, J., Sun, H., Zhang, X., McFadyen, I., & Mathews, D. H. (2017). 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. 45, 6168-6176.
• 106. Aytenfisu, A. H., Spasic, A., Grossfield, A., Stern, H. A., & Mathews, D. H. (2017). Revised RNA dihedral parameters for the Amber force field improve RNA molecular dynamics. Journal of Chemical Theory and Computation. 14, 900-915.
• 105. Mathews, D. H. Turner, D. H., & Watson, R. M. (2016). RNA Secondary Structure Prediction. Current Protocols in Nucleic Acid Chemistry. 67, 11.2.1 -11.2.19.
• 104. Sloma, M.F., & Mathews, D.H. (2016). Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. RNA. 22, 1808-1818. ArchiveII dataset of sequences and structures.
• 103. Xu, Z.Z., & Mathews, D.H. (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods in Molecular Biology. 1490, 15-34.
• 102. DiChiacchio, L., & Mathews, D.H. (2016). Predicting RNA-RNA Interactions Using RNAstructure. Methods in Molecular Biology. 1490, 51-62.
• 101. Xu, Z.Z., & Mathews, D.H. (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. Methods in Molecular Biology. 1490, 35-50.
• 100. Xu, Z.Z., & Mathews, D.H. (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods in Molecular Biology. 1490, 15-34.
• 99. Leamy, K.A., Assmann, S.M., Mathews, D.H., & Bevilacqua, P.C. (2016). Bridging the gap between in vitro and in vivo RNA folding. Quarterly Reviews of Biophysics. 49, e10.
• 98. DiChiacchio, L., Sloma, M. F., & Mathews, D. H. (2016). AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure. Bioinformatics. 32, 1033-1039.
• 97. Chen, J. L,. Bellaousov, S., Tubbs, J. D., Kennedy, S. D., Lopez, M. J., Mathews, D. H., &Turner, D. H. (2015). NMR-assisted prediction of secondary structure for RNA: Incorporation of direction-dependent chemical shift constraints. Biochemistry. 54, 6769-6782.
• 96. Aytenfisu, A., Liberman, J. A., Wedekind, J. E,. & Mathews, D. H. (2015). Molecular Mechanism for PreQ1-II Riboswitch Function Revealed by Molecular Dynamics. RNA. 21, 1898-1907.
• 95. Wu, Y., Shi, B., Ding, X., Liu, T., Hu, X., Yip, K. Y., Yang,  Z. R., Mathews, D. H., and Lu, Z. J. (2015). Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.  Nucleic Acids Research. 43, 7247-59.
• 94. Liberman, J. A., Suddala, K C., Aytenfisu, A,. Chan, D., Belashov, I. A., Salim, M.,Mathews, D. H., Spitale, R. C., Walter, N. G., & Wedekind, J. E. (2015). 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. 112, E3485-E3494.
• 93. Sloma, M. F., & Mathews, D. H. (2015). Improving RNA Secondary Structure Prediction with Structure Mapping Data. Methods in Enzymology. 553, 91-114.
• 92. Fu, Y., Xu, Z. Z., Lu, Z. J., Zhao, S., & Mathews, D. H. (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS One. 10, e0130200.
• 91. Fu, Y., Sharma, G., & Mathews, D. H. (2014). Dynalign II: Common Secondary Structure Prediction for RNA Homologs with Domain Insertions. Nucleic Acids Research. 42, 13939-13948.
• 90. Guy, M. P., Young, D. L., Payea, M. J., Zhang, X., Kon, Y., Dean, K. M., Grayhack, E. J., Mathews, D. H., Fields, S., & Phizicky, E. M. (2014).  Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high throughput in vivo analysis.  Genes & Development.  28,1721-1732.
• 89. Zhang, X., Walker, R. C., Phizicky, E. M., & Mathews, D. H. (2014). Influence of sequence and covalent modifications on yeast tRNA dynamics. Journal of Chemical Theory and Computation. 10, 3473-3483. Link to force field parameters for modified nucleotides on GitHub.
• 88. Mathews, D. H. (2014). RNA secondary structure analysis using RNAstructure. Current Protocols in Bioinformatics. 46, 12.6.1-12.6.25.
• 87. Mathews, D. H. (2014). Using the RNAstructure software package to predict conserved RNA structures. Current Protocols in Bioinformatics. 46, 12.4.1-12.4.22.
• 86. Aytenfisu, A. H., Spasic, A., Seetin, M. G., Serafini, J., & Mathews, D. H. (2014). Modified Amber force field correctly models the conformational preference for tandem GA pairs in RNA. Journal of Chemical Theory and Computation. 10, 1292-1301.
