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Accurate prediction of human miRNA targets via graph modeling of miRNA-target duplex

miRNAs are short sequences involved in regulating many critical cell activities such as proliferation, differentiation, cell death, growth control and developmental timing. To function, miRNAs bind to certain target locations in mRNAs that they regulate. There is a lack of experimental data about the tertiary structure of miRNAtarget binding duplexes. Correlations of nucleotides in the binding duplexes, not limited to canonical Watson Crick and the wobble base pairs, may carry information about how the bindings occur, especially where the targets are in the mRNAs. In this work, we modeled miRNA binding duplexes with a weighted bipartite graph, called a Correlation Graph, to capture the correlation between pairs of nucleotides appearing on a miRNA and its target sequences.