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David H. Mathews, M.D., Ph.D.


Showing all 117 journal articles & 0 books available

Journal Articles

Kayedkhordeh M, Yamagami R, Bevilacqua PC, Mathews DH. "Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots." Methods in molecular biology.. 2021 2167:113-143.

Zhang H, Zhang L, Li S, Mathews DH, Huang L. "LinearSampling: Linear-Time Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2." . 2020 Dec 29; Epub 2020 Dec 29.

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.. 2020 Nov 10; Epub 2020 Nov 10.

Zhang H, Zhang L, Mathews DH, Huang L. "LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities." Bioinformatics.. 2020 Jul 1; 36(Supplement_1):i258-i267.

Ermolenko DN, Mathews DH. "Making ends meet: New functions of mRNA secondary structure." Wiley interdisciplinary reviews. RNA.. 2020 Jun 29; :e1611. Epub 2020 Jun 29.

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.. 2020 Jun 29; Epub 2020 Jun 29.

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. "CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation." Nature communications.. 2019 Sep 6; 10(1):4056. Epub 2019 Sep 06.

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.. 2019 Jul 15; 35(14):i295-i304.

Mathews DH. "How to benchmark RNA secondary structure prediction accuracy." Methods : a companion to Methods in enzymology.. 2019 Jun 1; 162-163:60-67. Epub 2019 Apr 02.

Zuber J, Mathews DH. "Estimating uncertainty in predicted folding free energy changes of RNA secondary structures." RNA.. 2019 Jun 0; 25(6):747-754. Epub 2019 Apr 05.

Ward M, Sun H, Datta A, Wise M, Mathews DH. "Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change." Bioinformatics.. 2019 Mar 28; Epub 2019 Mar 28.

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.. 2018 Dec 21; Epub 2018 Dec 21.

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.. 2018 Dec 14; 46(22):12109-12125.

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.. 2018 Nov 27; Epub 2018 Nov 27.

Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC. "Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study." Nucleic acids research.. 2018 Nov 20; Epub 2018 Nov 20.

Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH. "Accelerated RNA secondary structure design using preselected sequences for helices and loops." RNA.. 2018 Nov 0; 24(11):1555-1567. Epub 2018 Aug 10.

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.. 2018 Nov 0; 24(11):1568-1582. Epub 2018 Aug 13.

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.. 2018 Oct 18; 9(1):4328. Epub 2018 Oct 18.

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.. 2018 Jul 27; 46(13):6401-6415.

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.. 2018 Jun 1; 46(10):4883-4892.

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.. 2018 May 0; 24(5):656-672. Epub 2018 Feb 06.

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.. 2018 Apr 10; 57(14):2121-2131. Epub 2018 Mar 23.

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.. 2018 Mar 0; 24(3):410-422. Epub 2017 Dec 19.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH. "Modeling RNA secondary structure folding ensembles using SHAPE mapping data." Nucleic acids research.. 2018 Jan 9; 46(1):314-323.

Tan Z, Fu Y, Sharma G, Mathews DH. "TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs." Nucleic acids research.. 2017 Nov 16; 45(20):11570-11581.

Sloma MF, Mathews DH. "Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs." PLoS computational biology.. 2017 Nov 0; 13(11):e1005827. Epub 2017 Nov 06.

Smith LG, Zhao J, Mathews DH, Turner DH. "Physics-based all-atom modeling of RNA energetics and structure." Wiley interdisciplinary reviews. RNA.. 2017 Sep 0; 8(5)

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.. 2017 Aug 21; 45(14):8541-8550.

Tan Z, Sharma G, Mathews DH. "Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data." Biophysical journal.. 2017 Jul 25; 113(2):330-338. Epub 2017 Jul 20.

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.. 2017 Jun 2; 45(10):6168-6176.

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.. 2017 Apr 26; 9(5)Epub 2017 Apr 26.

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.. 2017 Feb 14; 13(2):900-915. Epub 2017 Jan 24.

Mathews DH, Turner DH, Watson RM. "RNA Secondary Structure Prediction." Current protocols in nucleic acid chemistry. 2016 Dec 1; 67:11.2.1-11.2.19. Epub 2016 Dec 01.

