Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data

Soheila Montaseri; Mohammad Ganjtabesh; Fatemeh Zare-Mirakabad

doi:10.1371/journal.pone.0166965

Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data

PLoS ONE ◽

10.1371/journal.pone.0166965 ◽

2016 ◽

Vol 11 (11) ◽

pp. e0166965 ◽

Cited By ~ 4

Author(s):

Soheila Montaseri ◽

Mohammad Ganjtabesh ◽

Fatemeh Zare-Mirakabad

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Shape Data

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Impact of an enhanced thermodynamic model on RnaPredict, an evolutionary algorithm for RNA secondary structure prediction

2009 IEEE Congress on Evolutionary Computation ◽

10.1109/cec.2009.4983306 ◽

2009 ◽

Cited By ~ 2

Author(s):

Kay C. Wiese ◽

Andrew G. Hendriks

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Thermodynamic Model ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction

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Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures

Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753) ◽

10.1109/cec.2004.1330912 ◽

2004 ◽

Cited By ~ 13

Author(s):

A. Deschenes ◽

K.C. Wiese

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction

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RNA secondary structure prediction based on SHAPE data in helix regions

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2015.05.026 ◽

2015 ◽

Vol 380 ◽

pp. 178-182 ◽

Cited By ~ 4

Author(s):

Mohadeseh Lotfi ◽

Fatemeh Zare-Mirakabad ◽

Soheila Montaseri

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Shape Data

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Multimodal Optimization Evolutionary Algorithm for RNA Secondary Structure Prediction

The Fifth International Conference on Biological Information and Biomedical Engineering ◽

10.1145/3469678.3469714 ◽

2021 ◽

Author(s):

Yunfei Hu ◽

Kai Zhang

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Multimodal Optimization ◽

Rna Secondary Structure Prediction

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A Detailed Analysis of Parallel Speedup in P-RnaPredict - An Evolutionary Algorithm for RNA Secondary Structure Prediction

2006 IEEE International Conference on Evolutionary Computation ◽

10.1109/cec.2006.1688595 ◽

2006 ◽

Author(s):

K.C. Wiese ◽

A. Hendriks

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Detailed Analysis ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Parallel Speedup

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A parallel evolutionary algorithm for RNA secondary structure prediction using stacking-energies (INN and INN-HB)

IGARSS 2004 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat No 04CH37612) CIBCB-04 ◽

10.1109/cibcb.2004.1393957 ◽

2005 ◽

Cited By ~ 4

Author(s):

A. Hendriks ◽

A. Deschenes ◽

K.C. Wiese

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Parallel Evolutionary Algorithm

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RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2007.1054 ◽

2008 ◽

Vol 5 (1) ◽

pp. 25-41 ◽

Cited By ~ 39

Author(s):

K.C. Wiese ◽

A.A. Deschenes ◽

A.G. Hendriks

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction

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Faculty Opinions recommendation of COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718010599.793476797 ◽

2013 ◽

Author(s):

Scott Silverman

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Prediction Method ◽

Rna Secondary Structure Prediction ◽

Structure Prediction Method ◽

Secondary Structure Prediction Method

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A Discrete Hopfield Neural Network Based MIS Finding Algorithm for Stems Selecting and Its Application in RNA Secondary Structure Prediction

Chinese Journal of Computers ◽

10.3724/sp.j.1016.2008.00051 ◽

2009 ◽

Vol 31 (1) ◽

pp. 51-58

Author(s):

Qi LIU ◽

Yin ZHANG ◽

Xiu-Zi YE ◽

Rong-Dong YU

Keyword(s):

Neural Network ◽

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Hopfield Neural Network ◽

Rna Secondary Structure Prediction

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A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

RNA ◽

10.1261/rna.030049.111 ◽

2011 ◽

Vol 18 (2) ◽

pp. 193-212 ◽

Cited By ~ 50

Author(s):

E. Rivas ◽

R. Lang ◽

S. R. Eddy

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Probabilistic Models ◽

Nearest Neighbor ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction

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