David H. Mathews - Publications, H-index & Citations

David H. Mathews

university of rochester

55H指数

285论文数

2.2W被引数

收录论文 93

发表时间

SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling 采样设计：通过连续优化耦合变量和蒙特卡洛采样进行RNA设计

Nature Communications

IF15.7

2026-02-20

OAAI

Wei Yu Tang; Ning Dai; Tianshuo Zhou; David H. Mathews; Liang Huang

NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference NMR和分子动力学表明，RNA内含环GAGU是动态的，且相邻碱基对决定了构象偏好。

Biophysical Journal

IF3.1

2025-11-19

PREAI

Olayinka Akinyemi; Scott D. Kennedy; James P. McSally; David H. Mathews

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion 40S核糖体亚基通过一维扩散扫描mRNA寻找起始密码子。

RNA

IF5

2025-10-01

OAAI

Wakabayashi, Hironao; Zhu, Mingyi; Grayhack, Elizabeth J.; Mathews, David H.; Ermolenko, Dmitri N.

A Ψ–Ψ codon–anticodon pairing in nonsense suppression and translational recoding 无义抑制和翻译重编码中的Ψ–Ψ 密码子–反密码子配对

Nature Chemical Biology

IF13.7

2025-09-12

PREAI

Yi Pan; Elzbieta Kierzek; Ryszard Kierzek; David H. Mathews; Yi-Tao Yu

EnsembleDesign: messenger RNA design minimizing ensemble free energy via probabilistic lattice parsing EnsembleDesign：通过概率性格子解析最小化集合自由能的信使RNA设计

BIOINFORMATICS

IF5.4

2025-07-01

OAAI

Dai, Ning; Zhou, Tianshuo; Tang, Wei Yu; Mathews, David H.; Huang, Liang

Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops RNA茎环的Roquin结合偏好的综合分析

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

IF16.9

2024-11-06

OAAI

Oberstrass, Lasse; Tants, Jan-Niklas; Lichtenthaeler, Chiara; Ali, Sara E.; Koch, Louisa; Mathews, David H.; Schlundt, Andreas; Weigand, Julia E.

Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations

NUCLEIC ACIDS RESEARCH

IF13.1

2024-10-16

OAAI

Srivastava, Yoshita; Akinyemi, Olayinka; Rohe, Tiana C.; Pritchett, Elizabeth M.; Baker, Cameron D.; Sharma, Akshara; Jenkins, Jermaine L.; Mathews, David H.; Wedekind, Joseph E.

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

NATURE COMMUNICATIONS

IF15.7

2023-10-03

OAAI

Hedaya, Omar M.; Subbaiah, Kadiam C. Venkata; Jiang, Feng; Xie, Li Huitong; Wu, Jiangbin; Khor, Eng-Soon; Zhu, Mingyi; Mathews, David H.; Proschel, Chris; Yao, Peng

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

ACS SYNTHETIC BIOLOGY

IF3.9

2023-09-06

OAAI

Pham, Tuan M.; Miffin, Terrel; Sun, Hongying; Sharp, Kenneth K.; Wang, Xiaoyu; Zhu, Mingyi; Hoshika, Shuichi; Peterson, Raymond J.; Benner, Steven A.; Kahn, Jason D.; Mathews, David H.

LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules

NUCLEIC ACIDS RESEARCH

IF13.1

2023-08-31

OAAI

Zhang, He; Li, Sizhen; Dai, Ning; Zhang, Liang; Mathews, David H.; Huang, Liang

Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants

MICROORGANISMS

IF4.2

2023-07-25

OAAI

Zuber, Jeffrey; Sah, Sudisht K.; Mathews, David H.; Rustchenko, Elena; Blasi, Elisabetta

Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection

MBIO

IF4.7

2023-06-27

OAAI

Zhou, Terry; Gilliam, Nora J.; Li, Sizhen; Spandau, Simone; Osborn, Raven M.; Connor, Sarah; Anderson, Christopher S.; Mariani, Thomas J.; Thakar, Juilee; Dewhurst, Stephen; Mathews, David H.; Huang, Liang; Sun, Yan

In vivo secondary structural analysis of Influenza A virus genomic RNA

CELLULAR AND MOLECULAR LIFE SCIENCES

IF6.2

2023-05-02

OAAI

Mirska, Barbara; Wozniak, Tomasz; Lorent, Dagny; Ruszkowska, Agnieszka; Peterson, Jake M.; Moss, Walter N.; Mathews, David H.; Kierzek, Ryszard; Kierzek, Elzbieta

A riboswitch separated from its ribosome-binding site still regulates translation

NUCLEIC ACIDS RESEARCH

IF13.1

2023-02-10

OAAI

Schroeder, Griffin M.; Akinyemi, Olayinka; Malik, Jeffrey; Focht, Caroline M.; Pritchett, Elizabeth M.; Baker, Cameron D.; McSally, James P.; Jenkins, Jermaine L.; Mathews, David H.; Wedekind, Joseph E.

LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2

NUCLEIC ACIDS RESEARCH

IF13.1

2022-11-18

OAAI

Zhang, He; Li, Sizhen; Zhang, Liang; Mathews, David H.; Huang, Liang

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

ELIFE

IF0

2022-06-13

OAAI

Kumar, Jayashree; Lackey, Lela; Waldern, Justin M.; Dey, Abhishek; Mustoe, Anthony M.; Weeks, Kevin M.; Mathews, David H.; Laederach, Alain; Staley, Jonathan P.

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

NUCLEIC ACIDS RESEARCH

IF13.1

2022-05-07

OAAI

Zuber, Jeffrey; Schroeder, Susan J.; Sun, Hongying; Turner, Douglas H.; Mathews, David H.

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal

NUCLEIC ACIDS RESEARCH

IF13.1

2022-05-07

OAAI

Glasser, Eliezra; Maji, Debanjana; Biancon, Giulia; Puthenpeedikakkal, Anees Mohammed Keedakkatt; Cavender, Chapin E.; Tebaldi, Toma; Jenkins, Jermaine L.; Mathews, David H.; Halene, Stephanie; Kielkopf, Clara L.

Secondary structure prediction for RNA sequences including N6-methyladenosine

NATURE COMMUNICATIONS

IF15.7

2022-03-11

OAAI

Kierzek, Elzbieta; Zhang, Xiaoju; Watson, Richard M.; Kennedy, Scott D.; Szabat, Marta; Kierzek, Ryszard; Mathews, David H.

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

NATURE COMMUNICATIONS

IF15.7

2022-02-21

OAAI

Bao, Chen; Zhu, Mingyi; Nykonchuk, Inna; Wakabayashi, Hironao; Mathews, David H.; Ermolenko, Dmitri N.

研究方向