Sloma MF, Mathews DH. "Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures." RNA.. 2016 Dec 0; 22(12):1808-1818. Epub 2016 Oct 19.

DiChiacchio L, Sloma MF, Mathews DH. "AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure." Bioinformatics.. 2016 Apr 1; 32(7):1033-9. Epub 2015 Nov 20.

Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC. "Bridging the gap between in vitro and in vivo RNA folding." Quarterly reviews of biophysics.. 2016 Jan 0; 49:e10. Epub 2016 Jun 24.

Xu ZZ, Mathews DH. "Secondary Structure Prediction of Single Sequences Using RNAstructure." Methods in molecular biology.. 2016 1490:15-34.

Xu ZZ, Mathews DH. "Prediction of Secondary Structures Conserved in Multiple RNA Sequences." Methods in molecular biology.. 2016 1490:35-50.

DiChiacchio L, Mathews DH. "Predicting RNA-RNA Interactions Using RNAstructure." Methods in molecular biology.. 2016 1490:51-62.

Xu ZZ, Mathews DH. "Experiment-Assisted Secondary Structure Prediction with RNAstructure." Methods in molecular biology.. 2016 1490:163-76.

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. "Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints." Biochemistry.. 2015 Nov 17; 54(45):6769-82. Epub 2015 Nov 03.

Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. "Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics." RNA.. 2015 Nov 0; 21(11):1898-907. Epub 2015 Sep 14.

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.. 2015 Sep 3; 43(15):7247-59. Epub 2015 Jul 13.

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.. 2015 Jul 7; 112(27):E3485-94. Epub 2015 Jun 23.

Sloma MF, Mathews DH. "Improving RNA secondary structure prediction with structure mapping data." Methods in enzymology.. 2015 553:91-114. Epub 2015 Feb 03.

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.. 2015 10(6):e0130200. Epub 2015 Jun 15.

Fu Y, Sharma G, Mathews DH. "Dynalign II: common secondary structure prediction for RNA homologs with domain insertions." Nucleic acids research.. 2014 Dec 16; 42(22):13939-48.

Zhang X, Walker RC, Phizicky EM, Mathews DH. "Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics." Journal of chemical theory and computation.. 2014 Aug 12; 10(8):3473-3483. Epub 2014 May 28.

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.. 2014 Aug 1; 28(15):1721-32.

Mathews DH. "Using the RNAstructure Software Package to Predict Conserved RNA Structures." Current protocols in bioinformatics. 2014 Jun 17; 46:12.4.1-22. Epub 2014 Jun 17.

Mathews DH. "RNA Secondary Structure Analysis Using RNAstructure." Current protocols in bioinformatics. 2014 Jun 17; 46:12.6.1-25. Epub 2014 Jun 17.

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

Stern HA, Mathews DH. "Accelerating calculations of RNA secondary structure partition functions using GPUs." Algorithms for molecular biology : AMB. 2013 Nov 1; 8(1):29. Epub 2013 Nov 01.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH. "RNAstructure: Web servers for RNA secondary structure prediction and analysis." Nucleic acids research.. 2013 Jul 0; 41(Web Server issue):W471-4. Epub 2013 Apr 24.

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.. 2013 Apr 1; 41(6):3819-32. Epub 2013 Feb 07.

Schmidt K, Xu Z, Mathews DH, Butler JS. "Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance." RNA.. 2012 Oct 0; 18(10):1934-45. Epub 2012 Aug 24.

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.. 2012 Jul 10; 8(7):2497-2505. Epub 2012 Jun 05.

Seetin MG, Mathews DH. "TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots." Bioinformatics.. 2012 Mar 15; 28(6):792-8. Epub 2012 Jan 27.

Xu Z, Almudevar A, Mathews DH. "Statistical evaluation of improvement in RNA secondary structure prediction." Nucleic acids research.. 2012 Feb 0; 40(4):e26. Epub 2011 Dec 01.

Seetin MG, Mathews DH. "RNA structure prediction: an overview of methods." Methods in molecular biology.. 2012 905:99-122.

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.. 2011 Nov 8; 7(11):3779-3792.

