List of works - David H Mathews

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

scientific article

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

scientific article published on 11 January 2022

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.

scientific article published on 6 June 2017

Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove

scientific article published on 10 November 2020

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

scientific article published on 6 November 2017

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

scientific article published on 06 September 2019

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations

scientific article published on 27 November 2018

Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection

scientific article published on 01 February 2019

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study

scientific article published on 01 January 2019

How to benchmark RNA secondary structure prediction accuracy

scientific article published on 02 April 2019

Identification of new high affinity targets for Roquin based on structural conservation

scientific article published on 01 December 2018

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

scientific article published in June 2018

LinearSampling: Linear-Time Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2

scientific article published on 29 December 2020

Making ends meet: New functions of mRNA secondary structure

scientific article published on 29 June 2020

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

scientific article published on 21 November 2017

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

scientific article published on 3 January 2017

Secondary structure prediction for RNA sequences including N<sup>6</sup>-methyladenosine

scientific article published on 11 March 2022

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

article

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

scientific article published on 23 March 2018

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs