Biomedical subjects

James R J Haycocks

Publications and source records attributed to James R J Haycocks.

3 recordsLinked to original sources

PubMed2026

ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.

MOTIVATION: Chemical genomics is a powerful high-throughput approach to systematically link phenotypes to genotypes. However, the vast datasets generated remain challenging to explore due to the lack of integrated, interactive tools for visualization and analysis. Existing workflows often require multiple independent software tools, limiting data accessibility and collaboration. Therefore, we created a user-friendly platform that enables efficient exploration and sharing of chemical genomics data. RESULTS: We developed ChemGenXplore, a web-based Shiny application designed to streamline the visualization and analysis of chemical genomic screens. It offers two primary functionalities: one for exploring pre-implemented datasets and another for analysing user-uploaded datasets. ChemGenXplore enables users to visualize phenotypic profiles, assess gene-gene and condition-condition correlations, perform GO and KEGG enrichment analysis, and generate customizable, interactive heatmaps. To further support collaborative research, ChemGenXplore also facilitates the comparative analysis of chemical genomic and other omics datasets. By consolidating these features into a single interactive and accessible tool, ChemGenXplore facilitates data sharing, enhances reproducibility, and promotes collaboration within the research community. AVAILABILITY AND IMPLEMENTATION: ChemGenXplore is freely accessible as a web application at https://chemgenxplore.kaust.edu.sa/. Source code and documentation, including instructions for local installation, are provided on GitHub (https://github.com/Hudaahmadd/ChemGenXplore). A Docker image is also available on DockerHub (https://hub.docker.com/r/hudaahmad/chemgenxplore) to ensure reproducibility and simplify installation.

Software↗

PubMed2025

Genome-wide mapping of cyclic AMP receptor protein binding in Enteroaggregative Escherichia coli reveals targeting of virulence-associated genes.

Bacterial pathogens use a wide array of virulence factors to colonise and subsequently elicit disease in their host. These factors are often subject to extensive regulation at the transcriptional level, to ensure that their expression is timely. Although many pathogens use bespoke transcription factors that primarily target virulence genes, global transcription factors also sometimes play a role in controlling these genes. Enteroaggregative Escherichia coli (EAEC) is a significant cause of watery and mucoid diarrhoea globally. The organism colonises the small intestine before producing toxins that elicit disease, using a multitude of virulence factors that are encoded both chromosomally and on virulence plasmids. In this work, we have studied the cAMP Receptor Protein (CRP), a well-characterised bacterial global transcription factor, focusing on its role in pathogenicity of the prototype EAEC strain 042. We show that, although most functional CRP binding sites on the chromosome are conserved between E. coli K-12 and 042, CRP has been co-opted to couple the expression of some virulence genes to the nutritional state of the cell. We report novel mechanisms for CRP-dependent regulation of genes, whose products contribute to adhesion, production of a bacterial antibiotic, and export of a polysaccharide capsule.

CRP↗

PubMed2025

Genome-wide mapping of cAMP receptor protein binding in enteroaggregative Escherichia coli reveals targeting of virulence-associated genes.

Bacterial pathogens employ a diverse array of virulence factors to colonize and subsequently elicit disease in their host. These factors are often subject to extensive regulation at the transcriptional level to ensure that their expression is timely. Although many pathogens use bespoke transcription factors that primarily target virulence genes, global transcription factors also sometimes play a role in controlling these genes. Enteroaggregative Escherichia coli (EAEC) is a significant cause of watery and mucoid diarrhoea globally. The organism colonizes the small intestine before producing toxins that elicit disease, using a multitude of virulence factors that are encoded both chromosomally and on virulence plasmids. In this work, we have studied the cAMP receptor protein (CRP), a well-characterized bacterial global transcription factor, focusing on its role in the pathogenicity of the prototype EAEC strain 042. We show that, although most functional CRP binding sites on the chromosome are conserved between E. coli K-12 and 042, CRP has been co-opted to couple the expression of some virulence genes to the nutritional state of the cell. We report novel mechanisms for CRP-dependent regulation of genes whose products contribute to the maturation of a bacterial antibiotic, export of a polysaccharide capsule and production of a putative adhesin.

Escherichia coli↗