D
David H. Mathews
Researcher at University of Rochester
Publications - 188
Citations - 18341
David H. Mathews is an academic researcher from University of Rochester. The author has contributed to research in topics: RNA & Nucleic acid secondary structure. The author has an hindex of 47, co-authored 163 publications receiving 16394 citations. Previous affiliations of David H. Mathews include Pennsylvania State University & University of Texas at Dallas.
Papers
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Journal ArticleDOI
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
TL;DR: An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization and experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.
Journal ArticleDOI
RNAstructure: software for RNA secondary structure prediction and analysis
TL;DR: New extensions to RNAstructure are described, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces that serve to make RNA secondary structure prediction user- friendly.
Journal ArticleDOI
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
David H. Mathews,Matthew D. Disney,Jessica L. Childs,Susan J. Schroeder,Michael Zuker,Douglas H. Turner +5 more
TL;DR: A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch.
Book ChapterDOI
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
TL;DR: The details of the free energy rules and of the latest version 3.0 software are described and future plans are also discussed.
Journal ArticleDOI
Accurate SHAPE-directed RNA structure determination
TL;DR: It is demonstrated that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy, comparable to the best accuracies achievable by comparative sequence analysis.