Seetin MG, Mathews DH. "Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints." Journal of computational chemistry.. 2011 Jul 30; 32(10):2232-44. Epub 2011 Apr 21.

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.. 2011 Jul 1; 286(26):22965-70. Epub 2011 May 09.

Harmanci AO, Sharma G, Mathews DH. "TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences." BMC bioinformatics.. 2011 Apr 20; 12:108. Epub 2011 Apr 20.

Xu Z, Mathews DH. "Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences." Bioinformatics.. 2011 Mar 1; 27(5):626-32. Epub 2010 Dec 30.

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.. 2011 Feb 8; 50(5):640-53. Epub 2011 Jan 14.

Mathews DH, Moss WN, Turner DH. "Folding and finding RNA secondary structure." Cold Spring Harbor perspectives in biology.. 2010 Dec 0; 2(12):a003665. Epub 2010 Aug 04.

Bellaousov S, Mathews DH. "ProbKnot: fast prediction of RNA secondary structure including pseudoknots." RNA.. 2010 Oct 0; 16(10):1870-80. Epub 2010 Aug 10.

Reuter JS, Mathews DH. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC bioinformatics.. 2010 Mar 15; 11:129. Epub 2010 Mar 15.

Réblová K, St?elcová 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.. 2010 Mar 9; 6(3):910-29.

Liu B, Mathews DH, Turner DH. "RNA pseudoknots: folding and finding." F1000 biology reports. 2010 Jan 27; 2:8. Epub 2010 Jan 27.

Turner DH, Mathews DH. "NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure." Nucleic acids research.. 2010 Jan 0; 38(Database issue):D280-2. Epub 2009 Oct 30.

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.. 2010 Jan 0; 17(1):83-9. Epub 2009 Dec 06.

Mathews DH. "Using OligoWalk to identify efficient siRNA sequences." Methods in molecular biology.. 2010 629:109-21.

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.. 2009 Dec 11; 394(4):694-707. Epub 2009 Oct 21.

Lu ZJ, Gloor JW, Mathews DH. "Improved RNA secondary structure prediction by maximizing expected pair accuracy." RNA.. 2009 Oct 0; 15(10):1805-13. Epub 2009 Aug 24.

Harmanci AO, Sharma G, Mathews DH. "Stochastic sampling of the RNA structural alignment space." Nucleic acids research.. 2009 Jul 0; 37(12):4063-75. Epub 2009 May 08.

Deigan, K. E.; Li, T. W.; Mathews, D. H.; Weeks, K. M.;. "Accurate SHAPE-directed RNA structure determination". Proc Natl Acad Sci U S A. 2009; 106(31): 97-102.

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.. 2008 Aug 6; 130(31):10233-9. Epub 2008 Jul 10.

Lu ZJ, Mathews DH. "OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics." Nucleic acids research.. 2008 Jul 1; 36(Web Server issue):W104-8. Epub 2008 May 19.

Lu ZJ, Mathews DH. "Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design." Nucleic acids research.. 2008 Jun 0; 36(11):3738-45. Epub 2008 May 15.

Harmanci AO, Sharma G, Mathews DH. "PARTS: probabilistic alignment for RNA joinT secondary structure prediction." Nucleic acids research.. 2008 Apr 0; 36(7):2406-17. Epub 2008 Feb 26.

Lu ZJ, Mathews DH. "Efficient siRNA selection using hybridization thermodynamics." Nucleic acids research.. 2008 Feb 0; 36(2):640-7. Epub 2007 Dec 10.

Wilkinson, K. A.; Gorelick, R. J.; Vasa, S. M.; Guex, N.; Rein, A.; Mathews, D. H.; Giddings, M. C.; Weeks, K. M.;. "High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states". PLoS Biol. 2008; 6(34): e96.

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.. 2007 Nov 6; 46(44):12665-78. Epub 2007 Oct 11.

Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. "Efficient parameter estimation for RNA secondary structure prediction." Bioinformatics.. 2007 Jul 1; 23(13):i19-28.

Tyagi R, Mathews DH. "Predicting helical coaxial stacking in RNA multibranch loops." RNA.. 2007 Jul 0; 13(7):939-51. Epub 2007 May 16.

