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{"title"=>"MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern", "type"=>"journal", "authors"=>[{"first_name"=>"Wei", "last_name"=>"Shen", "scopus_author_id"=>"55574196327"}, {"first_name"=>"Ming", "last_name"=>"Chen", "scopus_author_id"=>"7406351617"}, {"first_name"=>"Guo", "last_name"=>"Wei", "scopus_author_id"=>"57199964386"}, {"first_name"=>"Yan", "last_name"=>"Li", "scopus_author_id"=>"57190386888"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84868135408", "sgr"=>"84868135408", "pui"=>"365953512", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"23118959", "doi"=>"10.1371/journal.pone.0048236"}, "id"=>"515532de-c142-3a77-a606-9fbf4a4a12b7", "abstract"=>"Predicting miRNAs is an arduous task, due to the diversity of the precursors and complexity of enzyme processes. Although several prediction approaches have reached impressive performances, few of them could achieve a full-function recognition of mature miRNA directly from the candidate hairpins across species. Therefore, researchers continue to seek a more powerful model close to biological recognition to miRNA structure. In this report, we describe a novel miRNA prediction algorithm, known as FOMmiR, using a fixed-order Markov model based on the secondary structural pattern. For a training dataset containing 809 human pre-miRNAs and 6441 human pseudo-miRNA hairpins, the model's parameters were defined and evaluated. The results showed that FOMmiR reached 91% accuracy on the human dataset through 5-fold cross-validation. Moreover, for the independent test datasets, the FOMmiR presented an outstanding prediction in human and other species including vertebrates, Drosophila, worms and viruses, even plants, in contrast to the well-known algorithms and models. Especially, the FOMmiR was not only able to distinguish the miRNA precursors from the hairpins, but also locate the position and strand of the mature miRNA. Therefore, this study provides a new generation of miRNA prediction algorithm, which successfully realizes a full-function recognition of the mature miRNAs directly from the hairpin sequences. And it presents a new understanding of the biological recognition based on the strongest signal's location detected by FOMmiR, which might be closely associated with the enzyme cleavage mechanism during the miRNA maturation.", "link"=>"http://www.mendeley.com/research/microrna-prediction-using-fixedorder-markov-model-based-secondary-structure-pattern-1", "reader_count"=>22, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>7, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>7, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>18}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>18}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "United States"=>1}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pone.0182629
• http://doi.org/10.1093/nar/gkx1115
• http://doi.org/10.3389/fgene.2020.00765
• http://doi.org/10.1371/journal.pone.0098263
• http://doi.org/10.1007/s12539-017-0223-x
• http://doi.org/10.1002/jmv.25505
• http://doi.org/10.5812/gct.103096
• http://doi.org/10.1142/S0219720013430099
• http://doi.org/10.1002/jcb.29367

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• {"id"=>"263386029845786624", "text"=>"MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern http://t.co/DSl2CX4U", "created_at"=>"2012-10-30T21:04:57Z", "user"=>"TestAllPLoSRSS", "user_name"=>"TestAllPLoSRSS", "user_profile_image"=>"http://a0.twimg.com/sticky/default_profile_images/default_profile_0_normal.png"}
• {"id"=>"263660200655986688", "text"=>"Mature miRNA recognition: MicroRNA prediction using a fixed-order markov model based on the secondary structure pattern http://t.co/L2zDgs4P", "created_at"=>"2012-10-31T15:14:25Z", "user"=>"BiomedRevon", "user_name"=>"mvelst@gmail.com", "user_profile_image"=>"http://a0.twimg.com/profile_images/1518893315/Arcimboldo_Librarian_Stokholm_normal.jpg"}

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Figshare

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• {"files"=>["https://ndownloader.figshare.com/files/552313"], "description"=>"<p>Distribution of the signal scores in positive and negative datasets.</p>", "links"=>[], "tags"=>["scores"], "article_id"=>222809, "categories"=>["Biological Sciences"], "users"=>["Wei Shen", "Ming Chen", "Guo Wei", "Yan Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048236.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_signal_scores_in_positive_and_negative_datasets_/222809", "title"=>"Distribution of the signal scores in positive and negative datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:09:13"}
• {"files"=>["https://ndownloader.figshare.com/files/552387"], "description"=>"<p>Receiver Operating Characteristic Curve of FOMmiR predictor.</p>", "links"=>[], "tags"=>["fommir"], "article_id"=>222884, "categories"=>["Biological Sciences"], "users"=>["Wei Shen", "Ming Chen", "Guo Wei", "Yan Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048236.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Receiver_Operating_Characteristic_Curve_of_FOMmiR_predictor_/222884", "title"=>"Receiver Operating Characteristic Curve of FOMmiR predictor.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:09:36"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime