Search results for "pseudoknot"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
101	Rune B. Lyngsø	Complexity of Pseudoknot Prediction in Simple Models.	ICALP	2004	DBLP DOI BibTeX RDF
82	Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar	RNA Pseudoknot Folding through Inference and Identification Using TAGRNA.	BICoB	2009	DBLP DOI BibTeX RDF
82	Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar	Pseudoknot Identification through Learning TAGRNA.	PRIB	2008	DBLP DOI BibTeX RDF
82	Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai	Profiling and Searching for RNA Pseudoknot Structures in Genomes.	Trans. Comp. Sys. Biology	2005	DBLP DOI BibTeX RDF
82	Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai	Profiling and Searching for RNA Pseudoknot Structures in Genomes.	International Conference on Computational Science (2)	2005	DBLP DOI BibTeX RDF
82	Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara	Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures.	CSB	2004	DBLP DOI BibTeX RDF
76	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
76	Yujin Lee, Wootaek Kim, Kyungsook Han	New Representation and Algorithm for Drawing RNA Structure with Pseudoknots.	DaWaK	2002	DBLP DOI BibTeX RDF
67	Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop 0004, Yinglei Zhao	HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding.	WABI	2007	DBLP DOI BibTeX RDF	Secondary Structure Prediction, Folding Pathways, Hierarchical Folding, RNA, Pseudoknot
48	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
44	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
44	Patricia A. Evans	Finding Common RNA Pseudoknot Structures in Polynomial Time.	CPM	2006	DBLP DOI BibTeX RDF
44	Xuezheng Fu, Hao Wang, William L. Harrison, Robert W. Harrison	RNA Pseudoknot Prediction Using Term Rewriting.	BIBE	2005	DBLP DOI BibTeX RDF
44	Dongkyu Lee, Kyungsook Han	A Genetic Algorithm for Predicting RNA Pseudoknot Structures.	International Conference on Computational Science	2003	DBLP DOI BibTeX RDF
44	Wootaek Kim, Yujin Lee, Kyungsook Han	Visualization of RNA Pseudoknot Structures.	VECPAR	2002	DBLP DOI BibTeX RDF
38	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
38	Mathias Möhl, Sebastian Will, Rolf Backofen	Lifting Prediction to Alignment of RNA Pseudoknots.	RECOMB	2009	DBLP DOI BibTeX RDF
38	Wenduo Zhou, David K. Lowenthal	A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction.	ICPP	2006	DBLP DOI BibTeX RDF
29	Hengwu Li	Approximation algorithm and scheme for RNA structure prediction.	ICIS	2009	DBLP DOI BibTeX RDF	approximation algorithm, approximation scheme, RNA structure, pseudoknot
29	Yinglei Song, Jizhen Zhao, Chunmei Liu, Kan Liu, Russell L. Malmberg, Liming Cai	RNA Structural Homology Search with a Succinct Stochastic Grammar Model.	J. Comput. Sci. Technol.	2005	DBLP DOI BibTeX RDF	RNA structural homology search, stochastic context-free grammar (SCFG), structure-sequence alignment, pseudoknot
26	Mateo Gray, Sebastian Will, Hosna Jabbari	SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.	Algorithms Mol. Biol.	2024	DBLP DOI BibTeX RDF
26	Luke Trinity, Ian Wark, Lance Lansing, Hosna Jabbari, Ulrike Stege	Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
26	Mateo Gray, Sebastian Will, Hosna Jabbari	SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles.	WABI	2023	DBLP DOI BibTeX RDF
26	Evangelos Makris, Angelos Kolaitis, Christos Andrikos, Vrettos Moulos, Panayiotis Tsanakas, Christos Pavlatos	An Intelligent Grammar-Based Platform for RNA H-type Pseudoknot Prediction.	AIAI Workshops	2022	DBLP DOI BibTeX RDF
26	Dustyn Eggers, Christian Höner zu Siederdissen, Peter F. Stadler	Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar.	BSB	2022	DBLP DOI BibTeX RDF
