Search results for "pseudoknots"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
140	Yujin Lee, Wootaek Kim, Kyungsook Han	New Representation and Algorithm for Drawing RNA Structure with Pseudoknots.	DaWaK	2002	DBLP DOI BibTeX RDF
123	Oyun-Erdene Namsrai, Kwang Su Jung, Sunshin Kim, Keun Ho Ryu	RNA Secondary Structure Prediction with Simple Pseudoknots Based on Dynamic Programming.	ICIC (3)	2006	DBLP DOI BibTeX RDF
123	Rune B. Lyngsø, Christian N. S. Pedersen	Pseudoknots in RNA secondary structures.	RECOMB	2000	DBLP DOI BibTeX RDF
120	Christina Witwer, Ivo L. Hofacker, Peter F. Stadler	Prediction of Consensus RNA Secondary Structures Including Pseudoknots.	IEEE ACM Trans. Comput. Biol. Bioinform.	2004	DBLP DOI BibTeX RDF	covariance, RNA secondary structure, pseudoknots
118	Xuezheng Fu, Hao Wang, William L. Harrison, Robert W. Harrison	RNA Pseudoknot Prediction Using Term Rewriting.	BIBE	2005	DBLP DOI BibTeX RDF
118	Wootaek Kim, Yujin Lee, Kyungsook Han	Visualization of RNA Pseudoknot Structures.	VECPAR	2002	DBLP DOI BibTeX RDF
106	Xiaolu Huang, Hesham H. Ali	Reducing Folding Scenario Candidates in Pseudoknots Detection Using PLMM_DPSS Algorithm Integrated With Energy Filters.	BIBE	2007	DBLP DOI BibTeX RDF
106	Fariza Tahi, Stefan Engelen, Mireille Régnier	A Fast Algorithm for NA Secondary Structure Prediction Including Pseudoknots.	BIBE	2003	DBLP DOI BibTeX RDF
98	Thomas K. F. Wong, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu	Structural Alignment of RNA with Complex Pseudoknot Structure.	WABI	2009	DBLP DOI BibTeX RDF	pseudoknots, Structural alignment, non-coding RNA
89	Qingfeng Chen, Yi-Ping Phoebe Chen	Discovery of Structural and Functional Features in RNA Pseudoknots.	IEEE Trans. Knowl. Data Eng.	2009	DBLP DOI BibTeX RDF
89	Oyun-Erdene Namsrai, Keun Ho Ryu	Characterizing Pseudobase and Predicting RNA Secondary Structure with Simple H-Type Pseudoknots Based on Dynamic Programming.	ADMA	2007	DBLP DOI BibTeX RDF	Pseudobase, H-type pseudo-knots, dynamic programming, RNA secondary structure prediction
89	Hengwu Li, Daming Zhu	A New Pseudoknots Folding Algorithm for RNA Structure Prediction.	COCOON	2005	DBLP DOI BibTeX RDF
86	Mathias Möhl, Sebastian Will, Rolf Backofen	Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots.	CPM	2008	DBLP DOI BibTeX RDF	RNA alignment, fixed parameter tractability, pseudoknots
84	Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara	Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures.	CSB	2004	DBLP DOI BibTeX RDF
84	Dongkyu Lee, Kyungsook Han	A Genetic Algorithm for Inferring Pseudoknotted RNA Structures from Sequence Data.	Discovery Science	2003	DBLP DOI BibTeX RDF
56	Xiang Chen, Simin He 0001, Dongbo Bu, Runsheng Chen, Wen Gao 0001	A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots.	BIBE	2007	DBLP DOI BibTeX RDF
56	Trilce Estrada, Abel Licon, Michela Taufer	compPknots: A Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots.	ISPA Workshops	2006	DBLP DOI BibTeX RDF
56	Jizhen Zhao, Russell L. Malmberg, Liming Cai	Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition.	WABI	2006	DBLP DOI BibTeX RDF
51	Minghui Jiang 0001, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser	K-Partite RNA Secondary Structures.	WABI	2009	DBLP DOI BibTeX RDF
