💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Scripts for reproducing results shown in Gupta VK et al. "A Predictive Index for Health Status using Species-level Gut Microbiome Profiling". Nature Communications, 2020. https://doi.org/10.1038/s41467-020-18476-8.

MicrobeRX

A computational tool for the prediction and identification of metabolites.

Data and analysis code for the Indian gut microbiota study

🔬 Resources and notes on studying the human microbiome

Gut microbiome study (from 2000 to 2020)

Analysis and visualization of bioenergetic pathways in human gut microbiome datasets.

Deciphering microbial interactions with functional redundancy in human microbial community with partial information decomposition.

An Android app to help people on the Specific Carbohydrate Diet (SCD) check if a food is allowed or not on the diet. This app is endorsed by Kirkton Press Limited, owner of the SCD trademark.

This repository provides the scripts used to analyze the metagenomics data from the paper Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.

MDPD - Microbiome Database of Pulmonary Diseases

Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico …

Analysis and machine learning of high-dimensional data from the human gut microbiome.

📑Reports and bioinformatics analyses from internship in Indonesia

Scripts to reproduce analysis and figures in Yang, J.C.; Jacobs, J.P.; Hwang, M.; Sabui, S.; Liang, F.; Said, H.M.; Skupsky, J. Biotin Deficiency Induces Intestinal Dysbiosis Associated with an Inflammatory Bowel Disease-like Phenotype. Nutrients 2023, 15, 264. https://doi.org/10.3390/nu15020264

Training classification models on human gut metagenomic signatures

agp data to understand gut microbiome and childhood obesity.

Snakemake workflow to calculate in vivo bacterial replication rates from single time point metagenomics sequencing

Scripts to reproduce analysis and figures in Yang JC, Lagishetty V, Aja E, et al. Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice. ISME J. Published online December 16, 2024. doi:10.1093/ismejo/wrae250