MOTIVATION: Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5' and 3' termini of exon(s) can be covalently ligated to form circRNAs through back-splicing (head-to-tail splicing). CircRNA...
With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typi...
MOTIVATION: One of the main challenges in machine learning (ML) is choosing an appropriate normalization method. Here, we examine the effect of various normalization methods on analyzing FPKM upper quartile (FPKM-UQ) RNA sequencing data sets. We coll...
Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task....
N 6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotes, and plays a pivotal role in various biological processes, such as splicing, RNA degradation and RNA-protein interaction. We report here a prediction fram...
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
Database : the journal of biological databases and curation
Jan 1, 2019
Next-generation sequencing technologies and the availability of an increasing number of mammalian and other genomes allow gene expression studies, particularly RNA sequencing, in many non-model organisms. However, incomplete genome annotation and ass...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2019
BACKGROUND: MicroRNAs (miRNAs) are small, non-coding RNA that regulate gene expression through post-transcriptional silencing. Differential expression observed in miRNAs, combined with advancements in deep learning (DL), have the potential to improve...
The current deluge of newly identified RNA transcripts presents a singular opportunity for improved assessment of coding potential, a cornerstone of genome annotation, and for machine-driven discovery of biological knowledge. While traditional, featu...
SUMMARY: Pathway analysis of alternative splicing would be biased without accounting for the different number of exons or junctions associated with each gene, because genes with higher number of exons or junctions are more likely to be included in th...
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