Search results for "RNA"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
136	Yujin Lee, Wootaek Kim, Kyungsook Han	New Representation and Algorithm for Drawing RNA Structure with Pseudoknots.	DaWaK	2002	DBLP DOI BibTeX RDF
134	Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato	Stem Kernels for RNA Sequence Analyses.	BIRD	2007	DBLP DOI BibTeX RDF	stem kernel, SVM, secondary structure, RNA, string kernel
131	Rojan Shrestha, Jisu Kim, Kyungsook Han	Prediction of RNA-Binding Residues in Proteins Using the Interaction Propensities of Amino Acids and Nucleotides.	ICIC (1)	2008	DBLP DOI BibTeX RDF	RNA-binding residues, protein-RNA interactions, support vector machine
116	Namshik Han, Hyunwoo Kim, Kyungsook Han	Computational Approach to Structural Analysis of Protein-RNA Complexes.	International Conference on Computational Science	2003	DBLP DOI BibTeX RDF
112	Shu-Yun Le, Jacob V. Maizel Jr., Kaizhong Zhang	An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes.	CSB	2004	DBLP DOI BibTeX RDF	RNA structure similarity, homologous structural RNA search, pattern recognition
107	Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang	RNA-RNA Interaction Prediction and Antisense RNA Target Search.	RECOMB	2005	DBLP DOI BibTeX RDF
107	Vineet Bafna, Haixu Tang, Shaojie Zhang	Consensus Folding of Unaligned RNA Sequences Revisited.	RECOMB	2005	DBLP DOI BibTeX RDF
107	Xuezheng Fu, Hao Wang, William L. Harrison, Robert W. Harrison	RNA Pseudoknot Prediction Using Term Rewriting.	BIBE	2005	DBLP DOI BibTeX RDF
107	Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara	Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures.	CSB	2004	DBLP DOI BibTeX RDF
102	Xiaoyong Fang, Zhigang Luo, Zhenghua Wang, Bo Yuan, Jinlong Shi	A Seed-Based Method for Predicting Common Secondary Structures in Unaligned RNA Sequences.	MDAI	2007	DBLP DOI BibTeX RDF	seed-based, unaligned RNA sequences, RNA secondary structure
97	Yelena Frid, Dan Gusfield	A Simple, Practical and Complete O(\fracn3 logn)O(\frac{n^3}{ \log n})-Time Algorithm for RNA Folding Using the Four-Russians Speedup.	WABI	2009	DBLP DOI BibTeX RDF
97	Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler	RNA Secondary Structure Prediction Via Energy Density Minimization.	RECOMB	2006	DBLP DOI BibTeX RDF
95	Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fangfang Pan, Liming Cai	Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes.	CSB	2005	DBLP DOI BibTeX RDF	RNA secondary structure profiling, Pseudo-knot search, Covariance model, Tree decomposition
87	Daeho Lim, Kyungsook Han	Mining RNA Structure Elements from the Structure Data of Protein-RNA Complexes.	Discovery Science	2003	DBLP DOI BibTeX RDF
87	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
87	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
87	Matthias Höchsmann, Björn Voss, Robert Giegerich	Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach.	IEEE ACM Trans. Comput. Biol. Bioinform.	2004	DBLP DOI BibTeX RDF
85	Xiaoyong Fang, Zhigang Luo, Zhenghua Wang	Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis.	J. Comput. Sci. Technol.	2008	DBLP DOI BibTeX RDF	phylogenic analysis, RNA secondary structure, stochastic context-free grammar
83	Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang	PMFastR: A New Approach to Multiple RNA Structure Alignment.	WABI	2009	DBLP DOI BibTeX RDF	multiple RNA alignment, RNA sequence-structure alignment, iterative alignment
