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David Mathews

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TOP 3
Matthew G Seetin; David H Mathews
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
Zhenjiang Xu; Anthony Almudevar; David H Mathews
Statistical evaluation of improvement in RNA secondary structure prediction.
Matthew G Seetin; David H Mathews
RNA structure prediction: an overview of methods.

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All Publications

2012: Matthew G Seetin; David H Mathews
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
Bioinformatics (Oxford, England) 2012;28(6):792-8.
2012: Zhenjiang Xu; Anthony Almudevar; David H Mathews
Statistical evaluation of improvement in RNA secondary structure prediction.
Nucleic acids research 2012;40(4):e26.
2012: Matthew G Seetin; David H Mathews
RNA structure prediction: an overview of methods.
Methods in molecular biology (Clifton, N.J.) 2012;905():99-122.
2011: Zhenjiang Xu; David H Mathews
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.
Bioinformatics (Oxford, England) 2011;27(5):626-32.
2011: Biao Liu; Joshua M Diamond; David H Mathews; Douglas H Turner
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.
Biochemistry 2011;50(5):640-53.
2011: Arif O Harmanci; Gaurav Sharma; David H Mathews
TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
BMC bioinformatics 2011;12():108.
2010: David H Mathews; Walter N Moss; Douglas H Turner
Folding and finding RNA secondary structure.
Cold Spring Harbor perspectives in biology 2010;2(12):a003665.
2010: David H Mathews
Using OligoWalk to identify efficient siRNA sequences.
Methods in molecular biology (Clifton, N.J.) 2010;629():109-21.
2010: Jessica S Reuter; David H Mathews
RNAstructure: software for RNA secondary structure prediction and analysis.
BMC bioinformatics 2010;11():129.
2010: Dorota Piekna-Przybylska; Laura DiChiacchio; David H Mathews; Robert A Bambara
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;17(1):83-9.
2010: Douglas H Turner; David H Mathews
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.
Nucleic acids research 2010;38(Database issue):D280-2.
2009: Sean T Rigby; Keith P Van Nostrand; April E Rose; Robert J Gorelick; David H Mathews; Robert A Bambara
Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site.
Journal of molecular biology 2009;394(4):694-707.
2009: Arif Ozgun Harmanci; Gaurav Sharma; David H Mathews
Stochastic sampling of the RNA structural alignment space.
Nucleic acids research 2009;37(12):4063-75.
2008: James M Hart; Scott D Kennedy; David H Mathews; Douglas H Turner
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;130(31):10233-9.
2008: Zhi John Lu; David H Mathews
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.
Nucleic acids research 2008;36(Web Server issue):W104-8.
2008: Zhi John Lu; David H Mathews
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.
Nucleic acids research 2008;36(11):3738-45.
2008: Arif Ozgun Harmanci; Gaurav Sharma; David H Mathews
PARTS: probabilistic alignment for RNA joinT secondary structure prediction.
Nucleic acids research 2008;36(7):2406-17.
2008: Zhi John Lu; David H Mathews
Efficient siRNA selection using hybridization thermodynamics.
Nucleic acids research 2008;36(2):640-7.
2007: Neelaabh Shankar; Tianbing Xia; Scott D Kennedy; Thomas R Krugh; David H Mathews; Douglas H Turner
NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.
Biochemistry 2007;46(44):12665-78.
2007: Rahul Tyagi; David H Mathews
Predicting helical coaxial stacking in RNA multibranch loops.
RNA (New York, N.Y.) 2007;13(7):939-51.
2007: Arif Ozgun Harmanci; Gaurav Sharma; David H Mathews
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.
BMC bioinformatics 2007;8():130.
2006: Shenghua Duan; David H Mathews; Douglas H Turner
Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.
Biochemistry 2006;45(32):9819-32.
2006: David H Mathews
Revolutions in RNA secondary structure prediction.
Journal of molecular biology 2006;359(3):526-32.
2006: David H Mathews; Douglas H Turner
Prediction of RNA secondary structure by free energy minimization.
Current opinion in structural biology 2006;16(3):270-8.
2006: David H Mathews; David A Case
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.
Journal of molecular biology 2006;357(5):1683-93.
2006: Zhi John Lu; Douglas H Turner; David H Mathews
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.
Nucleic acids research 2006;34(17):4912-24.
2006: Elzbieta Kierzek; David H Mathews; Anna Pasternak; Douglas H Turner; Ryszard Kierzek
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.
2006: Andrew V Uzilov; Joshua M Keegan; David H Mathews
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
BMC bioinformatics 2006;7():173.
2005: David H Mathews
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
Bioinformatics (Oxford, England) 2005;21(10):2246-53.
2005: Elzbieta Kierzek; Anna Pasternak; Karol Pasternak; David H Mathews; Douglas H Turner; Ryszard Kierzek
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.
2004: David H Mathews
Predicting the secondary structure common to two RNA sequences with Dynalign.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2004;Chapter 12():Unit 12.4.
2004: David H Mathews
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
RNA (New York, N.Y.) 2004;10(8):1178-90.
2004: Amy M Ruschak; David H Mathews; Arkadiusz Bibillo; Sherry L Spinelli; Jessica L Childs; Thomas H Eickbush; Douglas H Turner
Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.
RNA (New York, N.Y.) 2004;10(6):978-87.
2004: David H Mathews; Matthew D Disney; Jessica L Childs; Susan J Schroeder; Michael Zuker; Douglas H Turner
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;101(19):7287-92.
2003: Olga V Matveeva; David H Mathews; Alexander Tsodikov; Svetlana A Shabalina; Raymond F Gesteland; John F Atkins; Susan M Freier
Thermodynamic criteria for high hit rate antisense oligonucleotide design.
Nucleic acids research 2003;31(17):4989-94.
2002: David H Mathews; Douglas H Turner
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
Journal of molecular biology 2002;317(2):191-203.
2002: David H Mathews; Douglas H Turner
Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
Biochemistry 2002;41(3):869-80.
2001: J M Diamond; Douglas H Turner; David H Mathews
Thermodynamics of three-way multibranch loops in RNA.
Biochemistry 2001;40(23):6971-81.
1999: David H Mathews; Mark E Burkard; Susan M Freier; Jacqueline R Wyatt; Douglas H Turner
Predicting oligonucleotide affinity to nucleic acid targets.
RNA (New York, N.Y.) 1999;5(11):1458-69.
1999: David H Mathews; J Sabina; M Zuker; Douglas H Turner
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Journal of molecular biology 1999;288(5):911-40.
1997: David H Mathews; A R Banerjee; D D Luan; Thomas H Eickbush; Douglas H Turner
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.
RNA (New York, N.Y.) 1997;3(1):1-16.
1994: A E Walter; Douglas H Turner; J Kim; M H Lyttle; P Müller; David H Mathews; M Zuker
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;91(20):9218-22.