MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...
Long non-coding RNAs (lncRNAs) played essential roles in nearly every biological process and disease. Many algorithms were developed to distinguish lncRNAs from mRNAs in transcriptomic data and facilitated discoveries of more than 600 000 of lncRNAs....
MOTIVATION: Recent experimental evidence has shown that some long non-coding RNAs (lncRNAs) contain small open reading frames (sORFs) that are translated into functional micropeptides, suggesting that these lncRNAs are misannotated as non-coding. Cur...
As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification...
The increasing amount of transcriptomic data has brought to light vast numbers of potential novel RNA transcripts. Accurately distinguishing novel long non-coding RNAs (lncRNAs) from protein-coding messenger RNAs (mRNAs) has challenged bioinformatic ...
In biomedical networks, molecular associations are important to understand biological processes and functions. Many computational methods, such as link prediction methods based on graph neural networks (GNNs), have been successfully applied in discov...
Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. A growing amount of evidence reveals that subcellular localization of lncRNAs can provide valuable insights into their biological functions. Existing computat...
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncR...
LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. Since it was built based on MediaWiki as its database system, it fails to manage data in a structur...
As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems,...