51	Markus Bauer 0001, Gunnar W. Klau	Structural Alignment of Two RNA Sequences with Lagrangian Relaxation.	ISAAC	2004	DBLP DOI BibTeX RDF
39	Mathias Möhl, Sebastian Will, Rolf Backofen	Lifting Prediction to Alignment of RNA Pseudoknots.	RECOMB	2009	DBLP DOI BibTeX RDF
39	Herbert H. Tsang, Kay C. Wiese	SARNA-Predict-pk: Predicting RNA secondary structures including pseudoknots.	CIBCB	2008	DBLP DOI BibTeX RDF
39	Chunmei Liu, Yinglei Song, Louis W. Shapiro	RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound.	WABI	2007	DBLP DOI BibTeX RDF	path decomposition, maximum weighted independent set, free energy, pseudoknot, RNA secondary structure prediction
39	Minghui Jiang 0001	Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots.	AAIM	2007	DBLP DOI BibTeX RDF
39	Kay C. Wiese, Edward Glen	jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots.	CBMS	2006	DBLP DOI BibTeX RDF
39	Patricia A. Evans	Finding Common Subsequences with Arcs and Pseudoknots.	CPM	1999	DBLP DOI BibTeX RDF
34	Hengwu Li	Approximation algorithm and scheme for RNA structure prediction.	ICIS	2009	DBLP DOI BibTeX RDF	approximation algorithm, approximation scheme, RNA structure, pseudoknot
34	Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna	Structural Alignment of Pseudoknotted RNA.	RECOMB	2006	DBLP DOI BibTeX RDF
34	Patricia A. Evans	Finding Common RNA Pseudoknot Structures in Polynomial Time.	CPM	2006	DBLP DOI BibTeX RDF
34	Rune B. Lyngsø	Complexity of Pseudoknot Prediction in Simple Models.	ICALP	2004	DBLP DOI BibTeX RDF
34	Dongkyu Lee, Kyungsook Han	A Genetic Algorithm for Predicting RNA Pseudoknot Structures.	International Conference on Computational Science	2003	DBLP DOI BibTeX RDF
22	Gabriel Loyer, Vladimir Reinharz	Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.	Bioinform.	2024	DBLP DOI BibTeX RDF
22	Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty, Laurent Bulteau	Automated design of dynamic programming schemes for RNA folding with pseudoknots.	Algorithms Mol. Biol.	2023	DBLP DOI BibTeX RDF
22	Rohith Vedhthaanth Sekar, Patricia J. Oliva, Michael T. Woodside	Modelling the structures of frameshift-stimulatory pseudoknots from representative bat coronaviruses.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
22	Lina Yang, Yang Liu 0230, Huiwu Luo, Xichun Li, Yuan Yan Tang	Visualization of RNA secondary structure with pseudoknots.	Int. J. Wavelets Multiresolution Inf. Process.	2022	DBLP DOI BibTeX RDF
22	Kengo Sato, Yuki Kato	Prediction of RNA secondary structure including pseudoknots for long sequences.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
22	Md. Shahidul Islam, Md. Rafiqul Islam 0002	A hybrid framework based on genetic algorithm and simulated annealing for RNA structure prediction with pseudoknots.	J. King Saud Univ. Comput. Inf. Sci.	2022	DBLP DOI BibTeX RDF
22	Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty	Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots.	WABI	2022	DBLP DOI BibTeX RDF
22	Liyu Huang, Qingfeng Chen, Yongjie Li, Cheng Luo	Classifying Conserved RNA Secondary Structures With Pseudoknots by Vector-Edit Distance.	IEEE Access	2021	DBLP DOI BibTeX RDF
22	Yongna Yuan, Shaowei Fu, Dongxu Huo, Wei Su 0008, Ruisheng Zhang, Jiaxuan Wei	Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function.	J. Comput. Chem.	2021	DBLP DOI BibTeX RDF
