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2020 – today
- 2024
[c6]Tianshuo Zhou
, Wei Yu Tang, David H. Mathews, Liang Huang:
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. RECOMB 2024: 270-287- [i7]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 abs/2401.00037 (2024) - [i6]Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang:
Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs. CoRR abs/2402.17206 (2024) - 2023
- [j21]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): 563-571 (2023) - [j20]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): 396-403 (2023) - [i5]Sizhen Li, Ning Dai, He Zhang, Apoorv Malik, David H. Mathews, Liang Huang:
LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs. CoRR abs/2307.09580 (2023) - 2022
- [j19]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): 3892-3899 (2022) - [i4]Liang Zhang, Sizhen Li, He Zhang, David H. Mathews, Liang Huang:
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments. CoRR abs/2206.14794 (2022) - [i3]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 abs/2210.14982 (2022) - 2021
- [j18]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): e2116269118 (2021) - 2020
- [j17]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): i258-i267 (2020) - [i2]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 abs/2001.04020 (2020)
2010 – 2019
- 2019
- [j16]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): i295-i304 (2019) - [j15]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): 4298-4306 (2019) - [i1]He Zhang, Liang Zhang, David H. Mathews, Liang Huang:
LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities. CoRR abs/1912.13190 (2019) - 2017
- [j14]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) - 2016
- [j13]Laura DiChiacchio, Michael F. Sloma, David H. Mathews:
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinform. 32(7): 1033-1039 (2016) - 2013
- [j12]Harry A. Stern, David H. Mathews:
Accelerating calculations of RNA secondary structure partition functions using GPUs. Algorithms Mol. Biol. 8: 29 (2013) - [j11]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): 471-474 (2013) - 2012
- [j10]Matthew G. Seetin, David H. Mathews:
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinform. 28(6): 792-798 (2012) - 2011
- [j9]Zhenjiang Xu, David H. Mathews:
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinform. 27(5): 626-632 (2011) - [j8]Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform. 12: 108 (2011) - [j7]Matthew G. Seetin, David H. Mathews:
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem. 32(10): 2232-2244 (2011) - [c5]Gaurav Sharma, Arif Ozgun Harmanci, David H. Mathews:
Iterative estimation of structures of multiple RNA homologs: Turbofold. ICASSP 2011: 529-532 - 2010
- [j6]Jessica S. Reuter, David H. Mathews:
RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform. 11: 129 (2010) - [j5]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): 280-282 (2010)
2000 – 2009
- 2009
- [c4]Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Joint stochastic sampling for RNA secondary structure prediction. GENSiPS 2009: 1-4 - 2008
- [j4]Zhi John Lu, David H. Mathews:
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res. 36(Web-Server-Issue): 104-108 (2008) - [c3]Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Probabilistic structural alignment of RNA sequences. ICASSP 2008: 645-648 - 2007
- [j3]Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinform. 8 (2007) - [c2]Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Toward Turbo Decoding of RNA Secondary Structure. ICASSP (1) 2007: 365-368 - [c1]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: 19-28 - 2006
- [j2]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: 173 (2006) - 2005
- [j1]David H. Mathews:
Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinform. 21(10): 2246-2253 (2005)
Coauthor Index
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