• 85. Andronescu, M., Condon, A., Turner, D. H., & Mathews, D. H. (2014).  The Determination of RNA folding nearest neighbor parameters.  Methods in Molecular Biology.  1097, 45-70.
• 84. Stern, H. A., & Mathews, D. H. (2013). Accelerating calculations of RNA secondary structure partition functions using GPUs. Algorithms for Molecular Biology. 8, 29.
• 83. Bellaousov, S., Reuter, J. S., Seetin, M. G., & Mathews, D. H. (2013).  RNAstructure: Web servers for RNA Secondary Structure Prediction and Analysis.  Nucleic Acids Research.  41, W471-W474.
• 82. Hajdin, C. E., Bellaousov, S., Huggins, W., Leonard, C. W., Mathews, D. H., & Weeks, K. M. (2013).  Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.  Proceedings of the National Academy of Sciences, USA.  110, 5498-5503.
• 81. Leonard, C. W., Hajdin, C. E., Karabiber, F., Mathews, D. H., Favorov, O. V., Dokholyan, N. V., & Weeks, K. M. (2013).  Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.  Biochemistry.  52: 588-595.
• 80. Shen, M., Bellaousov, S., Hiller, M., de La Grange, P., Creamer, T. P., Malina, O., Sperling, R., Mathews, D. H., Stoilov, P., & Stamm, S.  (2013).  Pyrvinium Pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.  Nucleic Acids Research. 41, 3819-3832.
• 79. Spasic, A., Serafini, J., & Mathews, D. H. (2012). The Amber ff99 force field predicts relative free energy changes for RNA helix formation. Journal of Chemical Theory and Computation. 8, 2497-2505.
• 78. Schmidt, K., Xu, Z., Mathews, D. H., & Butler, J. S. (2012). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA. 18, 1934-1945.
• 77. Seetin, M. G., & Mathews, D. H. (2012). RNA structure prediction: an overview of methods. Methods in Molecular Biology. 905, 99-122.
• 76. Seetin, M. G., & Mathews, D. H. (2012). TurboKnot: Rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics. 28, 792-798.
• 75. Xu, Z., Almudevar, A., & Mathews, D. H. (2012). Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research. 40, e26.
• 74. Van Nostrand, K. P., Kennedy, S. D., Turner, D. H., & Mathews, D. H. (2011). Molecular mechanics investigation of an adenine-adenine non-canonical pair conformational change. Journal of Chemical Theory and Computation. 7, 3779-3792.
• 73. Rocca-Serra, P., Bellaousov, S., Birmingham, A., Chen, C., Cordero, P., Das, R., Davis-Neulander, L., Duncan, C. D., Halvorsen, M., Knight, R., Leontis, N. B., Mathews, D. H., Ritz, J., Stombaugh, J., Weeks, K. M., Zirbel, C. L., Laederach, A. (2011). Sharing and archiving nucleic acid structure mapping data. RNA. 17, 1204-1212.
• 72. Noble, E., Mathews, D. H., Chen, J. L., Turner, D. H., Takimoto, T., & Kim, B. (2011). Biophysical analysis of influenza a virus RNA promoter at physiological temperatures. Journal of Biological Chemistry. 286, 22965-22970.
• 71. Seetin, M. G., & Mathews, D. H. (2011). Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. Journal of Computational Chemistry. 32, 2232-2244.
• 70. Harmanci, A. O., Sharma, G., & Mathews, D. H. (2011). TurboFold: Iterative probabilistic estimation of secondary structure for multiple RNA sequences. BMC Bioinformatics. 20, 108.
• 69. Vockenhuber, M., Sharma, C., Statt, M. G., Schmidt, D., Xu, Z., Dietrich, S., Liesegang, H., Mathews, D. H., & Suess, B. (2011). Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biology. 8, 468-477.
• 68. Xu, Z., & Mathews, D. H. (2011). Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics. 27, 626-632.
• 67. Liu, B., Diamond, J. M., Mathews, D. H., & Turner, D. H. (2011). Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters. Biochemistry. 50, 640-653.
• 66. Nasrallah, C. A., Mathews D. H., Huelsenbeck, J. P. (2011). Quantifying the impact of dependent evolution among sites in phylogenetic inference. Systems Biology. 60, 60-73.
• 65. Underwood, J. G., Uzilov, A. V., Katzman, S., Onodera, C. S., Mainzer, J. E., Mathews, D. H., Lowe, T. M., Salama, S. R., & Haussler, D. (2010). FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods. 7, 995-1001.