22	Md. Rafiqul Islam 0002, Md. Shahidul Islam, Nazmus Shaker Nafi	RNA Secondary Structure Prediction with Pseudoknots Using Chemical Reaction Optimization Algorithm.	IEEE ACM Trans. Comput. Biol. Bioinform.	2021	DBLP DOI BibTeX RDF
22	Alan Zammit, Leon S. Helwerda, René C. L. Olsthoorn, Fons J. Verbeek, Alexander P. Gultyaev	A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions.	Bioinform.	2021	DBLP DOI BibTeX RDF
22	Vo Hong Thanh, Dani Korpela, Pekka Orponen	Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots.	J. Comput. Biol.	2021	DBLP DOI BibTeX RDF
22	Louis Becquey, Eric Angel, Fariza Tahi	BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules.	Bioinform.	2020	DBLP DOI BibTeX RDF
22	Michela Quadrini, Luca Tesei, Emanuela Merelli	ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots.	Bioinform.	2020	DBLP DOI BibTeX RDF
22	Michela Quadrini	Searching RNA Substructures with Arbitrary Pseudoknots.	PACBB	2020	DBLP DOI BibTeX RDF
22	Michela Quadrini, Luca Tesei, Emanuela Merelli	An algebraic language for RNA pseudoknots comparison.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
22	Louis Petingi, Tamar Schlick	Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots.	AlCoB	2019	DBLP DOI BibTeX RDF
22	Audrey Legendre	Prédiction de structures secondaires d'ARN et de complexes d'ARN avec pseudonoeuds - Approches basées sur la programmation mathématique multi-objectif. (RNA and RNA complex secondary structure prediction with pseudoknots - Multi-objective mathematical programming based approaches).		2019	RDF
22	Zhendong Liu, Daming Zhu, Qionghai Dai	Predicting Model and Algorithm in RNA Folding Structure Including Pseudoknots.	Int. J. Pattern Recognit. Artif. Intell.	2018	DBLP DOI BibTeX RDF
22	Audrey Legendre, Eric Angel, Fariza Tahi	Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.	BMC Bioinform.	2018	DBLP DOI BibTeX RDF
22	Ya-Zhou Shi, Lei Jin, Chen-Jie Feng, Ya-Lan Tan, Zhi-Jie Tan	Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.	PLoS Comput. Biol.	2018	DBLP DOI BibTeX RDF
22	Michela Quadrini, Emanuela Merelli	Loop-loop Interaction Metrics on RNA Secondary Structures with Pseudoknots.	BIOINFORMATICS	2018	DBLP DOI BibTeX RDF
22	Kai Zhang, Yulin Lv	A Novel Efficient Simulated Annealing Algorithm for the RNA Secondary Structure Predicting with Pseudoknots.	ICIC (2)	2018	DBLP DOI BibTeX RDF
22	Zhendong Liu, Fanghan Liu, Qingxia Kong, Fanchang Hao, Hongluan Zhao	Algorithm and Scheme in RNA Structure Prediction Including Pseudoknots.	CIS	2018	DBLP DOI BibTeX RDF
22	Boris Shabash, Kay C. Wiese	RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots.	IEEE ACM Trans. Comput. Biol. Bioinform.	2017	DBLP DOI BibTeX RDF
22	Qingxia Kong, Yaoyao Fu, Zhendong Liu	Possible Transitions Between Types of Pseudoknots of RNA Structure.	CIS	2017	DBLP DOI BibTeX RDF
22	Zhendong Liu, Qingxia Kong, Yaoyao Fu, Hongchao Ye, Shimin Zhao, Xinhong Su, Kai Jiang, Hui Wang, Kunle Dong, Zhenxiong Song, Yujie Wang	The Algorithm and Scheme of Prediction in RNA Folding Structure with Pseudoknots.	CIS	2017	DBLP DOI BibTeX RDF
22	Rune B. Lyngsø	RNA Secondary Structure Prediction Including Pseudoknots.	Encyclopedia of Algorithms	2016	DBLP DOI BibTeX RDF
