David H. Mathews

41 papers B 2Misc 2Journal 34Unranked 3

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Designing RNAs with Language Models. CoRR Milan Gautam, Ning Dai, Tianshuo Zhou, Bowen Xie, David H. Mathews, Liang Huang
2026	J	`jnl`	Probabilistic RNA Designability via Interpretable Ensemble Approximation and Dynamic Decomposition. CoRR Tianshuo Zhou, David H. Mathews, Liang Huang
2026	J	`jnl`	Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs. J. Comput. Biol. Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang
2025	J	`jnl`	Differentiable Folding for Nearest Neighbor Model Optimization. CoRR Ryan K. Krueger, Sharon Aviran, David H. Mathews, Jeffrey Zuber, Max Ward
2025	J	`jnl`	EnsembleDesign: messenger RNA design minimizing ensemble free energy via probabilistic lattice parsing. Bioinform. Ning Dai, Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
2025	B	`conf`	Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance. RECOMB Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang
2024	J	`jnl`	Messenger and Non-Coding RNA Design via Expected Partition Function and Continuous Optimization. CoRR Ning Dai, Wei Yu Tang, Tianshuo Zhou, David H. Mathews, Liang Huang
2024	J	`jnl`	Sampling-based Continuous Optimization with Coupled Variables for RNA Design. CoRR Wei Yu Tang, Ning Dai, Tianshuo Zhou, David H. Mathews, Liang Huang
2024	J	`jnl`	Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs. CoRR Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
2024	B	`conf`	Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. RECOMB Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
2023	J	`jnl`	Algorithm for optimized mRNA design improves stability and immunogenicity. Nat. 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
2023	J	`jnl`	LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs. CoRR Sizhen Li, Ning Dai, He Zhang, Apoorv Malik, David H. Mathews, Liang Huang
2023	J	`jnl`	RNA design via structure-aware multifrontier ensemble optimization. Bioinform. Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H. Mathews, Liang Huang
2022	J	`jnl`	Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. Bioinform. Marcell Szikszai, Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews
2022	J	`jnl`	LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. CoRR Liang Zhang, Sizhen Li, He Zhang, David H. Mathews, Liang Huang
2022	J	`jnl`	LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules. CoRR He Zhang, Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang
2021	J	`jnl`	LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2. Proc. Natl. Acad. Sci. USA Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang
2020	J	`jnl`	LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. CoRR Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews
2020	J	`jnl`	LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities. Bioinform. He Zhang, Liang Zhang, David H. Mathews, Liang Huang
2019	J	`jnl`	Determining parameters for non-linear models of multi-loop free energy change. Bioinform. Max Ward, Hongying Sun, Amitava Datta, Michael J. Wise, David H. Mathews
2019	J	`jnl`	LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinform. Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews
2019	J	`jnl`	LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities. CoRR He Zhang, Liang Zhang, David H. Mathews, Liang Huang
2017	J	`jnl`	Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput. Biol. Michael F. Sloma, David H. Mathews
2016	J	`jnl`	AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinform. Laura DiChiacchio, Michael F. Sloma, David H. Mathews
2013	J	`jnl`	Accelerating calculations of RNA secondary structure partition functions using GPUs. Algorithms Mol. Biol. Harry A. Stern, David H. Mathews
2013	J	`jnl`	RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. Stanislav Bellaousov, Jessica S. Reuter, Matthew G. Seetin, David H. Mathews
2012	J	`jnl`	TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinform. Matthew G. Seetin, David H. Mathews
2011	J	`jnl`	Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem. Matthew G. Seetin, David H. Mathews
2011	Misc	`conf`	Iterative estimation of structures of multiple RNA homologs: Turbofold. ICASSP Gaurav Sharma, Arif Ozgun Harmanci, David H. Mathews
2011	J	`jnl`	Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinform. Zhenjiang Xu, David H. Mathews
2011	J	`jnl`	TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform. Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
2010	J	`jnl`	NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. Douglas H. Turner, David H. Mathews
2010	J	`jnl`	RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform. Jessica S. Reuter, David H. Mathews
2009	—	`conf`	Joint stochastic sampling for RNA secondary structure prediction. GENSiPS Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
2008	J	`jnl`	OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res. Zhi John Lu, David H. Mathews
2008	Misc	`conf`	Probabilistic structural alignment of RNA sequences. ICASSP Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
2007	J	`jnl`	Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinform. Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
2007	—	`conf`	Efficient parameter estimation for RNA secondary structure prediction. ISMB/ECCB (Supplement of Bioinformatics) Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy
2007	—	`conf`	Toward Turbo Decoding of RNA Secondary Structure. ICASSP (1) Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
2006	J	`jnl`	Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinform. Andrew V. Uzilov, Joshua M. Keegan, David H. Mathews
2005	J	`jnl`	Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinform. David H. Mathews