In the present study, we demonstrate a tunneling nanogap technique to identify individual RNA nucleotides, which can be used as a mechanism to read the nucleobases for direct sequencing of RNA in a solid-state nanopore. The tunneling nanogap is compo...
RNA sequencing (RNA-seq) is becoming a prevalent approach to quantify gene expression and is expected to gain better insights into a number of biological and biomedical questions compared to DNA microarrays. Most importantly, RNA-seq allows us to qua...
RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these meth...
Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which...
This study examines accurate and efficient computational method for identification of 5-methylcytosine sites in RNA modification. The occurrence of 5-methylcytosine (mC) plays a vital role in a number of biological processes. For better comprehension...
RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, tim...
RNA 5-methylcytosine (mC) is an important post-transcriptional modification that plays an indispensable role in biological processes. The accurate identification of mC sites from primary RNA sequences is especially useful for deeply understanding the...
The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable nature of RNA structure predictions further e...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 7, 2017
Disease gene prediction is a challenging task that has a variety of applications such as early diagnosis and drug development. The existing machine learning methods suffer from the imbalanced sample issue because the number of known disease genes (po...
BACKGROUND: RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs. How the RBPs correctly recog...