22	Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin 0006	Pseudoknots in RNA folding landscapes.	Bioinform.	2016	DBLP DOI BibTeX RDF
22	Yanga Byun, Kyungsook Han	An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type.	J. Bioinform. Comput. Biol.	2016	DBLP DOI BibTeX RDF
22	Kai Zhang 0002, Shangyi Li, Juanjuan He, Yunyun Niu	Nucleic Acid Secondary Structures Prediction with Planar Pseudoknots Using Genetic Algorithm.	BIC-TA (2)	2016	DBLP DOI BibTeX RDF
22	Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen	Efficient Conversion of RNA Pseudoknots to Knot-Free Structures Using a Graphical Model.	IEEE Trans. Biomed. Eng.	2015	DBLP DOI BibTeX RDF
22	Yinglei Song, Chunmei Liu, Yongzhong Li	A New Parameterized Algorithm for Predicting the Secondary Structure of RNA Sequences Including Pseudoknots.	Comput. J.	2015	DBLP DOI BibTeX RDF
22	Kwok-Kit Tong, Kwan-Yau Cheung, Kin-Hong Lee, Kwong-Sak Leung	Classification of RNA sequences with pseudoknots using features based on partial sequences.	CIBCB	2015	DBLP DOI BibTeX RDF
22	Linkon Chowdhury, Mohammad Ibrahim Khan	Pseudoknots Prediction on RNA Secondary Structure Using Term Rewriting.	IWBBIO (1)	2015	DBLP DOI BibTeX RDF
22	Zhendong Liu, Daming Zhu, Qionghai Dai	Predicting Algorithm of RNA Folding Structure with Pseudoknots.	CIS	2015	DBLP DOI BibTeX RDF
22	Cong Zeng	Classification of RNA Pseudoknots and Comparison of Structure Prediction Methods. (Classification de Pseudo-nœuds d'ARN et Comparaison de Méthodes de Prédiction de Structure).		2015	RDF
22	Zhendong Liu, Daming Zhu, Hongwei Ma	Predicting scheme of RNA folding structure including pseudoknots.	Int. J. Sens. Networks	2014	DBLP DOI BibTeX RDF
22	Fei Xia, Guoqing Jin	Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.	J. Bioinform. Comput. Biol.	2014	DBLP DOI BibTeX RDF
22	Kai Zhang 0002, Xinquan Huang, Wei Hu 0001, Jun Liu 0011	Prediction Nucleic Acid Secondary Structure with Planar Pseudoknots and Genetic Algorithm.	BIC-TA	2014	DBLP DOI BibTeX RDF
22	Rujira Achawanantakun, Yanni Sun	Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.	BMC Bioinform.	2013	DBLP DOI BibTeX RDF
22	Cheng Yuan, Yanni Sun	Efficient known ncRNA search including pseudoknots.	BMC Bioinform.	2013	DBLP DOI BibTeX RDF
22	Zhendong Liu, Daming Zhu	New Heuristic Algorithm of RNA Structure Prediction Including Pseudoknots.	J. Comput.	2013	DBLP BibTeX RDF
22	Kwan-Yau Cheung, Kwok-Kit Tong, Kin-Hong Lee, Kwong-Sak Leung	Classification of RNAs with pseudoknots using k-mer occurrences count as attributes.	BIBE	2013	DBLP DOI BibTeX RDF
22	Kwok-Kit Tong, Kwan-Yau Cheung, Kin-Hong Lee, Kwong-Sak Leung	Modified free energy model to improve RNA secondary structure prediction with pseudoknots.	BIBE	2013	DBLP DOI BibTeX RDF
22	Kwok-Kit Tong, Kwan-Yau Cheung, Kin-Hong Lee, Kwong-Sak Leung	GAknot: RNA secondary structures prediction with pseudoknots using genetic algorithm.	CIBCB	2013	DBLP DOI BibTeX RDF
22	Zhendong Liu, Daming Zhu, Wei Cui, Nan Liu	An Approximation Scheme for RNA Folding Structure Prediction Including Pseudoknots.	CIS	2013	DBLP DOI BibTeX RDF
22	Thomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu	Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots.	IEEE ACM Trans. Comput. Biol. Bioinform.	2012	DBLP DOI BibTeX RDF
