Journal of chemical information and modeling
Jul 14, 2025
Microorganisms such as bacteria and fungi have been used for natural products that translate to drugs. However, assessing the bioactivity of extract from culture to identify novel natural molecules remains a strenuous process due to the cumbersome or...
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...
Combinatorial chemistry & high throughput screening
Jan 1, 2019
AIM AND OBJECTIVE: It is interesting to find the gene signatures of cancer stages based on the omics data. The aim of study was to evaluate and to enrich the array data using gene ontology and ncRNA databases in colorectal cancer.
Combinatorial chemistry & high throughput screening
Jan 1, 2019
OBJECTIVE: A significant proportion of patients with early non-small cell lung cancer (NSCLC) can be cured by surgery. The distant metastasis of tumors is the most common cause of treatment failure. Precisely predicting the likelihood that a patient ...
Reduction of dimensionality has emerged as a routine process in modelling complex biological systems. A large number of feature selection techniques have been reported in the literature to improve model performance in terms of accuracy and speed. In ...
Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approac...
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