David H. Mathews

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 17

Top Topics

Partition Function

Secondary Structure

Top Venues

Proc. Natl. Acad. Sci. USA

Publications

Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs. CoRR (2024)
Ning Dai, Wei Yu Tang, Tianshuo Zhou, David H. Mathews, Liang Huang
Messenger and Non-Coding RNA Design via Expected Partition Function and Continuous Optimization. CoRR (2024)
Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. RECOMB (2024)
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
Algorithm for optimized mRNA design improves stability and immunogenicity. Nat. 621 (7978) (2023)
Sizhen Li, Ning Dai, He Zhang, Apoorv Malik, David H. Mathews, Liang Huang
LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs. CoRR (2023)
Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H. Mathews, Liang Huang
RNA design via structure-aware multifrontier ensemble optimization. Bioinform. 39 (Supplement-1) (2023)
He Zhang, Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang
LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules. CoRR (2022)
Marcell Szikszai, Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. Bioinform. 38 (16) (2022)
Liang Zhang, Sizhen Li, He Zhang, David H. Mathews, Liang Huang
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. CoRR (2022)
Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang
LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2. Proc. Natl. Acad. Sci. USA 118 (52) (2021)
Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. CoRR (2020)
He Zhang, Liang Zhang, David H. Mathews, Liang Huang
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities. Bioinform. 36 (Supplement-1) (2020)
Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinform. 35 (14) (2019)
Max Ward, Hongying Sun, Amitava Datta, Michael J. Wise, David H. Mathews
Determining parameters for non-linear models of multi-loop free energy change. Bioinform. 35 (21) (2019)
He Zhang, Liang Zhang, David H. Mathews, Liang Huang
LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities. CoRR (2019)
Michael F. Sloma, David H. Mathews
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput. Biol. 13 (11) (2017)
Laura DiChiacchio, Michael F. Sloma, David H. Mathews
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinform. 32 (7) (2016)
Harry A. Stern, David H. Mathews
Accelerating calculations of RNA secondary structure partition functions using GPUs. Algorithms Mol. Biol. 8 (2013)
Stanislav Bellaousov, Jessica S. Reuter, Matthew G. Seetin, David H. Mathews
RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Matthew G. Seetin, David H. Mathews
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinform. 28 (6) (2012)
Matthew G. Seetin, David H. Mathews
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem. 32 (10) (2011)
Gaurav Sharma, Arif Ozgun Harmanci, David H. Mathews
Iterative estimation of structures of multiple RNA homologs: Turbofold. ICASSP (2011)
Zhenjiang Xu, David H. Mathews
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinform. 27 (5) (2011)
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform. 12 (2011)
Jessica S. Reuter, David H. Mathews
RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform. 11 (2010)
Douglas H. Turner, David H. Mathews
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. 38 (Database-Issue) (2010)
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
Joint stochastic sampling for RNA secondary structure prediction. GENSiPS (2009)
Zhi John Lu, David H. Mathews
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
Probabilistic structural alignment of RNA sequences. ICASSP (2008)
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinform. 8 (2007)
Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy
Efficient parameter estimation for RNA secondary structure prediction. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
Toward Turbo Decoding of RNA Secondary Structure. ICASSP (1) (2007)
Andrew V. Uzilov, Joshua M. Keegan, David H. Mathews
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinform. 7 (2006)
David H. Mathews
Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinform. 21 (10) (2005)