Abubaker Patan

The paper expands a bile acid and steroidal MS/MS spectral library across three repositories, capturing diverse structures and providing a resource for classifying unknown spectra.

The paper develops an agentic AI system using LLMs and domain tools to hypothesize and validate structures of unknown drug metabolites from mass spectrometry data.

This paper introduces molecular community networking to organize metabolite data, revealing hidden connections and discovering novel dipeptide-conjugated bile acids.

The paper identifies alkamines as a previously hidden class of metabolites formed via reductive amination, revealing significant gaps in metabolomics and drug metabolism understanding.

This study examines how maternal antibiotic use during breastfeeding affects the infant gut microbiome and metabolome, finding altered microbial profiles and increased BMI in some infants.

The paper systematically extracts and catalogs acylcarnitine metabolites from multiple repositories, identifying previously unknown carnitines and providing a resource for further metabolic research.

The paper identifies microbial bile acid conjugation as a drug-activating function for 5-ASA, revealing its therapeutic relevance through metabolomics analysis.

This study maps conjugated metabolites by analyzing MS/MS spectra from public repositories, identifying potential conjugation events and providing a resource for structural discovery.

The paper introduces microbiomeMASST, a metadata network graph linking metabolites across datasets, enabling cross-study analysis of microbial metabolites and their biological context.

The paper introduces a collaborative platform for curating microbial metabolite knowledge to enhance metabolomics data interpretation.

ChemEmbed improves metabolite identification by combining enhanced MS/MS data with multidimensional molecular embeddings, achieving high accuracy in benchmark tests.

The paper develops a multidimensional bile acid reference library and evaluates workflows for accurate bile acid measurement in biological samples.

The paper uses synthetic multiplexing to annotate uncharacterized metabolites, identifying ibuprofen-carnitine as a metabolite linked to muscle toxicity.

The paper examines how environmental and maternal factors influence infant gut metabolism through microbiome and metabolome profiling in Bangladeshi mother-infant pairs.

The paper presents a multi-organ metabolomics atlas in AD mouse models, identifying dysregulated metabolites and microbiome associations linked to oxidative stress and cognitive impairment.

This study identifies distinct microbial and metabolic signatures in VEO-IBD compared to healthy controls, linking microbiome changes to metabolic dysregulation.

This paper introduces a mass spectrometry filtering tree to distinguish bile acid isomers in LC-MS/MS data and identifies a novel deoxycholyl-2-aminophenol amidate linked to whole grain consumption.

The paper creates a spectral library of N-acyl lipids from metabolomics data, identifies novel compounds, and links them to health conditions like HIV and cognitive impairment.