David H Mathews

ORCID

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 28

Top Venues

Nucleic acids research

Nature communications

Cellular and molecular life sciences : CMLS

Journal of chemical theory and computation

University of Rochester Medical Center

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Rochester Medical Center

United States

Professor :: Biochemistry & Biophysics

Publications

Griffin M Schroeder, Olayinka Akinyemi, Jeffrey Malik, Caroline M Focht, Elizabeth M Pritchett, Cameron D Baker, James P McSally, Jermaine L Jenkins, David H Mathews, Joseph E Wedekind
A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic acids research 51 (5) (2023)
Omar M Hedaya, Kadiam C Venkata Subbaiah, Feng Jiang, Li Huitong Xie, Jiangbin Wu, Eng-Soon Khor, Mingyi Zhu, David H Mathews, Chris Proschel, Peng Yao
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nature communications 14 (1) (2023)
Griffin M Schroeder, Olayinka Akinyemi, Jeffrey Malik, Caroline M Focht, Elizabeth M Pritchett, Cameron D Baker, James P McSally, Jermaine L Jenkins, David H Mathews, Joseph E Wedekind
A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic acids research 51 (5) (2023)
Barbara Mirska, Tomasz Wozniak, Dagny Lorent, Agnieszka Ruszkowska, Jake M Peterson, Walter N Moss, David H Mathews, Ryszard Kierzek, Elzbieta Kierzek
In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and molecular life sciences : CMLS 80 (5) (2023)
Jeffrey Zuber, Sudisht K Sah, David H Mathews, Elena Rustchenko
Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants. Microorganisms 11 (8) (2023)
Tuan M Pham, Terrel Miffin, Hongying Sun, Kenneth K Sharp, Xiaoyu Wang, Mingyi Zhu, Shuichi Hoshika, Raymond J Peterson, Steven A Benner, Jason D Kahn, David H Mathews
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. ACS synthetic biology (2023)
Griffin M Schroeder, Olayinka Akinyemi, Jeffrey Malik, Caroline M Focht, Elizabeth M Pritchett, Cameron D Baker, James P McSally, Jermaine L Jenkins, David H Mathews, Joseph E Wedekind
A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic acids research 51 (5) (2023)
Barbara Mirska, Tomasz Wozniak, Dagny Lorent, Agnieszka Ruszkowska, Jake M Peterson, Walter N Moss, David H Mathews, Ryszard Kierzek, Elzbieta Kierzek
In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and molecular life sciences : CMLS 80 (5) (2023)
He Zhang, Sizhen Li, Ning Dai, Liang Zhang, David H Mathews, Liang Huang
LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules. Nucleic acids research (2023)
Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H Mathews, Liang Huang
RNA design via structure-aware multifrontier ensemble optimization. Bioinformatics (Oxford, England) 39 (39 Suppl 1) (2023)
Barbara Mirska, Tomasz Wozniak, Dagny Lorent, Agnieszka Ruszkowska, Jake M Peterson, Walter N Moss, David H Mathews, Ryszard Kierzek, Elzbieta Kierzek
In vivo secondary structural analysis of Influenza A virus genomic RNA. Cellular and molecular life sciences : CMLS 80 (5) (2023)
Griffin M Schroeder, Olayinka Akinyemi, Jeffrey Malik, Caroline M Focht, Elizabeth M Pritchett, Cameron D Baker, James P McSally, Jermaine L Jenkins, David H Mathews, Joseph E Wedekind
A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic acids research (2023)
He Zhang, Liang Zhang, Ang Lin, Congcong Xu, Ziyu Li, Kaibo Liu, Boxiang Liu, Xiaopin Ma, Fanfan Zhao, Huiling Jiang, Chunxiu Chen, Haifa Shen, Hangwen Li, David H Mathews, Yujian Zhang, Liang Huang
Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity. Nature (2023)
Griffin M Schroeder, Chapin E Cavender, Maya E Blau, Jermaine L Jenkins, David H Mathews, Joseph E Wedekind
A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nature communications 13 (1) (2022)
Chen Bao, Mingyi Zhu, Inna Nykonchuk, Hironao Wakabayashi, David H Mathews, Dmitri N Ermolenko
Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation. Nature communications 13 (1) (2022)
Eliezra Glasser, Debanjana Maji, Giulia Biancon, Anees Mohammed Keedakkatt Puthenpeedikakkal, Chapin E Cavender, Toma Tebaldi, Jermaine L Jenkins, David H Mathews, Stephanie Halene, Clara L Kielkopf
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic acids research 50 (9) (2022)
Jeffrey Zuber, Susan J Schroeder, Hongying Sun, Douglas H Turner, David H Mathews
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic acids research 50 (9) (2022)
Elzbieta Kierzek, Xiaoju Zhang, Richard M Watson, Scott D Kennedy, Marta Szabat, Ryszard Kierzek, David H Mathews
Secondary structure prediction for RNA sequences including N 6 -methyladenosine. Nature communications 13 (1) (2022)
He Zhang, Sizhen Li, Liang Zhang, David H Mathews, Liang Huang
LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2. Nucleic acids research (2022)
Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H Mathews, Liang Huang
LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2. bioRxiv : the preprint server for biology (2021)
Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H Mathews, Liang Huang
LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 118 (52) (2021)
Sai Shashank Chavali, Chapin E Cavender, David H Mathews, Joseph E Wedekind
Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. Journal of the American Chemical Society 142 (47) (2020)
Dmitri N Ermolenko, David H Mathews
Making ends meet: New functions of mRNA secondary structure. Wiley interdisciplinary reviews. RNA 12 (2) (2020)
Rubina Tuladhar, Yunku Yeu, John Tyler Piazza, Zhen Tan, Jean Rene Clemenceau, Xiaofeng Wu, Quinn Barrett, Jeremiah Herbert, David H Mathews, James Kim, Tae Hyun Hwang, Lawrence Lum
CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nature communications 10 (1) (2019)
Kyle D Berger, Scott D Kennedy, Susan J Schroeder, Brent M Znosko, Hongying Sun, David H Mathews, Douglas H Turner
Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. Biochemistry 57 (14) (2018)
Louis G Smith, Zhen Tan, Aleksandar Spasic, Debapratim Dutta, Leslie A Salas-Estrada, Alan Grossfield, David H Mathews
Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. Journal of chemical theory and computation 14 (12) (2018)
Michael F Sloma, David H Mathews
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS computational biology 13 (11) (2017)
Asaminew H Aytenfisu, Aleksandar Spasic, Alan Grossfield, Harry A Stern, David H Mathews
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. Journal of chemical theory and computation 13 (2) (2017)

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Publication Activity (10 Years)

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David H Mathews