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Background Ubiquitination, which is also called “lysine ubiquitination”, occurs when an ubiquitin is attached to lysine (K) residues in targeting proteins. As one of the most important post translational modifications (PTMs), it plays the significant role not only in protein degradation, but also in other cellular functions. Thus, systematic anatomy of the ubiquitination proteome is an appealing and...
Background Small interfering RNA (siRNA) can be used to post-transcriptional gene regulation by knocking down targeted genes. In functional genomics, biomedical research and cancer therapeutics, siRNA design is a critical research topic. Various computational algorithms have been developed to select the most effective siRNA, whereas the efficacy prediction accuracy is not so satisfactory. Many existing...
In eukaryotes, protein ubiquitylation is an important type of post-translation modification, in which the ubiquitin conjugates to a substrate protein. To have a better insight of the mechanisms underlying ubiquitylation, a key step is to identify protein ubiquitylation sites. Many existing computational methods are based on feature engineering, which may lead to biased and incomplete features. Deep...
In functional genomics, small interfering RNA (siRNA) can be used to knockdown gene expression. Usually, a target gene has numerous potential siRNAs, but their efficiencies of gene silencing often varies. Thus, for a successful RNA interference (RNAi), selecting the most effective siRNA is a critical step. Despite various computational algorithms have been developed, the efficacy prediction accuracy...
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