22	Christopher Ma, Thomas K. F. Wong, Tak Wah Lam, Wing-Kai Hon, Kunihiko Sadakane, Siu-Ming Yiu	An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence.	IEEE ACM Trans. Comput. Biol. Bioinform.	2012	DBLP DOI BibTeX RDF
22	Gero Doose, Dirk Metzler	Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.	Bioinform.	2012	DBLP DOI BibTeX RDF
22	Matthew G. Seetin, David H. Mathews	TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.	Bioinform.	2012	DBLP DOI BibTeX RDF
22	Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel	Addendum: topology and prediction of RNA pseudoknots.	Bioinform.	2012	DBLP DOI BibTeX RDF
22	Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise	Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots.	CoRR	2012	DBLP BibTeX RDF
22	Saad Sheikh, Rolf Backofen, Yann Ponty	Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots.	CPM	2012	DBLP DOI BibTeX RDF
22	Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise	Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract).	WABI	2012	DBLP DOI BibTeX RDF
22	Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai	IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.	Bioinform.	2011	DBLP DOI BibTeX RDF
22	Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel	Topology and prediction of RNA pseudoknots.	Bioinform.	2011	DBLP DOI BibTeX RDF
22	Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon	NP-completeness of the energy barrier problem without pseudoknots and temporary arcs.	Nat. Comput.	2011	DBLP DOI BibTeX RDF
22	Christian M. Reidys	Combinatorial Computational Biology of RNA - Pseudoknots and Neutral Networks.		2011	DOI RDF
22	Thomas K. F. Wong, Siu-Ming Yiu	Structural Alignment of RNAs with Pseudoknots.	Handbook of Research on Computational and Systems Biology	2011	DBLP DOI BibTeX RDF
22	Zhendong Liu, Yuxiao Dong, Hengwu Li, Huijian Han	Approximating algorithm for RNA structure prediction including pseudoknots.	ICAL	2011	DBLP DOI BibTeX RDF
22	Zhendong Liu, Zhijun Zhang, Zaixue Liu, Daming Zhu	New Heuristic Algorithm of RNA Secondary Structure Prediction with Pseudoknots.	CIS	2011	DBLP DOI BibTeX RDF
22	Cédric Saule	Modèles combinatoires des structures d'ARN avec ou sans pseudonoeuds, application à la comparaison de structures. (Combinatorial models for RNA structures, with or without pseudoknots and application to structures comparison).		2011	RDF
22	Zhibin Huang	Computational search of RNA pseudoknots and structural variations in genomes.		2011	RDF
22	Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp	Sparsification of RNA structure prediction including pseudoknots.	Algorithms Mol. Biol.	2010	DBLP DOI BibTeX RDF
22	Minghui Jiang 0001	Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots.	IEEE ACM Trans. Comput. Biol. Bioinform.	2010	DBLP DOI BibTeX RDF
22	Sanguthevar Rajasekaran, Sahar Al Seesi, Reda A. Ammar	Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots.	IEEE ACM Trans. Comput. Biol. Bioinform.	2010	DBLP DOI BibTeX RDF
22	Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro	CyloFold: secondary structure prediction including pseudoknots.	Nucleic Acids Res.	2010	DBLP DOI BibTeX RDF
22	Uwe Schöning, Monika von Knop	Using Stochastic Indexed Grammars for RNA Structure PredictionWith Pseudoknots.	Bull. EATCS	2010	DBLP BibTeX RDF