Publications by authors named "David Mathews"

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Solid Organ Malignancy After Pancreas Transplantation: A Four Decade Single-Center Experience.
Michael G Megaly, Todd DeFor, Xianghua Luo, Michael Dryden, Joseph Sushil Rao, David Mathews

Clin Transplant· December 2025

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Decrease in Psoas Muscle Mass and Density Following Liver Transplantation Is Greatest in Patients With the Highest Muscle Quantity and Density Pre-Transplant.
Michael G Megaly, William C Miller, Jessica Thul, Peter Gullickson, Abraham J Matar, David Mathews

Clin Transplant· December 2025

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NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.
Olayinka Akinyemi, Scott D Kennedy, James P McSally, David H Mathews

Biophys J· November 2025

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Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.
Marcell Szikszai, Ting-Yuan Wang, Ryan Krueger, David H Mathews, Max Ward

bioRxiv· November 2025

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Feasibility of Using Dynamic Appraisal of Situational Aggression to Reduce Agitation in an Inpatient Psychiatric Unit.
Diane E Mathew, David P Mathews, Dongliang Wang, Derek W Empey, Elena C Nichita

Cureus· November 2025

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40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.
Hironao Wakabayashi, Mingyi Zhu, Elizabeth J Grayhack, David H Mathews, Dmitri N Ermolenko

RNA· September 2025

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A Ψ-Ψ codon-anticodon pairing in nonsense suppression and translational recoding.
Yi Pan, Elzbieta Kierzek, Ryszard Kierzek, David H Mathews, Yi-Tao Yu

Nat Chem Biol· September 2025

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Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.
Kyle D Berger, Anees M K Puthenpeedikakkal, David H Mathews, Dragony Fu

J Mol Biol· August 2025

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Computational Resources for Molecular Biology 2025.
David H Mathews, Rita Casadio, Michael J E Sternberg

J Mol Biol· August 2025

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EnsembleDesign: messenger RNA design minimizing ensemble free energy via probabilistic lattice parsing.
Ning Dai, Tianshuo Zhou, Wei Yu Tang, David H Mathews, Liang Huang

Bioinformatics· July 2025

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AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.
Abhinav Mittal, David H Mathews

bioRxiv· July 2025

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Differentiable Folding for Nearest Neighbor Model Optimization.
Ryan K Krueger, Sharon Aviran, David H Mathews, Jeffrey Zuber, Max Ward

ArXiv· May 2025

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Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.
Justin M Waldern, Colin Taylor, Catherine A Giannetti, Patrick S Irving, Scott R Allen, David H Mathews

Nucleic Acids Res· May 2025

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Bariatric surgery prior to pancreas transplantation: a retrospective matched case-control study.
Abraham J Matar, Matthew Wright, Michael Megaly, Michael Dryden, Karthik Ramanathan, David V Mathews

Surg Obes Relat Dis· April 2025

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mutants are temperature sensitive due to decay of tRNA by the 5'-3' exonuclease Dhp1, primarily targeting the unspliced pre-tRNA.
Franziska Stegemann, Erin Marcus, Savanah Neupert, Sarah Ostrowski, David H Mathews

RNA· March 2025

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memerna: Sparse RNA folding including coaxial stacking.
Eliot Courtney, Amitava Datta, David H Mathews, Max Ward

J Mol Biol· February 2025

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40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.
Hironao Wakabayashi, Mingyi Zhu, Elizabeth J Grayhack, David H Mathews, Dmitri N Ermolenko

bioRxiv· January 2025

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An oligo walk to identify siRNAs against the circular Tau 12->7 RNA.
Justin R Welden, Giorgi Margvelani, Megan Miaro, David Mathews, David W Rodgers

bioRxiv· January 2025

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Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.
Lasse Oberstrass, Jan-Niklas Tants, Chiara Lichtenthaeler, Sara E Ali, Louisa Koch, David H Mathews

Angew Chem Int Ed Engl· December 2024

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Sampling-based Continuous Optimization with Coupled Variables for RNA Design.
Wei Yu Tang, Ning Dai, Tianshuo Zhou, David H Mathews, Liang Huang

ArXiv· December 2024

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Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.
Yoshita Srivastava, Olayinka Akinyemi, Tiana C Rohe, Elizabeth M Pritchett, Cameron D Baker, David H Mathews

Nucleic Acids Res· November 2024

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Using the RNAstructure Software Package to Predict Conserved RNA Structures.
Abhinav Mittal, Sara E Ali, David H Mathews

Curr Protoc· November 2024

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Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.
Carly R Reed, Scott D Kennedy, Rachel H Horowitz, Anees Mohammed Keedakkatt Puthenpeedikakkal, Harry A Stern, David H Mathews

J Phys Chem B· November 2024

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Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA.
Kyle D Berger, Anees M K Puthenpeedikakkal, David H Mathews, Dragony Fu

bioRxiv· November 2024

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DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.
Mingyi Zhu, Jeffrey Zuber, Zhen Tan, Gaurav Sharma, David H Mathews

bioRxiv· October 2024

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