IEEE/ACM transactions on computational biology and bioinformatics
Jun 21, 2018
To describe the cellular functions of proteins and genes, a potential dynamic vocabulary is Gene Ontology (GO), which comprises of three sub-ontologies namely, Biological-process, Cellular-component, and Molecular-function. It has several application...
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular...
UNLABELLED: In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In...
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...
SUMMARY: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computati...
Non-ribosomal peptides (NRPs) are promising lead compounds for novel antibiotics. Bioinformatic mining of silent microbial NRPS gene clusters provide crucial insights for the discovery and de novo design of bioactive peptides. Here, we describe the e...
Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC predict...
MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information i...
MOTIVATION: Clustering spatial-resolved gene expression is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2020
The GOSemSim package, an R-based tool within the Bioconductor project, offers several methods based on information content and graph structure for measuring semantic similarity among GO terms, gene products and gene clusters. In this chapter, I illus...
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