78	Shibin Qiu, Terran Lane	The RNA String Kernel for siRNA Efficacy Prediction.	BIBE	2007	DBLP DOI BibTeX RDF
78	Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, Abel Licon	RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology.	IPDPS	2007	DBLP DOI BibTeX RDF
78	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
78	Daeho Lim, Kyungsook Han	PairAnalyzer: Extracting and Visualizing RNA Structure Elements Formed by Base Pairing.	International Conference on Computational Science	2004	DBLP DOI BibTeX RDF
78	Wootaek Kim, Yujin Lee, Kyungsook Han	Visualization of RNA Pseudoknot Structures.	VECPAR	2002	DBLP DOI BibTeX RDF
75	Carsten Maus	Component-Based Modelling of RNA Structure Folding.	CMSB	2008	DBLP DOI BibTeX RDF	RNA folding, model components, DEVS, secondary structure, multi-level
75	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
75	Eli Hershkovitz, Guillermo Sapiro, Allen R. Tannenbaum, Loren Dean Williams	Statistical Analysis of RNA Backbone.	IEEE ACM Trans. Comput. Biol. Bioinform.	2006	DBLP DOI BibTeX RDF	RNA backbone, local conformations, torsion angles, conformational motifs, statistical analysis, vector quantization
75	Gilles Bailly, Laurence Nigay, David Auber	NAVRNA: visualization - exploration - editing of RNA.	AVI	2006	DBLP DOI BibTeX RDF	distributed display environment, visualization, tabletop display, two-handed interaction, RNA structure
68	Kejie Li, Reazur Rahman, Aditi Gupta 0001, Prasad Siddavatam, Michael Gribskov	Pattern Matching in RNA Structures.	ISBRA	2008	DBLP DOI BibTeX RDF
68	Herbert H. Tsang, Kay C. Wiese	SARNA-Predict-pk: Predicting RNA secondary structures including pseudoknots.	CIBCB	2008	DBLP DOI BibTeX RDF
68	Xinyu Tang, Shawna L. Thomas, Lydia Tapia, Nancy M. Amato	Tools for Simulating and Analyzing RNA Folding Kinetics.	RECOMB	2007	DBLP DOI BibTeX RDF
68	Hiroshi Sankoh, Koichiro Doi, Akihiro Yamamoto	An Intentional Kernel Function for RNA Classification.	Discovery Science	2007	DBLP DOI BibTeX RDF
68	Xiaoyong Fang, Zhigang Luo, Bo Yuan, Zhenghua Wang	Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences.	BIBE	2007	DBLP DOI BibTeX RDF
68	Mohammad Anwar, Marcel Turcotte	Evaluation of RNA Secondary Structure Motifs using Regression Analysis.	CCECE	2006	DBLP DOI BibTeX RDF
68	Oriel Bergig, Danny Barash, Klara Kedem	RNA Motif Search Using the Structure to String (STR2) Method.	CSB	2004	DBLP DOI BibTeX RDF
68	Christine E. Heitsch, Anne Condon, Holger H. Hoos	From RNA Secondary Structure to Coding Theory: A Combinatorial Approach.	DNA	2002	DBLP DOI BibTeX RDF
68	Guohui Lin, Bin Ma 0002, Kaizhong Zhang	Edit distance between two RNA structures.	RECOMB	2001	DBLP DOI BibTeX RDF
66	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
66	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
64	Vineet Bafna, Shaojie Zhang	FastR: Fast Database Search Tool for Non-Coding RNA.	CSB	2004	DBLP DOI BibTeX RDF	non-coding RNA genes, dynamic programming, sequence alignment, RNA, filtration, database search
63	Xiaoyong Fang, Zhenghua Wang, Zhigang Luo, Bo Yuan, Fan Ding	The detection and assessment of possible RNA secondary structure using multiple sequence alignment.	SAC	2007	DBLP DOI BibTeX RDF	multiple sequence alignment, RNA secondary structure, non-coding RNA
