Predicting a set of minimal free energy RNA secondary structures common to two sequences. - David H. Mathews (Bioinform., 2005)

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)

Toward Turbo Decoding of RNA Secondary Structure. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (ICASSP (1), 2007)

Efficient parameter estimation for RNA secondary structure prediction. - Mirela Andronescu; Anne Condon; Holger H. Hoos; David H. Mathews; Kevin P. Murphy (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (BMC Bioinform., 2007)

Probabilistic structural alignment of RNA sequences. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (ICASSP, 2008)

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. - Zhi John Lu; David H. Mathews (Nucleic Acids Res., 2008)

Joint stochastic sampling for RNA secondary structure prediction. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (GENSiPS, 2009)

RNAstructure: software for RNA secondary structure prediction and analysis. - Jessica S. Reuter; David H. Mathews (BMC Bioinform., 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)

Iterative estimation of structures of multiple RNA homologs: Turbofold. - Gaurav Sharma 001; Arif Ozgun Harmanci; David H. Mathews (ICASSP, 2011)

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. - Zhenjiang Xu; David H. Mathews (Bioinform., 2011)

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (BMC Bioinform., 2011)

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. - Matthew G. Seetin; David H. Mathews (J. Comput. Chem., 2011)

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. - Matthew G. Seetin; David H. Mathews (Bioinform., 2012)

Accelerating calculations of RNA secondary structure partition functions using GPUs. - Harry A. Stern; David H. Mathews (Algorithms Mol. Biol., 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)

AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. - Laura DiChiacchio; Michael F. Sloma; David H. Mathews (Bioinform., 2016)

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. - Michael F. Sloma; David H. Mathews (PLoS Comput. Biol., 2017)

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. - Liang Huang 001; He Zhang; Dezhong Deng; Kai Zhao 003; Kaibo Liu; David A. Hendrix; David H. Mathews (Bioinform., 2019)

Determining parameters for non-linear models of multi-loop free energy change. - Max Ward 001; Hongying Sun; Amitava Datta; Michael J. Wise; David H. Mathews (Bioinform., 2019)

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities. - He Zhang; Liang Zhang; David H. Mathews; Liang Huang 001 (Bioinform., 2020)

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 001 (Proc. Natl. Acad. Sci. USA, 2021)

Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. - Marcell Szikszai; Michael J. Wise; Amitava Datta; Max Ward 001; David H. Mathews (Bioinform., 2022)

LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. - Liang Zhang; Sizhen Li; He Zhang; David H. Mathews; Liang Huang 001 (CoRR, 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 001 (CoRR, 2022)

RNA design via structure-aware multifrontier ensemble optimization. - Tianshuo Zhou; Ning Dai; Sizhen Li; Max Ward 001; David H. Mathews; Liang Huang 001 (Bioinform., 2023)

LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs. - Sizhen Li; Ning Dai; He Zhang; Apoorv Malik; David H. Mathews; Liang Huang 001 (CoRR, 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; et al. (Nat., 2023)

Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. - Tianshuo Zhou; Wei Yu Tang; David H. Mathews; Liang Huang 001 (RECOMB, 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 001 (CoRR, 2024)

Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs. - Tianshuo Zhou; Wei Yu Tang; David H. Mathews; Liang Huang 001 (CoRR, 2024)

Sampling-based Continuous Optimization with Coupled Variables for RNA Design. - Wei Yu Tang; Ning Dai; Tianshuo Zhou; David H. Mathews; Liang Huang 001 (CoRR, 2024)

Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance. - Tianshuo Zhou; Apoorv Malik; Wei Yu Tang; David H. Mathews; Liang Huang 001 (RECOMB, 2025)

Differentiable Folding for Nearest Neighbor Model Optimization. - Ryan K. Krueger; Sharon Aviran; David H. Mathews; Jeffrey Zuber; Max Ward 001 (CoRR, 2025)