• 64. Andronescu, M., Condon, A., Hoos, H. H., Mathews, D. H., & Murphy, K. P. (2010). Computational approaches for RNA energy parameter estimation. RNA. 16, 2304-2318.
• 63. Bellaousov, S., & Mathews, D. H. (2010). ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA. 16, 1870-1880.
• 62. Liu, B., Mathews, D. H., & Turner, D. H. (2010). RNA pseudoknots: folding and finding. F1000 Biology Reports. 2, 8.
• 61. Reuter, J. S., & Mathews, D. H. (2010). RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 11,129.
• 60. Reblova, K., Strelcova, Z., Kuthanek, P., Besseova, I., Mathews, D. H., Van Nostrand, K., Yildirim, I., Turner, D. H., & Sponer, J. (2010). 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, 910-929.
• 59. Piekna-Przybylska, D., DiChiacchio, L., Mathews, D. H., & Bambara, R. A.  (2010).  A sequence similar to tRNA3Lys gene is embedded in HIV-1 U3/R and promotes minus strand transfer. Nature Structural & Molecular Biology. 17, 83-89. 
• 58. Mathews, D. H., Moss, W. N., & Turner, D. H.. (2010).  Folding and finding RNA secondary structure. Cold Spring Harbor Perspectives in Biology. 2, a003665.
• 57. Mathews, D. H.  (2010).  Using OligoWalk to iIdentify efficient siRNA sequences. Methods in Molecular Biology. 629, 109-121.
• 56. Turner, D. H.& Mathews, D. H..  (2009).  NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.  Nucleic Acids Research.  38, D280-D282.
• 55. Rigby, S. T., Van Nostrand, K. P., Rose, A. E., Gorelick, R. J., Mathews, D. H., & Bambara, R.A. (2009).  Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site.  Journal of Molecular Biology.  394, 694-707.
• 54. Lu, Z. J., Gloor, J. W., & Mathews, D. H.  (2009).  Improved RNA secondary structure prediction by maximizing expected pair accuracy.  RNA. 15, 1805-1813.
• 53. Harmanci, A. O., Sharma, G., & Mathews, D. H. (2009).  Stochastic sampling of the RNA structural alignment space.  Nucleic Acids Research.  37, 4063-4075. 
• 52. Harmanci, A. O., Sharma, G., & Mathews, D. H. (2009). Joint stochastic sampling for RNA secondary structure prediction. Proceedings IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), May 17-20, 2009, Minneapolis, MN.
• 51. Deigan, K. E., Li, T. W., Mathews, D. H., & Weeks, K. M. (2009). Accurate SHAPE-directed RNA structure determination. Proceedings of the National Academy of Sciences, USA. 106, 97 - 102.
• 50. Hart, J. M., Kennedy, S. D., Mathews, D. H., & Turner, D. H.(2008). NMR-assisted prediction of RNA secondary structrure. JACS. 103, 10233 - 10239.
• 49. Lu, Z. J., & Mathews, D. H. (2008). Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotides. Nucleic Acids Research. 36, 3738 - 3745.
• 48. Lu, Z. J., & Mathews, D. H. (2008). OligoWalk: An online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research. 36, W104 - W108.
• 47. Wilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A., Mathews, D. H., Giddings, M. C., & Weeks, K. M. (2008). High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLOS Biology. 6, e96.
• 46. Harmanci, A. O., Sharma, G., & Mathews, D. H. (2008). Probabilistic structural alignment of RNA sequences. Proceedings IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), March 30-April 4, 2008, Las Vegas, NV, 1685-1688.
• 45. Harmanci, A. O., Sharma, G., & Mathews, D. H. (2008). PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction. Nucleic Acids Research. 36, 2406-2417.
• 44. Lu, Z. J., & Mathews, D. H. (2008). Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research. 36, 640-647.
• 43. Shankar, N., Xia, T., Kennedy, S. D., Krugh, T. R., Mathews, D. H., & Turner, D. H. (2007). NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA. Biochemistry. 46, 12665-12678.
• 42. Andronescu, M., Condon, A., Hoos, H. H., Mathews, D. H., & Murphy, K. P. (2007). Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics. 23, i19-i28.
• 41. Sharma, G., Harmanci, A. O., & Mathews, D. H. (2007). Probabilistic methods for improving efficiency of RNA secondary structure prediction across multiple sequences. Proceedings 41 st Asilomar Conference on Signals, Systems & Computers, Nov. 4-7, 2007, Pacific Grove, CA.