59	Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel 0002, Peter F. Stadler, Ivo L. Hofacker	Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics.	BIRD	2008	DBLP DOI BibTeX RDF
58	Kay C. Wiese, Edward Glen	jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots.	CBMS	2006	DBLP DOI BibTeX RDF
58	Kay C. Wiese, Andrew Hendriks	A hybrid clustering/evolutionary algorithm for RNA folding.	CIBCB	2008	DBLP DOI BibTeX RDF
58	Herbert H. Tsang, Kay C. Wiese	The significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.	IEEE Congress on Evolutionary Computation	2007	DBLP DOI BibTeX RDF
58	Jean-Eudes Duchesne, Mathieu Giraud, Nadia El-Mabrouk	Seed-Based Exclusion Method for Non-coding RNA Gene Search.	COCOON	2007	DBLP DOI BibTeX RDF
58	Xueyi Wang, Jun Huan, Jack Snoeyink, Wei Wang 0010	Mining RNA Tertiary Motifs with Structure Graphs.	SSDBM	2007	DBLP DOI BibTeX RDF
58	Xiaoyong Fang, Zhigang Luo, Bo Yuan, Zhenghua Wang, Fan Ding	Constructing Structural Alignment of RNA Sequences by Detecting and Assessing Conserved Stems.	LSMS (2)	2007	DBLP DOI BibTeX RDF
58	Markus Bauer 0001, Gunnar W. Klau, Knut Reinert	Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization.	CompLife	2005	DBLP DOI BibTeX RDF
58	Tong Liu, Bertil Schmidt	Parallel RNA Sequence-Structure Alignment.	IPDPS	2004	DBLP DOI BibTeX RDF
58	Zhuozhi Wang, Kaizhong Zhang	Multiple RNA Structure Alignment.	CSB	2004	DBLP DOI BibTeX RDF
58	Kay C. Wiese, Edward Glen	RNA Structure as Permutation: A GA Approach Comparing Different Genetic Sequencing Operators.	ISMIS	2003	DBLP DOI BibTeX RDF	Evolutionary Computation, Bioinformatics, Soft Computing
58	Matthias Höchsmann, Thomas Töller, Robert Giegerich, Stefan Kurtz	Local Similarity in RNA Secondary Structures.	CSB	2003	DBLP DOI BibTeX RDF
58	Giulio Pavesi, Giancarlo Mauri, Graziano Pesole	Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences.	ICTAI	2003	DBLP DOI BibTeX RDF
58	Barry Cohen, Steven Skiena	Designing RNA structures: natural and artificial selection.	RECOMB	2002	DBLP DOI BibTeX RDF
58	Rune B. Lyngsø, Christian N. S. Pedersen	Pseudoknots in RNA secondary structures.	RECOMB	2000	DBLP DOI BibTeX RDF
57	Étienne Ogoubi, David Pouliot, Marcel Turcotte, Abdelhakim Hafid	Parallel Multiprocessor Approaches to the RNA Folding Problem.	PPAM	2007	DBLP DOI BibTeX RDF	message passing, folding, parallel computer architecture, secondary structure, RNA
57	Xinyu Tang, Bonnie Kirkpatrick, Shawna L. Thomas, Guang Song, Nancy M. Amato	Using motion planning to study RNA folding kinetics.	RECOMB	2004	DBLP DOI BibTeX RDF	folding kinetics, motion planning, RNA
56	Jennifer A. Smith 0001	RNA Search with Decision Trees and Partial Covariance Models.	IEEE ACM Trans. Comput. Biol. Bioinform.	2009	DBLP DOI BibTeX RDF	covariance models, RNA database search, decision trees, Bioinformatics, computational intelligence
56	Mario Alberto Garcia Martinez, Rubén Posada-Gómez, Giner Alor-Hernández	Novel Architecture for RNA Secondary Structure Prediction.	IDEAL	2009	DBLP DOI BibTeX RDF	RNA-problem, FPGA, hardware implementation, secondary structure
56	Shu-Yun Le, Jih-Hsiang Chen	Statistical Inference on Distinct RNA Stem-Loops in Genomic Sequences.	BIRD	2007	DBLP DOI BibTeX RDF	well-ordered RNA structure, microRNA stem-loops, dynamic programming, statistical inference
56	Guillaume Blin, Guillaume Fertin, Gaël Herry, Stéphane Vialette	Comparing RNA Structures: Towards an Intermediate Model Between the Editand the LapcsProblems.	BSB	2007	DBLP DOI BibTeX RDF	arc-annotated sequences, motif extraction, RNA structures
