David H. Mathews

According to our database, David H. Mathews authored at least 32 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of four.

2024

Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs.

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

CoRR, 2024

Messenger and Non-Coding RNA Design via Expected Partition Function and Continuous Optimization.

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

CoRR, 2024

Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition.

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

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Algorithm for optimized mRNA design improves stability and immunogenicity.

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

Nat., 2023

LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs.

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

CoRR, 2023

RNA design via structure-aware multifrontier ensemble optimization.

Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H. Mathews, Liang Huang

Bioinform., 2023

2022

LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules.

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

CoRR, 2022

LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments.

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

CoRR, 2022

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

Marcell Szikszai, Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews

Bioinform., 2022

2021

LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.

Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang

Proc. Natl. Acad. Sci. USA, 2021

2020

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.

He Zhang, Liang Zhang, David H. Mathews, Liang Huang

Bioinform., 2020

2019

Determining parameters for non-linear models of multi-loop free energy change.

Max Ward, Hongying Sun, Amitava Datta, Michael J. Wise, David H. Mathews

Bioinform., 2019

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews

Bioinform., 2019

2017

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

Michael F. Sloma, David H. Mathews

PLoS Comput. Biol., 2017

2016

AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.

Laura DiChiacchio, Michael F. Sloma, David H. Mathews

Bioinform., 2016

2013

RNAstructure: web servers for RNA secondary structure prediction and analysis.

Stanislav Bellaousov, Jessica S. Reuter, Matthew G. Seetin, David H. Mathews

Nucleic Acids Res., 2013

Accelerating calculations of RNA secondary structure partition functions using GPUs.

Harry A. Stern, David H. Mathews

Algorithms Mol. Biol., 2013

2012

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.

Matthew G. Seetin, David H. Mathews

Bioinform., 2012

2011

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints.

Matthew G. Seetin, David H. Mathews

J. Comput. Chem., 2011

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews

BMC Bioinform., 2011

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

Zhenjiang Xu, David H. Mathews

Bioinform., 2011

Iterative estimation of structures of multiple RNA homologs: Turbofold.

Gaurav Sharma, Arif Ozgun Harmanci, David H. Mathews

Proceedings of the IEEE International Conference on Acoustics, 2011

2010

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.

Douglas H. Turner, David H. Mathews

Nucleic Acids Res., 2010

RNAstructure: software for RNA secondary structure prediction and analysis.

Jessica S. Reuter, David H. Mathews

BMC Bioinform., 2010

2009

Joint stochastic sampling for RNA secondary structure prediction.

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews

Proceedings of the 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 2009

2008

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.

Zhi John Lu, David H. Mathews

Nucleic Acids Res., 2008

Probabilistic structural alignment of RNA sequences.

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews

Proceedings of the IEEE International Conference on Acoustics, 2008

2007

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews

BMC Bioinform., 2007

Efficient parameter estimation for RNA secondary structure prediction.

Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Toward Turbo Decoding of RNA Secondary Structure.

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews

Proceedings of the IEEE International Conference on Acoustics, 2007

2006

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

Andrew V. Uzilov, Joshua M. Keegan, David H. Mathews

BMC Bioinform., 2006

2005

Predicting a set of minimal free energy RNA secondary structures common to two sequences.

David H. Mathews

Bioinform., 2005