• 40. Harmanci, A., Sharma, G., & Mathews, D. H. (2007). Toward turbo decoding of RNA secondary structure. Proceedings IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), April 15-20, 2007, Honolulu, HI, I, 365–368.
• 39. Tyagi, R., & Mathews, D.H. (2007). Predicting helical coaxial stacking in RNA multibranch loops. RNA. 13, 939 - 951. Supplementary Material and Erratum.
• 38. Harmanci, A., Sharma, G., & Mathews, D. H. (2007). Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics. 8,130.
• 37. Lu, Z. J., Turner, D. H., & Mathews, D. H. (2006). A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research. 34, 4912-4924.
• 36. Mathews, D. H. (2006). RNA secondary structure analysis using RNAstructure. In Current Protocols in Bioinformatics (Baxevanis, A. D., Davidson, D. B., Page, R. D. M., Petsko, G. A., Stein, L. D., & Stormo, G. D., eds.), pp. 12.6.1-12.6.14. John Wiley & Sons, Inc.
• 35. Duan, S., Mathews, D. H., & Turner, D. H. (2006). Interpreting oligonucleotide microarray data to determine RNA secondary structure: Application to the 3' end of Bombyx mori R2 RNA. Biochemistry. 45, 9819-9832
• 34. Kierzek, E., Mathews, D. H., Ciesielska, A., Turner, D. H., & Kierzek, R. (2006). Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides. Nucleic Acids Research. 34, 3609-3614.
• 33. Leontis, N. B., Altman, R. B., Berman, H. M., Brenner, S. E., Brown, J. W., Engelke, D. R., Harvey, S. C., Holbrook, S. R., Jossinet, F., Lewis, S. E., Major, F., Mathews, D. H., Richardson, J. S., Williamson, J. R., Westhof, E. (2006). The RNA Ontology Consortium: an open invitation to the RNA community. RNA. 12, 533-541.
• 32. Uzilov, A. V., Keegan, J. M., & Mathews, D. H. (2006). Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics. 7:173. [pdf]
• 31. Mathews, D. H., & Case, D. A. (2006). Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair. Journal of Molecular Biology. 357: 1683-1693.
• 30. Mathews, D. H. & Turner, D. H. (2006). Prediction of RNA secondary structure by free energy minimization. Current Opinion in Structural Biology. 16: 270-278.
• 29. Mathews, D. H. (2006). Revolutions in RNA secondary structure prediction. Journal of Molecular Biology. 359: 526-532.
• 28. Mathews, D. H. (2005). Predicting RNA secondary structure by free energy minimization. Theoretical Chemistry Accounts. 116, 160-168.
• 27. Mathews, D. H. (2005). Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics. 21, 2246-2253. Supplementary Material.
• 26. Mathews, D. H., Schroeder, S. J., Turner, D. H., & Zuker, M. (2005). Predicting RNA secondary structure. In The RNA World, Third Edition (Gesteland, R. F., Cech, T. R., & Atkins, J. F., eds.), pp. 631-657. Cold Spring Harbor Laboratory Press.
• 25. Kierzek, E., Ciesielska, A., Pasternak, K., Mathews, D. H., Turner, D. H., & Kierzek, R. (2005). The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heterduplexes. Nucleic Acids Research. 33, 5082-5093.
• 24. Mathews, D. H. (2005). Predicting the secondary structure common to two sequences with Dynalign. In Current Protocols in Bioinformatics (Baxevanis, A. D., Davidson, D. B., Page, R. D. M., Petsko, G. A., Stein, L. D., & Stormo, G. D., eds.), pp. 12.4.1-12.4.11. John Wiley & Sons, Inc.
• 23. Mathews, D. H. & Zuker, M. (2005). RNA secondary structure prediction. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (Subramaniam, S., Kuspa, A., Salzburg, S. L., Aravind, L., Lewin, H., Quackenbush, J., Taylor, W. R., Altman, R. B., & Clote, P., eds.) John Wiley & Sons, Inc.
• 22. Mathews, D. H., & Zuker, M. (2004). Predictive methods using RNA sequences. In Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins (Baxevanis, A. D., & Ouellette, B. F. F., eds.), pp. 143-170. John Wiley & Sons, Inc.
• 21. Mathews, D. H. (2004). Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA. 10, 1178-1190.
• 20. Ruschak, A. M., Mathews, D. H., Bibillo, A., Spinelli, S. L., Childs, J. L., Eickbush, T. H. & Turner, D. H. (2004). Secondary structure models of the 3' untranslated regions of diverse R2 RNAs. RNA. 10, 978-87.