56	Tetsuo Shibuya	Generalization of a Suffix Tree for RNA Structural Pattern Matching.	Algorithmica	2004	DBLP DOI BibTeX RDF	Suffix tree generalization, Parameterized suffix tree, RNA structure matching, Pattern matching, Computational biology
53	Scott F. Smith 0002	A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA.	ISBRA	2007	DBLP DOI BibTeX RDF	functional RNA, covariance models, dynamic programming, database search, gene finding, Non-coding RNA
49	Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar	RNA Pseudoknot Folding through Inference and Identification Using TAGRNA.	BICoB	2009	DBLP DOI BibTeX RDF
49	Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Vandanaben Patel, Marvin K. Nakayama	Constrained RNA Structural Alignment: Algorithms and Application to Motif Detection in the Untranslated Regions of Trypanosoma brucei mRNAs.	BIBE	2007	DBLP DOI BibTeX RDF
49	Mugdha Khaladkar, Jason T. L. Wang	Detecting Conserved RNA Secondary Structures in Viral Genomes: The RADAR Approach.	BioSurveillance	2007	DBLP DOI BibTeX RDF
49	Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann	Local Alignment of RNA Sequences with Arbitrary Scoring Schemes.	CPM	2006	DBLP DOI BibTeX RDF
49	Patricia A. Evans	Finding Common RNA Pseudoknot Structures in Polynomial Time.	CPM	2006	DBLP DOI BibTeX RDF
49	Gilles Bailly, David Auber, Laurence Nigay	From Visualization to Manipulation of RNA Secondary and Tertiary Structures.	IV	2006	DBLP DOI BibTeX RDF	bioinformtics, multi-surface interaction, graph drawing, two-handed interaction, multiple cursors
49	Zhuozhi Wang, Elisabeth R. M. Tillier	A Bayesian approach to pairwise RNA Secondary Structure Alignment.	CIBCB	2006	DBLP DOI BibTeX RDF
49	Carlos A. M. Del Carpio, Mohamed Ismael, Eiichiro Ichiishi, Michihisa Koyama, Momoji Kubo, Akira Miyamoto	An Evolving Automaton for RNA Secondary Structure Prediction.	IJCNN	2006	DBLP DOI BibTeX RDF
49	Qi Liu, Xiuzi Ye, Yin Zhang 0006	A Hopfield Neural Network Based Algorithm for RNA Secondary Structure Prediction.	IMSCCS (1)	2006	DBLP DOI BibTeX RDF
49	Wenduo Zhou, David K. Lowenthal	A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction.	ICPP	2006	DBLP DOI BibTeX RDF
49	Jizhen Zhao, Russell L. Malmberg, Liming Cai	Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition.	WABI	2006	DBLP DOI BibTeX RDF
49	Markus Bauer 0001, Gunnar W. Klau	Structural Alignment of Two RNA Sequences with Lagrangian Relaxation.	ISAAC	2004	DBLP DOI BibTeX RDF
49	Richard F. Meraz, Xiaofeng He, Chris H. Q. Ding, Stephen R. Holbrook	Positive Sample Only Learning (PSOL) for Predicting RNA Genes in E. coli.	CSB	2004	DBLP DOI BibTeX RDF
49	Dongkyu Lee, Kyungsook Han	A Genetic Algorithm for Inferring Pseudoknotted RNA Structures from Sequence Data.	Discovery Science	2003	DBLP DOI BibTeX RDF
49	Phillip A. Sharp	RNA biology and the genome (abstract only).	RECOMB	2001	DBLP DOI BibTeX RDF
49	Zhuozhi Wang, Kaizhong Zhang	Alignment between Two RNA Structures.	MFCS	2001	DBLP DOI BibTeX RDF
49	Kaizhong Zhang, Lusheng Wang 0001, Bin Ma 0002	Computing Similarity between RNA Structures.	CPM	1999	DBLP DOI BibTeX RDF
48	Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar	Pseudoknot Identification through Learning TAGRNA.	PRIB	2008	DBLP DOI BibTeX RDF
