Current Bioinformatics - Volume 19, Issue 1, 2024

Over the past two decades, studies have discovered a special form of alternative splicing (AS) that produces a circular form of RNA. This stands in contrast to normal AS, which produces a linear form of RNA. Although these circRNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on the regulatory role of circRNAs with the assumptio Read More

Long non-coding RNAs (lncRNAs) typically refer to non-protein coding RNAs that are longer than 200 nucleotides. Historically dismissed as junk DNA, over two decades of research have revealed that lncRNAs bind to other macromolecules (e.g., DNA, RNA, and/or proteins) to modulate signaling pathways and maintain organism viability. Their discovery has been significantly aided by the development of bioinformatics tools in rec Read More

Treatment of many human diseases involves small-molecule drugs.Some target proteins, however, are not druggable with traditional strategies. Innovative RNA-targeted therapeutics may overcome such a challenge. Long noncoding RNAs (lncRNAs) are transcribed RNAs that do not translate into proteins. Their ability to interact with DNA, RNA, microRNAs (miRNAs), and proteins makes them an interesting target for regulating Read More

Today, the bioinformatics tool and database development are one of the most significant research areas in computational biology. Computational biologists are developing diverse bioinformatics tools and databases in the various fields of biological science. Nowadays, several non-coding RNAs (ncRNA) have been studied extensively, which act as a mediator of the regulation of gene expression. ncRNA is a functional RNA molecu Read More

Objective: Representation learning in the context of biological concepts involves acquiring their numerical representations through various sources of biological information, such as sequences, interactions, and literature. This study has conducted a comprehensive systematic review by analyzing both quantitative and qualitative data to provide an overview of this field. Methods: Our systematic review involved searching f Read More

Background: Intricacy in the pathological processes of type 2 diabetes (T2D) invites a need to understand gene regulation at the systems level. However, deciphering the complex gene modulation requires regulatory network construction. Objective: The study aims to construct a six-node feed-forward loop (FFL) to analyze all the diverse inter- and intra- interactions between microRNAs (miRNA) and transcription factors (TF Read More

Background: Root is a desirable trait for modern plant breeding programs, as the roots play a pivotal role in the growth and development of plants. Therefore, identification of the genes governing the root traits is an essential research component. With regard to the identification of root-associated genes/proteins, the existing wet-lab experiments are resource intensive and the gene expression studies are species-specific. Read More