• 19. Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M. & Turner, D. H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.Proceedings of the National Academy of Sciences, USA. 101, 7287-7292.
• 18. Matveeva, O. V., Mathews, D. H., Tsodikov, A. D., Shabalina, S. A., Gesteland, R. F., Atkins, J. F. & Freier, S. M. (2003). Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Research. 31, 4989-4994.
• 17. Mathews, D. H. & Turner, D. H. (2002). Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology. 317, 191-203.
• 16. Mathews, D. H. & Turner, D. H. (2002). Experimentally derived nearest neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry. 41, 869-880.
• 15. Mathews, D. H. & Turner, D. H. (2002). Use of chemical modification to elucidate RNA folding pathways. In Current Protocols in Nucleic Acid Chemistry (Beaucage, S. L., Bergstrum, D. E., Glick, G. D. & Jones, R. A., eds.), pp. 11.9.1-11.9.4. John Wiley & Sons, Inc.
• 14. Diamond, J. M., Turner, D. H. & Mathews, D. H. (2001). Thermodynamics of three-way multibranch loops in RNA. Biochemistry. 40, 6971-6981.
• 13. Mathews, D. H., Diamond, J. M. & Turner, D. H. (2000). The application of thermodynamics to the modeling of RNA secondary structure. In Thermodynamics in Biology (Di Cera, E., ed.), pp. 177-201. Oxford University Press.
• 12. Mathews, D. H., Turner, D. H. & Zuker, M. (2000). RNA secondary structure prediction. In Current Protocols in Nucleic Acid Chemistry (Beaucage, S. L., Bergstrum, D. E., Glick, G. D. & Jones, R. A., eds.), Vol. 11, pp. 2.1-2.10. John Wiley and Sons, New York.
• 11. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. (1999a). Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA Secondary Structure. Journal of Molecular Biology. 288, 911-940.
• 10. Mathews, D. H., Burkard, M. E., Freier, S. M., Wyatt, J. R. & Turner, D. H. (1999). Predicting oligonucleotide affinity to nucleic acid targets. RNA. 5, 1458-1469.
• 9. Xia, T., Mathews, D. H. & Turner, D. H. (1999). Thermodynamics of RNA secondary structure formation. In Prebiotic Chemistry, Molecular Fossils, Nucleosides, and RNA (Söll, D. G., Nishimura, S. & Moore, P. B., eds.), pp. 21-47. Elsevier, New York.
• 8. Zuker, M., Mathews, D. H. & Turner, D. H. (1999). Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA Biochemistry and Biotechnology (Barciszewski, J. & Clark, B. F. C., eds.), pp. 11-43. Kluwer Academic Publishers, Boston.
• 7. Mathews, D. H., Andre, T. C., Kim, J., Turner, D. H. & Zuker, M. (1998). An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. In Molecular Modeling of Nucleic Acids (Leontis, N. B. & SantaLucia, J., Jr., eds.), pp. 246-257. American Chemical Society.
• 6. Mathews, D. H., Banerjee, A. R., Luan, D. D., Eickbush, T. H. & Turner, D. H. (1997). Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA. 3, 1-16.
• 5. Li, Y., Bevilacqua, P. C., Mathews, D. & Turner, D. H. (1995). Thermodynamics and activation parameters for binding of pyrene-labeled substrate by the Tetrahymena ribozyme: Docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry. 34, 14394-14399.
• 4. Herrick, D. M., Wolfs, F. L. H., Bryan, D. C., Freeman, C. G., Kurtz, K. L., Mathews, D. H., Perera, P. A. A. & Zanni, M. T. (1995). Elastic Scattering and Quasielastic Transfer for ³²S + ^96,100Mo at E_lab=180 MeV. Physical Review C. 52, 744-754.
• 3. Freeman, C. G., Herrick, D. M., Bryan, D. C., Kurtz, K. L., Mathews, D. H., Perera, P. A. A., Wolfs, F. L. H. & Zanni, M. T. (1995). New Focal Plane Detector System for the Rochester Recoil Mass Spectrometer. Nuclear Instruments and Methods, A. 357, 450-457.
• 2. Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H. & Zuker, M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.Proceedings of the National Academy of Sciences, USA. 91, 9218-9222.
• 1. Wolfs, F. L. H., White, C. A., Bryan, D. C., Freeman, C. G., Herrick, D. M., Kurtz, K. L., Mathews, D. H., Perera, P. A. A. & Zanni, M. T. (1994). Breakup of 87 MeV ¹¹B. Physical Review C. 49, 2538-2548.

© 2020 Mathews group | Page design derived from a template supplied by Styleshout.