Human microRNA prediction through a probabilistic co-learning model of sequence and structure
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- @Article{Nam:2005:NAR,
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author = "Jin-Wu Nam and Ki-Roo Shin and Jinju Han and
Yoontae Lee and V. Narry Kim and Byoung-Tak Zhang",
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title = "Human microRNA prediction through a probabilistic
co-learning model of sequence and structure",
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journal = "Nucleic Acids Research",
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year = "2005",
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volume = "33",
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number = "11",
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pages = "3570--3581",
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keywords = "genetic algorithms, genetic programming",
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DOI = "doi:10.1093/nar/gki668",
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abstract = "MicroRNAs (miRNAs) are small regulatory RNAs of ~22
nt. Although hundreds of miRNAs have been identified
through experimental complementary DNA cloning methods
and computational efforts, previous approaches could
detect only abundantly expressed miRNAs or close
homologs of previously identified miRNAs. Here, we
introduce a probabilistic co-learning model for miRNA
gene finding, ProMiR, which simultaneously considers
the structure and sequence of miRNA precursors
(pre-miRNAs). On 5-fold cross-validation with 136
referenced human datasets, the efficiency of the
classification shows 73percent sensitivity and
96percent specificity. When applied to genome screening
for novel miRNAs on human chromosomes 16, 17, 18 and
19, ProMiR effectively searches distantly homologous
patterns over diverse pre-miRNAs, detecting at least 23
novel miRNA gene candidates. Importantly, the miRNA
gene candidates do not demonstrate clear sequence
similarity to the known miRNA genes. By quantitative
PCR followed by RNA interference against Drosha, we
experimentally confirmed that 9 of the 23
representative candidate genes express transcripts that
are processed by the miRNA biogenesis enzyme Drosha in
HeLa cells, indicating that ProMiR may successfully
predict miRNA genes with at least 40percent accuracy.
Our study suggests that the miRNA gene family may be
more abundant than previously anticipated, and confer
highly extensive regulatory networks on eukaryotic
cells.",
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notes = "PMID: Compares with esRCSG \cite{nam:evows04}",
- }
Genetic Programming entries for
Jin-Wu Nam
Ki-Roo Shin
Jinju Han
Yoontae Lee
V Narry Kim
Byoung-Tak Zhang
Citations