VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.

The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment.

Circular RNA circ_0026218 Suppressed Atherosclerosis Progression via miR-338-3p/SIRT6 Axis.

Background: Multiple circular RNAs (circRNAs) are implicated in atherosclerosis (AS) pathogenesis. In fact, how circRNA 0026218 (circ_0026218) functions in AS remains unknown, and thus the functions and mechanisms of circ_0026218 in the injury of vascular endothelial cells are to be investigated.

Methods: Microarray analysis was employed to screen out differentially expressed circRNAs in AS.

MethBank 4.0: an updated database of DNA methylation across a variety of species.

DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species.

ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers.

Alternative splicing (AS) is a fundamental process that governs almost all aspects of cellular functions, and dysregulation in this process has been implicated in tumor initiation, progression and treatment resistance. With accumulating studies of carcinogenic mis-splicing in cancers, there is an urgent demand to integrate cancer-associated splicing changes to better understand their internal cross-talks and functional consequences from a global view. However, a resource of key functional AS events in human cancers is still lacking.

Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.

Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy.

scMethBank: a database for single-cell whole genome DNA methylation maps.

Single-cell bisulfite sequencing methods are widely used to assess epigenomic heterogeneity in cell states. Over the past few years, large amounts of data have been generated and facilitated deeper understanding of the epigenetic regulation of many key biological processes including early embryonic development, cell differentiation and tumor progression. It is an urgent need to build a functional resource platform with the massive amount of data.