26	Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski, Michael T. Woodside	Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
26	Luke Trinity, Lance Lansing, Hosna Jabbari, Ulrike Stege	SARS-CoV-2 Ribosomal Frameshifting Pseudoknot: Detection of Inter-viral Structural Similarity.	ICHI	2021	DBLP DOI BibTeX RDF
26	Tomasz Zok, Jan Badura, Sylwester Swat, Kacper Figurski, Mariusz Popenda, Maciej Antczak	New models and algorithms for RNA pseudoknot order assignment.	Int. J. Appl. Math. Comput. Sci.	2020	DBLP DOI BibTeX RDF
26	Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will	Knotty: efficient and accurate prediction of complex RNA pseudoknot structures.	Bioinform.	2018	DBLP DOI BibTeX RDF
26	Da-Jung Cho, Yo-Sub Han, Timothy Ng 0001, Kai Salomaa	Pseudoknot-generating operation.	Theor. Comput. Sci.	2017	DBLP DOI BibTeX RDF
26	Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will	Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice.	WABI	2017	DBLP DOI BibTeX RDF
26	Da-Jung Cho, Yo-Sub Han, Timothy Ng 0001, Kai Salomaa	Pseudoknot-Generating Operation.	SOFSEM	2016	DBLP DOI BibTeX RDF
26	Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, Martin Mann	antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
26	Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang	Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.	BMC Bioinform.	2015	DBLP DOI BibTeX RDF
26	William B. Langdon, Mark Harman	Grow and Graft a Better CUDA pknotsRG for RNA Pseudoknot Free Energy Calculation.	GECCO (Companion)	2015	DBLP DOI BibTeX RDF
26	Fenix W. D. Huang, Markus E. Nebel, Christian M. Reidys	Uniform generation of RNA pseudoknot structures with genus filtration	CoRR	2013	DBLP BibTeX RDF
26	Jikai Lei, Prapaporn Techa-angkoon, Yanni Sun, Rujira Achawanantakun	ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools.	BCB	2013	DBLP DOI BibTeX RDF
26	Markus E. Nebel, Frank Weinberg	Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications.	J. Comput. Biol.	2012	DBLP DOI BibTeX RDF
26	Qingfeng Chen, Yi-Ping Phoebe Chen	Function Annotation for Pseudoknot Using Structure Similarity.	IEEE ACM Trans. Comput. Biol. Bioinform.	2011	DBLP DOI BibTeX RDF
26	Patricia A. Evans	Finding common RNA pseudoknot structures in polynomial time.	J. Discrete Algorithms	2011	DBLP DOI BibTeX RDF
26	Markus E. Nebel, Christian M. Reidys, Rita R. Wang	Loops in Canonical RNA Pseudoknot Structures.	J. Comput. Biol.	2011	DBLP DOI BibTeX RDF
26	Thomas K. F. Wong, Tak Wah Lam, Wing-Kin Sung, Brenda W. Y. Cheung, Siu-Ming Yiu	Structural Alignment of RNA with Complex Pseudoknot Structure.	J. Comput. Biol.	2011	DBLP DOI BibTeX RDF
26	Thomas K. F. Wong, Hui-Ting Yu, Bay-Yuan Hsu, Tak Wah Lam, Wing-Kai Hon, Siu-Ming Yiu	Algorithms for pseudoknot classification.	BCB	2011	DBLP DOI BibTeX RDF
26	James Z. M. Gao, Linda Y. M. Li, Christian M. Reidys	Inverse folding of RNA pseudoknot structures.	Algorithms Mol. Biol.	2010	DBLP DOI BibTeX RDF
26	Emma Yu Jin, Christian M. Reidys	RNA pseudoknot structures with arc-length >=3 and stack-length >=sigma.	Discret. Appl. Math.	2010	DBLP DOI BibTeX RDF
26	Christian M. Reidys, Rita R. Wang	Shapes of RNA Pseudoknot Structures.	J. Comput. Biol.	2010	DBLP DOI BibTeX RDF
26	Thomas K. F. Wong, Siu-Ming Yiu	Prediction of Minimum Free Energy Structure for Simple Non-standard Pseudoknot.	BIOSTEC (Selected Papers)	2010	DBLP DOI BibTeX RDF
26	Thomas K. F. Wong, Siu-Ming Yiu	Structure Prediction of Simple Non-standard Pseudoknot.	BIOINFORMATICS	2010	DBLP BibTeX RDF
26	Emma Yu Jin, Christian M. Reidys	Combinatorial design of pseudoknot RNA.	Adv. Appl. Math.	2009	DBLP DOI BibTeX RDF
