Related papers: Systematic identification of abundant A-to-I editi…
A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues.…
A-To-I RNA editing is common to all eukaryotes, associated with various neurological functions. Recently, A-to-I editing was found to occur abundantly in the human transcriptome. Here we show that the frequency of A-to-I editing in humans…
A number of recent studies have hypothesized that sense-antisense RNA transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA editing. Here we studied human and mouse genomic antisense regions, and found that the editing…
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing…
Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome. Results: We compiled…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is…
Human genetic diseases often arise from point mutations, emphasizing the critical need for precise genome editing techniques. Among these, base editing stands out as it allows targeted alterations at the single nucleotide level. However,…
Human genetic diseases often arise from point mutations, emphasizing the critical need for precise genome editing techniques. Among these, base editing stands out as it allows targeted alterations at the single nucleotide level. However,…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Current biological AI models lack interpretability -- their internal representations do not correspond to biological relationships that researchers can examine. Understanding gene regulation requires models whose learned structure can be…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
The human annotations are imperfect, especially when produced by junior practitioners. Multi-expert consensus is usually regarded as golden standard, while this annotation protocol is too expensive to implement in many real-world projects.…
Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient implementation compared to traditional pharmaceutical treatments. Current trends emphasize the…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
CRISPR-based genome editing has revolutionized biotechnology, yet optimizing guide RNA (gRNA) design for efficiency and safety remains a critical challenge. Recent advances (2020--2025, updated to reflect current year if needed) demonstrate…