50. Hart, J., Kennedy, S., Mathews, D., & Turner, D. (2008). NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon. JACS. In Press.

49. Lu, Z. J., & Mathews, D. H. (2008). Fundamental Differences in the Equilibrium Considerations for siRNA and Antisense Oligodeoxynucleotide Design. Nucleic Acids Research. In Press.

48. Lu, Z. J., & Mathews, D. H. (2008). OligoWalk: An Online siRNA Design Tool Utilizing Hybridization Thermodynamics. Nucleic Acids Research. In Press.

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 Intl. Conf. Acoustics Speech and Signal Processing, March 30-April 4, 2008, Las Vegas, NV, accepted.

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 Conf. 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 Intl. Conf. Acoustics Speech and Signal Processing, 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., Lweis, 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. J. Mol. Biol. 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. J. Mol. Biol. 359: 526-532.

28. Mathews, D. H. (2005). Predicting RNA secondary structure by free energy minimization. Theoretical Chemistry Accounts. Published online 12/3/2005.

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. Proc. Natl. Acad. Sci. 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 Res. 31, 4989-4994.

17. Mathews, D. H. & Turner, D. H. (2002). Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 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. J. Mol. Biol. 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. Proc. Natl. Acad. Sci. 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.