David H. Mathews

Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities

This study shows that longer equilibration times in umbrella sampling can alter free energy landscapes and reduce agreement with experimental data for RNA hairpin folding.

Markov models of SHAPE data improve secondary structure prediction

This paper improves RNA secondary structure prediction by incorporating Markov models to capture context dependencies in SHAPE data, enhancing prediction accuracy.

Nearest Neighbor Parameters for Estimating RNA Folding Stability with In Vivo-like Conditions

The paper develops a new RNA folding model using in vivo-like ionic conditions, improving tRNA structure prediction but showing minimal overall impact on secondary structure predictions.

40S ribosomal subunits move along the 5' UTR through an eIF4A-independent mechanism in higher eukaryotes

This study shows that 40S ribosomal subunits move along 5' UTRs via a helicase-independent mechanism, as eIF4A inhibition does not affect translation efficiency in mRNAs with varying 5' UTR lengths.

Reparameterization of the Amber RNA Force Field Non-Bonded Terms

This paper improves RNA force field parameters by fitting them to quantum mechanics data, enhancing stability of native structures and conformational preferences.

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine

This paper presents nearest neighbor parameters for estimating RNA folding stability with pseudouridine, derived from optical melting experiments, and demonstrates their application in modeling RNA secondary structures.

RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine

This paper develops new RNA folding nearest neighbor parameters for sequences containing 1-methyl-pseudouridine, showing it stabilizes RNA folding and improves tRNA ensemble modeling.

Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing

This study introduces PRIME, a method to measure RNA structural energetics, finding that RNA base pairs and tertiary interactions dynamically open with low-energy fluctuations.

Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

This paper evaluates deep learning methods for RNA secondary structure prediction, highlights generalization challenges, and discusses integration with traditional methods.

NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference

This paper uses NMR and MD simulations to show that the RNA internal loop GAGU is dynamic, with flanking base pairs influencing its conformational preferences.

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion

The paper shows that 40S ribosomal subunits scan mRNA via one-dimensional diffusion rather than helicase-driven translocation in yeast.

AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction

This paper introduces AlignmentFold and AlignmentPartition to improve RNA secondary structure prediction using fixed alignments and new thermodynamic parameters, achieving accuracy comparable to existing tools.

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

The paper investigates the structural determinants of inverted Alu-mediated backsplicing in the HIPK3 gene using SHAPE-JuMP and finds that long-range Alu-mediated base pairs are required for circularization, but not full-length Alu elements.

An oligo walk to identify siRNAs against the circular Tau 12->7 RNA

The paper identifies an siRNA effective against a modified circRNA, showing it can be targeted but with variable efficacy.

memerna: Sparse RNA Folding Including Coaxial Stacking

The paper introduces memerna, a fast RNA folding algorithm that incorporates coaxial stacking and sparsity, achieving the fastest exact RNA folding implementation among popular packages supporting this feature.

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences

DecoyFinder identifies contaminant sequences in homologous RNA sets using machine learning trained on TurboFold features, detecting 45% of non-homologs with 5% false positives.

Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA

This study investigates how 3-methylcytosine modification at position 32 of tRNA-Arg-UCU affects the structure of the anticodon stem loop and its functional implications.

Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy

The paper identifies dsRNA structures in uORFs that regulate translation and shows ASO targeting can modulate mORF translation and reduce cardiac hypertrophy.

LazySampling and LinearSampling: Fast Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2

The paper introduces LazySampling and LinearSampling algorithms for fast RNA secondary structure sampling, achieving linear-time performance and enabling analysis of full-genome RNA structures like SARS-CoV-2.

Deep learning models for RNA secondary structure prediction (probably) do not generalise across families

The paper shows that deep learning models for RNA secondary structure prediction do not generalize across families, using rigorous cross-validation methods.

Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing

The paper predicts variant effects on alternative splicing using structural probing data and a computational framework, achieving 90% accuracy for splice-altering variants.

Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine

The paper introduces updated RNA secondary structure prediction tools and parameters for N6-methyladenosine, enabling analysis of modified RNA structures.

LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2

LinearTurboFold predicts conserved RNA structures for SARS-CoV-2 homologs efficiently, capturing long-range interactions and enabling global structural analysis of full-length genomes.

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

This study shows that CRISPR/Cas9-induced INDELs can lead to mRNA misregulation by creating foreign mRNAs or proteins in about half of edited cell lines.

LinearFold: Linear-Time Prediction of RNA Secondary Structures

LinearFold predicts RNA secondary structures in linear time using dynamic programming with beam search pruning, achieving higher accuracy on long sequences and long-range base pairs.