A. Jayaraman

A microfluidic model of colonocyte-microbiota interaction mimicking the colorectal cancer microenvironment

The paper develops a microfluidic model to study interactions between colonocytes, microbiota, and Fusobacterium nucleatum in a colorectal cancer microenvironment, showing altered gene expression and microbiota composition.

Machine Learning-Guided Antibody Engineering That Leverages Domain Knowledge To Overcome The Small Data Problem

This paper presents a machine learning platform that enhances antibody affinity and neutralizing potency using domain knowledge and limited experimental data.

A Chemical Reaction Similarity-Based Prediction Algorithm Identifies the Multiple Taxa Required to Catalyze an Entire Metabolic Pathway of Dietary Flavonoids

The paper predicts and validates bacterial taxa capable of catalyzing the entire metabolic pathway of the flavonoid tilianin using a chemical reaction similarity-based algorithm.

Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice

This study shows that oral administration of indole-3-acetate reduces liver steatosis and inflammation in mice fed a high-fat diet.

Microbe-derived indole tunes organ-function and links microbe metabolites to biological ageing

This study shows that indole, a gut microbe metabolite, is essential for maintaining organ function and metabolic homeostasis, and its deficiency leads to multiorgan decline and accelerated biological ageing.

A Chalcone Synthase-Like Bacterial Protein Catalyzes Heterocyclic C-Ring Cleavage of Naringenin to Alter Bioactivity Against Nuclear Receptors in Colonic Epithelial Cells

The paper identifies a bacterial enzyme that cleaves naringenin, altering its bioactivity against nuclear receptors in intestinal cells, and shows how gut microbiota influence flavonoid metabolism and inflammation.

A metabolically engineered bacterium controls autoimmunity by remodeling the pro-inflammatory microenvironment

A metabolically engineered bacterium produces indole to modulate macrophages and Tregs, reducing autoimmune arthritis by altering the pro-inflammatory microenvironment.

Platelet proteome analysis reveals an early hyperactive phenotype in SARS-CoV-2-infected humanized ACE2 mice

This paper uses proteomics to analyze platelet changes in SARS-CoV-2-infected humanized mice, finding early activation of coagulation and complement pathways.

Epigenetic reprogramming ameliorates type 1 diabetes by decreasing the generation of Th1 and Th17 subsets and restoring self-tolerance in CD4+ T cells

This study shows that the histone modifier TSA reduces Th1 and Th17 cell generation and restores self-tolerance in CD4+ T cells, ameliorating type 1 diabetes in NOD mice.

Epigenetic modulation of selected immune response genes and altered functions of T lymphocytes and macrophages collectively contribute to autoimmune diabetes protection.

This study shows that TSA treatment reduces T cell and macrophage infiltration and alters gene expression in NOD mice, contributing to autoimmune diabetes protection.

Evaluation of Antibiotic Tolerance in Pseudomonas aeruginosa for Aminoglycosides and its Predicted Gene Regulations Through In-silico Transcriptomic Analysis

This study evaluates antibiotic tolerance in Pseudomonas aeruginosa to aminoglycosides and identifies gene expression changes, finding tobramycin shows superior in vitro response and potential for combating resistance.

Environmental chemical diethylhexyl phthalate alters intestinal microbiota community structure and metabolite profile in mice

This study shows DEHP alters gut microbiota composition and metabolite profiles in mice, increasing p-cresol and decreasing butyrate, linked to neurodevelopmental disorders.

Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics

The paper introduces EMMA, a computational workflow for untargeted metabolomics annotation, increasing candidate set size and identifying novel metabolites in CHO cells and murine cecal microbiota.