26	Fenix W. D. Huang, Linda Y. M. Li, Christian M. Reidys	Sequence-structure relations of pseudoknot RNA.	BMC Bioinform.	2009	DBLP DOI BibTeX RDF
26	Lila Kari, Shinnosuke Seki	On pseudoknot-bordered words and their properties.	J. Comput. Syst. Sci.	2009	DBLP DOI BibTeX RDF
26	Fenix W. D. Huang, Wade W. J. Peng, Christian M. Reidys	Folding 3-Noncrossing RNA Pseudoknot Structures.	J. Comput. Biol.	2009	DBLP DOI BibTeX RDF
26	Kay C. Wiese, Andrew Hendriks	RNA pseudoknot prediction via an evolutionary algorithm.	IEEE Congress on Evolutionary Computation	2009	DBLP DOI BibTeX RDF
26	Mathias Möhl	Dynamic programming based RNA pseudoknot alignment.		2009	RDF
26	Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg, Liming Cai	Fast and accurate search for non-coding RNA pseudoknot structures in genomes.	Bioinform.	2008	DBLP DOI BibTeX RDF
26	Xuezheng Fu, Hao Wang, Robert W. Harrison, William L. Harrison	A rule-based approach for RNA pseudoknot prediction.	Int. J. Data Min. Bioinform.	2008	DBLP DOI BibTeX RDF
26	Hillary S. W. Han, Christian M. Reidys	Pseudoknot RNA Structures with Arc-Length >= 4.	J. Comput. Biol.	2008	DBLP DOI BibTeX RDF
26	Gang Ma, Christian M. Reidys	Canonical RNA Pseudoknot Structures.	J. Comput. Biol.	2008	DBLP DOI BibTeX RDF
26	Jens Reeder, Peter Steffen, Robert Giegerich	pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.	Nucleic Acids Res.	2007	DBLP DOI BibTeX RDF
26	Lila Kari, Shinnosuke Seki	Towards the Sequence Design Preventing Pseudoknot Formation.	IWNC	2007	DBLP DOI BibTeX RDF
26	Yuki Kato, Hiroyuki Seki, Tadao Kasami	Stochastic Multiple Context-Free Grammar for RNA Pseudoknot Modeling.	TAG	2006	DBLP BibTeX RDF
26	Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara	Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.	Bioinform.	2005	DBLP DOI BibTeX RDF
26	Jens Reeder, Robert Giegerich	Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.	BMC Bioinform.	2004	DBLP DOI BibTeX RDF
26	Rune B. Lyngsø, Christian N. S. Pedersen	RNA Pseudoknot Prediction in Energy-Based Models.	J. Comput. Biol.	2000	DBLP DOI BibTeX RDF
26	Pieter H. Hartel, Marc Feeley, Martin Helmut Alt, Lennart Augustsson, Peter Baumann, Marcel Beemster, Emmanuel Chailloux, Christine H. Flood, Wolfgang Grieskamp, John H. G. van Groningen, Kevin Hammond, Bogumil Hausman, Melody Y. Ivory, Richard E. Jones, Jasper Kamperman, Peter Lee 0001, Xavier Leroy, Rafael Dueire Lins, Sandra Loosemore, Niklas Röjemo, Manuel Serrano, Jean-Pierre Talpin, Jon Thackray, Stephen Thomas, Pum Walters, Pierre Weis, Peter Wentworth	Benchmarking Implementations of Functional Languages with 'Pseudoknot', a Float-Intensive Benchmark.	J. Funct. Program.	1996	DBLP DOI BibTeX RDF
26	Claude Philippe, Lionel Bénard, Claude Portier, E. Westhof, Bernard Ehresmann, Chantal Ehresmann	Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15.	Nucleic Acids Res.	1995	DBLP DOI BibTeX RDF
26	Jih-Hsiang Chen, Shu-Yun Le, Jacob V. Maizel	A procedure for RNA pseudoknot prediction.	Comput. Appl. Biosci.	1992	DBLP DOI BibTeX RDF
19	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
19	Herbert H. Tsang, Kay C. Wiese	SARNA-Predict-pk: Predicting RNA secondary structures including pseudoknots.	CIBCB	2008	DBLP DOI BibTeX RDF
19	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
19	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
19	Markus Bauer 0001, Gunnar W. Klau, Knut Reinert	Multiple Structural RNA Alignment with Lagrangian Relaxation.	WABI	2005	DBLP DOI BibTeX RDF
19	Fariza Tahi, Stefan Engelen, Mireille Régnier	A Fast Algorithm for NA Secondary Structure Prediction Including Pseudoknots.	BIBE	2003	DBLP DOI BibTeX RDF
19	Yuh-Jyh Hu	Mining A Set of Coregulated RNA Sequences.	ICDM	2002	DBLP DOI BibTeX RDF