Harmanci AO, Sharma G, Mathews DH. "Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign." BMC bioinformatics.. 2007 Apr 19; 8:130. Epub 2007 Apr 19.

Mathews DH, Turner DH, Zuker M. "RNA secondary structure prediction." Current protocols in nucleic acid chemistry. 2007 Mar 0; Chapter 11:Unit 11.2.

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.. 2006 Aug 15; 45(32):9819-32.

Mathews DH. "Revolutions in RNA secondary structure prediction." Journal of molecular biology.. 2006 Jun 9; 359(3):526-32. Epub 2006 Feb 06.

Mathews DH, Turner DH. "Prediction of RNA secondary structure by free energy minimization." Current opinion in structural biology.. 2006 Jun 0; 16(3):270-8. Epub 2006 May 19.

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.. 2006 Apr 14; 357(5):1683-93. Epub 2006 Feb 03.

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.. 2006 Apr 0; 12(4):533-41. Epub 2006 Feb 16.

Uzilov AV, Keegan JM, Mathews DH. "Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change." BMC bioinformatics.. 2006 Mar 27; 7:173. Epub 2006 Mar 27.

Mathews DH. "RNA secondary structure analysis using RNAstructure." Current protocols in bioinformatics. 2006 Mar 0; Chapter 12:Unit 12.6.

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.. 2006 34(13):3609-14. Epub 2006 Jul 26.

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.. 2006 34(17):4912-24. Epub 2006 Sep 18.

Mathews DH. "Predicting a set of minimal free energy RNA secondary structures common to two sequences." Bioinformatics.. 2005 May 15; 21(10):2246-53. Epub 2005 Feb 24.

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.. 2005 33(16):5082-93. Epub 2005 Sep 09.

Mathews D. "Predicting the secondary structure common to two RNA sequences with Dynalign." Current protocols in bioinformatics. 2004 Dec 0; Chapter 12:Unit 12.4.

Mathews DH. "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization." RNA.. 2004 Aug 0; 10(8):1178-90.

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.. 2004 Jun 0; 10(6):978-87.

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.. 2004 May 11; 101(19):7287-92. Epub 2004 May 03.

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.. 2003 Sep 1; 31(17):4989-94.

Mathews DH, Turner DH. "Use of chemical modification to elucidate RNA folding pathways." Current protocols in nucleic acid chemistry. 2002 Aug 0; Chapter 11:Unit 11.9.

Mathews DH, Turner DH. "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences." Journal of molecular biology.. 2002 Mar 22; 317(2):191-203.

Mathews DH, Turner DH. "Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops." Biochemistry.. 2002 Jan 22; 41(3):869-80.

Diamond JM, Turner DH, Mathews DH. "Thermodynamics of three-way multibranch loops in RNA." Biochemistry.. 2001 Jun 12; 40(23):6971-81.

Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. "Predicting oligonucleotide affinity to nucleic acid targets." RNA.. 1999 Nov 0; 5(11):1458-69.

Mathews DH, Sabina J, Zuker M, Turner DH. "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure." Journal of molecular biology.. 1999 May 21; 288(5):911-40.

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.. 1997 Jan 0; 3(1):1-16.

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.. 1995 Nov 7; 34(44):14394-9.

Herrick DM, Wolfs FL, Bryan DC, Freeman CG, Kurz KL, Mathews DH, Perera PA, Zanni MT. "Elastic scattering and quasielastic transfer for 32S+96,100Mo at Elab=180 MeV." Physical review. C, Nuclear physics.. 1995 Aug 0; 52(2):744-754.

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. ;. "New Focal Plane Detector System for the Rochester Recoil Mass Spectrometer". Nuclear Instruments and Methods. 1995; 357(3): 450-457.

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.. 1994 Sep 27; 91(20):9218-22.

Wolfs FL, White CA, Bryan DC, Freeman CG, Herrick DM, Kurz KL, Mathews DH, Perera PA, Zanni MT. "Breakup of 87 MeV 11B." Physical review. C, Nuclear physics.. 1994 May 0; 49(5):2538-2548.