Predicting RNA secondary structure based on the class information and Hopfield network

[1]  Yin Zhang,et al.  A Discrete Hopfield Neural Network Based MIS Finding Algorithm for Stems Selecting and Its Application in RNA Secondary Structure Prediction: A Discrete Hopfield Neural Network Based MIS Finding Algorithm for Stems Selecting and Its Application in RNA Secondary Structure Prediction , 2009 .

[2]  Peter F. Stadler,et al.  SnoReport: computational identification of snoRNAs with unknown targets , 2008, Bioinform..

[3]  Liu Qi.  A Discrete Hopfield Neural Network Based MIS Finding Algorithm for Stems Selecting and Its Application in RNA Secondary Structure Prediction , 2008 .

[4]  Andrew Hendriks,et al.  RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction , 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[5]  Peng Jiang,et al.  MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features , 2007, Nucleic Acids Res..

[6]  Yanga Byun,et al.  PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures , 2006, Nucleic Acids Res..

[7]  Andrew Hendriks,et al.  Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction , 2006, Bioinform..

[8]  Kaizhong Zhang,et al.  RNA Secondary Structure Prediction Via Energy Density Minimization , 2006, RECOMB.

[9]  Fei Li,et al.  Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine , 2005, BMC Bioinformatics.

[10]  Maozu Guo,et al.  A Permutation-Based Genetic Algorithm for Predicting RNA Secondary Structure-A Practicable Approach , 2005, FSKD.

[11]  Rolf Backofen,et al.  Backofen R: MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons , 2005 .

[12]  Yi Zhao,et al.  NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..

[13]  Sean R. Eddy,et al.  Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..

[14]  Robert Giegerich,et al.  A comprehensive comparison of comparative RNA structure prediction approaches , 2004, BMC Bioinformatics.

[15]  Peter F. Stadler,et al.  Alignment of RNA base pairing probability matrices , 2004, Bioinform..

[16]  J. Clarke,et al.  Atomic force microscopy: mechanical unfolding of proteins. , 2004, Methods.

[17]  D. Mathews.  Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.

[18]  Hélène Touzet,et al.  CARNAC: folding families of related RNAs , 2004, Nucleic Acids Res..

[19]  Sean R. Eddy,et al.  Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction , 2004, BMC Bioinformatics.

[20]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  K. Wiese,et al.  A permutation-based genetic algorithm for the RNA folding problem: a critical look at selection strategies, crossover operators, and representation issues. , 2003, Bio Systems.

[22]  C. Hammann.  Web Site: RNA for everyone! The RNA World Website at IMB Jena , 2003 .

[23]  Bjarne Knudsen,et al.  Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .

[24]  Hélène Touzet,et al.  Finding the common structure shared by two homologous RNAs , 2003, Bioinform..

[25]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[26]  Yuh-Jyh Hu.  Prediction of consensus structural motifs in a family of coregulated RNA sequences. , 2002, Nucleic acids research.

[27]  Kyungsook Han,et al.  PseudoViewer: automatic visualization of RNA pseudoknots , 2002, ISMB.

[28]  G. Stormo,et al.  Discovering common stem-loop motifs in unaligned RNA sequences. , 2001, Nucleic acids research.

[29]  Jin Chu Wu,et al.  The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation , 2001, Bioinform..

[30]  Daniel J. Müller,et al.  Observing single biomolecules at work with the atomic force microscope , 2000, Nature Structural Biology.

[31]  J. Zlatanova,et al.  Single molecule force spectroscopy in biology using the atomic force microscope. , 2000, Progress in biophysics and molecular biology.

[32]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[33]  S. Le,et al.  Prediction of common secondary structures of RNAs: a genetic algorithm approach. , 2000, Nucleic acids research.

[34]  Christian N. S. Pedersen,et al.  Fast evaluation of internal loops in RNA secondary structure prediction , 1999, Bioinform..

[35]  Bjarne Knudsen,et al.  RNA secondary structure prediction using stochastic context-free grammars and evolutionary history , 1999, Bioinform..

[36]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[37]  Peter F. Stadler,et al.  RNA In Silico The Computational Biology of RNA Secondary Structures , 1999, Adv. Complex Syst..

[38]  James W. Brown.  The ribonuclease P database , 1998, Nucleic Acids Res..

[39]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[40]  Y Takefuji,et al.  Comments on 'Parallel algorithms for finding a near-maximum independent set of a circle graph' [with reply] , 1991, IEEE Trans. Neural Networks.

[41]  Yoshiyasu Takefuji,et al.  Parallel algorithms for finding a near-maximum independent set of a circle graph , 1990, IEEE Trans. Neural Networks.

[42]  M. Zuker.  On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[43]  Stephen Grossberg,et al.  Absolute stability of global pattern formation and parallel memory storage by competitive neural networks , 1983, IEEE Transactions on Systems, Man, and Cybernetics.

[44]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..