Matthew Madgwick

Macrophage signature-based prediction of cancer treatment response using MIL-attention

The paper predicts cancer treatment response using a MIL-attention framework that analyzes macrophage states from single-cell RNA data, showing improved performance over existing methods.

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

This paper identifies a microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state linked to mucosal inflammation and treatment resistance in ulcerative colitis.

RNA foundation models enable generalizable endometriosis disease classification and stable gene-level interpretation

This paper uses RNA foundation models to improve endometriosis classification across cohorts and identifies stable gene-level predictors.

Decoding Non-coding SNPs: Systems Genomics Modelling Dissects the Heterogeneity of IBD

The paper models the impact of non-coding SNPs on gene regulatory networks in IBD to stratify patients based on gene dysregulation and therapeutic response.

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

AutophagyNet is an updated database providing curated interactions and annotations for autophagy proteins, enabling analysis of autophagy regulation across different contexts.

Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease

This study shows that extracellular vesicles from Bacteroides thetaiotaomicron affect host immune pathways differently in various cell types and disease states, with implications for IBD therapy.

Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

SalmoNet2 provides an updated multi-layered network resource for 20 Salmonella strains, enhancing strain comparisons through protein-protein, transcriptional regulatory, and metabolic interactions.

CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases

CytokineLink maps cytokine interactions to analyze immune responses in inflammatory and infectious diseases, revealing rewiring in ulcerative colitis and cytokine storm patterns in COVID-19.

Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection

This study uses single-cell RNA-seq data to analyze how SARS-CoV-2 infection alters intestinal epithelial-immune cell interactions and identifies potential drug targets and repurposing strategies for COVID-19.

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

ViralLink is a systems biology workflow that reconstructs and analyzes intracellular signaling networks affected by viruses, using transcriptomics data to identify key pathways and proteins in the cellular response to infection.

A systems genomics approach to uncover patient-specific pathogenic pathways in a complex disease

This paper introduces iSNP, a workflow to identify patient-specific pathogenic pathways in ulcerative colitis by integrating SNP profiles with regulatory networks.