48	Rna Ghallab, Mona Shokair, Atef E. Abou-El-azm, Ali A. Sakr, Waleed Saad, Ahmed Naguib	Performance enhancement using multiple-input multiple-output (MIMO) electronic relay in massive MIMO cellular networks.	IET Networks	2019	DBLP DOI BibTeX RDF
48	Rna Ghallab, Ali A. Sakr, Mona Shokair, Atef E. Abou-El-azm	Electronic relay performance in the inband device-to-device (D2D) communication system.	Telecommun. Syst.	2019	DBLP DOI BibTeX RDF
47	Yong Dou, Fei Xia, Jingfei Jiang	Fine-grained parallel application specific computing for RNA secondary structure prediction using SCFGS on FPGA.	CASES	2009	DBLP DOI BibTeX RDF	SCFGS, reconfigurable algorithm accelerator, secondary structure prediction, FPGA, RNA
47	Guillaume Rizk, Dominique Lavenier	GPU Accelerated RNA Folding Algorithm.	ICCS (1)	2009	DBLP DOI BibTeX RDF	minimum free energy, GPGPU, secondary structure, RNA
47	Weijia Xu, Stuart Ozer, Robin Ray Gutell	Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.	SSDBM	2009	DBLP DOI BibTeX RDF	Bioinformatics, Sequence Analysis, RNA, Biological database
47	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
47	Julien Allali, Marie-France Sagot	A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison.	SPIRE	2005	DBLP DOI BibTeX RDF	Graph layers, graph comparison, edit distance, secondary structure, RNA
47	Gerald Gainant, David Auber	ARNA: Interactive Comparison and Alignment of RNA Secondary Structure.	INFOVIS	2004	DBLP DOI BibTeX RDF	visualization, bioinformatics, graph drawing, sequence alignment, combinatorics, RNA
47	Julien Allali, Marie-France Sagot	Novel Tree Edit Operations for RNA Secondary Structure Comparison.	WABI	2004	DBLP DOI BibTeX RDF	edit operation, distance, secondary structure, RNA, tree comparison
46	Hengwu Li	Approximation algorithm and scheme for RNA structure prediction.	ICIS	2009	DBLP DOI BibTeX RDF	approximation algorithm, approximation scheme, RNA structure, pseudoknot
46	Kay C. Wiese, Alain Deschênes, Andrew Hendriks	RnaPredict-An Evolutionary Algorithm for RNA Secondary Structure Prediction.	IEEE ACM Trans. Comput. Biol. Bioinform.	2008	DBLP DOI BibTeX RDF	RnaPredict, Evolutionary Computation, RNA Secondary Structure Prediction
46	Matthias Zytnicki, Christine Gaspin, Thomas Schiex	DARN! A Weighted Constraint Solver for RNA Motif Localization.	Constraints An Int. J.	2008	DBLP DOI BibTeX RDF	DARN, RNA motif localization, ncRNA
46	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
46	Dandan Song, Zhidong Deng	A fuzzy model of predicting RNA secondary structure.	Sci. China Ser. F Inf. Sci.	2007	DBLP DOI BibTeX RDF	fuzzy dynamic programming, fuzzy model, RNA secondary structure
46	Sergey Bereg, Marcin Kubica, Tomasz Walen, Binhai Zhu	RNA multiple structural alignment with longest common subsequences.	J. Comb. Optim.	2007	DBLP DOI BibTeX RDF	RNA multiple structure alignment, Dynamic programming, Longest common subsequence
46	Guillaume Blin, Guillaume Fertin, Irena Rusu, Christine Sinoquet	Extending the Hardness of RNA Secondary Structure Comparison.	ESCAPE	2007	DBLP DOI BibTeX RDF	arc-annotated sequences, NP-hardness, computational biology, edit distance, RNA structures
46	Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna	Searching Genomes for Noncoding RNA Using FastR.	IEEE ACM Trans. Comput. Biol. Bioinform.	2005	DBLP DOI BibTeX RDF	Noncoding RNA, riboswitch, bacterial genome, filtration, database search
46	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