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David H. Mathews

university of rochester medical center
H-index:55
Citation Count:2.1万
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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
2026-02-200
OA
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
2025-11-190
PRE
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
2025-10-010
OA
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
2025-09-120
PRE
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
2025-07-010
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
2024-11-060
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
2024-10-161
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
2023-10-032
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
2023-09-061
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
2023-08-311
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
2023-07-253
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
2023-06-2719
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
2023-05-029
OAAI
Mirska, Barbara; Wozniak, Tomasz; Lorent, Dagny; Ruszkowska, Agnieszka; Peterson, Jake M.; Moss, Walter N.; Mathews, David H.; Kierzek, Ryszard; Kierzek, Elzbieta
Algorithm for optimized mRNA design improves stability and immunogenicity

优化的mRNA设计算法提高了稳定性和免疫原性

Nature
IF48.5
2023-05-020
OAAI
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
A riboswitch separated from its ribosome-binding site still regulates translation
NUCLEIC ACIDS RESEARCH
IF13.1
2023-02-1010
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
2022-11-183
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
2022-06-138
OA
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
2022-05-0719
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
2022-05-0714
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
2022-03-1135
OAAI
Kierzek, Elzbieta; Zhang, Xiaoju; Watson, Richard M.; Kennedy, Scott D.; Szabat, Marta; Kierzek, Ryszard; Mathews, David H.

Research Directions

The data has not been retrieved yet.
D
Douglas H. Turner
H-index:75Papers:361Citations:2.6万
J
Joseph E. Wedekind
H-index:38Papers:156Citations:4,053
A
Aleksandar Spasic
H-index:11Papers:38Citations:534
S
Stanislav Bellaousov
H-index:12Papers:33Citations:1,450
C
Chapin E. Cavender
H-index:7Papers:31Citations:261
张笑菊 cover
张笑菊
H-index:37Papers:336Citations:5,139
G
Gaurav Sharma
H-index:53Papers:601Citations:1.7万
J
Jermaine L. Jenkins
H-index:26Papers:94Citations:1,640
Z
Zhen Tan
H-index:9Papers:16Citations:807
L
Louis G. Smith
H-index:7Papers:32Citations:186