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

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

Contact Information

University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, NY 14642

Fax: (585) 275-6007
Office: (585) 275-1734

Journal Articles

Showing all 78 journal articles available.

2016 Apr 1
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.
2015 Nov 17
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.
2015 Nov
Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. "Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics." RNA. 2015 Nov; 21(11):1898-907. Epub 2015 Sep 14.
2015 Sep 3
"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.
2015 Jul 7
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.
2014 Aug 12
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.
2014 Aug 1
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.
2014 Mar 11
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.
Fu Y, Sharma G, Mathews DH. "Dynalign II: common secondary structure prediction for RNA homologs with domain insertions." Nucleic acids research. 2014 42(22):13939-48.
Mathews DH. "Using the RNAstructure Software Package to Predict Conserved RNA Structures." Current protocols in bioinformatics. 2014 46:12.4.1-22. Epub 2014 Jun 17.
Mathews DH. "RNA Secondary Structure Analysis Using RNAstructure." Current protocols in bioinformatics. 2014 46:12.6.1-25. Epub 2014 Jun 17.
2013 Jul
"RNAstructure: Web servers for RNA secondary structure prediction and analysis." Nucleic acids research. 2013 Jul; 41(Web Server issue):W471-4. Epub 2013 Apr 24.
2013 Apr 1
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.
Stern HA, Mathews DH. "Accelerating calculations of RNA secondary structure partition functions using GPUs." Algorithms for molecular biology : AMB. 2013 8(1):29. Epub 2013 Nov 01.
2012 Oct
Schmidt K, Xu Z, Mathews DH, Butler JS. "Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance." RNA. 2012 Oct; 18(10):1934-45. Epub 2012 Aug 24.
2012 Jul 10
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.
2012 Mar 15
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.
2012 Feb
Xu Z, Almudevar A, Mathews DH. "Statistical evaluation of improvement in RNA secondary structure prediction." Nucleic acids research. 2012 Feb; 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.
2011 Nov 8
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.
2011 Jul 30
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.
2011 Jul 1
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.
2011 Mar 1
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.
2011 Feb 8
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.
Harmanci AO, Sharma G, Mathews DH. "TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences." BMC bioinformatics. 2011 12:108. Epub 2011 Apr 20.
2010 Oct
Bellaousov S, Mathews DH. "ProbKnot: fast prediction of RNA secondary structure including pseudoknots." RNA. 2010 Oct; 16(10):1870-80. Epub 2010 Aug 10.
2010 Mar 9
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.
2010 Jan
Turner DH, Mathews DH. "NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure." Nucleic acids research. 2010 Jan; 38(Database issue):D280-2. Epub 2009 Oct 30.
2010 Jan
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; 17(1):83-9. Epub 2009 Dec 06.
Reuter JS, Mathews DH. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC bioinformatics. 2010 11:129. Epub 2010 Mar 15.
Mathews DH. "Using OligoWalk to identify efficient siRNA sequences." Methods in molecular biology. 2010 629:109-21.
Liu B, Mathews DH, Turner DH. "RNA pseudoknots: folding and finding." F1000 biology reports. 2010 2:8. Epub 2010 Jan 27.
Mathews DH, Moss WN, Turner DH. "Folding and finding RNA secondary structure." Cold Spring Harbor perspectives in biology. 2010 2(12):a003665. Epub 2010 Aug 04.
2009 Oct
Lu ZJ, Gloor JW, Mathews DH. "Improved RNA secondary structure prediction by maximizing expected pair accuracy." RNA. 2009 Oct; 15(10):1805-13. Epub 2009 Aug 24.
2009 Jul
Harmanci AO, Sharma G, Mathews DH. "Stochastic sampling of the RNA structural alignment space." Nucleic acids research. 2009 Jul; 37(12):4063-75. Epub 2009 May 08.
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 394(4):694-707. Epub 2009 Oct 21.
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. Link
2008 Aug 6
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.
2008 Jul 1
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.
2008 Jun
Lu ZJ, Mathews DH. "Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design." Nucleic acids research. 2008 Jun; 36(11):3738-45. Epub 2008 May 15.
2008 Apr
Harmanci AO, Sharma G, Mathews DH. "PARTS: probabilistic alignment for RNA joinT secondary structure prediction." Nucleic acids research. 2008 Apr; 36(7):2406-17. Epub 2008 Feb 26.
2008 Feb
Lu ZJ, Mathews DH. "Efficient siRNA selection using hybridization thermodynamics." Nucleic acids research. 2008 Feb; 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. Link
2007 Nov 6
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.
2007 Jul 1
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.
2007 Jul
Tyagi R, Mathews DH. "Predicting helical coaxial stacking in RNA multibranch loops." RNA. 2007 Jul; 13(7):939-51. Epub 2007 May 16.
2007 Mar
Mathews DH, Turner DH, Zuker M. "RNA secondary structure prediction." Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.]. 2007 Mar; Chapter 11:Unit 11.2.
Harmanci AO, Sharma G, Mathews DH. "Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign." BMC bioinformatics. 2007 8:130. Epub 2007 Apr 19.
2006 Aug 15
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.
2006 Jun 9
Mathews DH. "Revolutions in RNA secondary structure prediction." Journal of molecular biology. 2006 Jun 9; 359(3):526-32. Epub 2006 Feb 06.
2006 Jun
Mathews DH, Turner DH. "Prediction of RNA secondary structure by free energy minimization." Current opinion in structural biology. 2006 Jun; 16(3):270-8. Epub 2006 May 19.
2006 Apr 14
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.
2006 Apr
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; 12(4):533-41. Epub 2006 Feb 16.
2006 Mar
Mathews DH. "RNA secondary structure analysis using RNAstructure." Current protocols in bioinformatics. 2006 Mar; Chapter 12:Unit 12.6.
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 7:173. Epub 2006 Mar 27.
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.
2005 May 15
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.
2004 Aug
Mathews DH. "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization." RNA. 2004 Aug; 10(8):1178-90.
2004 Jun
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; 10(6):978-87.
2004 May 11
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.
Mathews D. "Predicting the secondary structure common to two RNA sequences with Dynalign." Current protocols in bioinformatics. 2004 Chapter 12:Unit 12.4.
2003 Sep 1
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.
2002 Aug
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.]. 2002 Aug; Chapter 11:Unit 11.9.
2002 Mar 22
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.
2002 Jan 22
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.
2001 Jun 12
Diamond JM, Turner DH, Mathews DH. "Thermodynamics of three-way multibranch loops in RNA." Biochemistry. 2001 Jun 12; 40(23):6971-81.
1999 Nov
Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. "Predicting oligonucleotide affinity to nucleic acid targets." RNA. 1999 Nov; 5(11):1458-69.
1999 May 21
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.
1997 Jan
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; 3(1):1-16.
1995 Nov 7
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.
1995 Aug
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; 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. Link
1994 Sep 27
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.
1994 May
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; 49(5):2538-2548.