MDPD - Microbiome Database of Pulmonary Diseases

My professional repository of project and publication data files in computational biology and data science.

📑Reports and bioinformatics analyses from internship in Indonesia

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

MicrobeRX

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.

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

🔬 Resources and notes on studying the human microbiome

Gut microbiome study (from 2000 to 2020)

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 …

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

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.

A computational tool for the prediction and identification of metabolites.

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

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.

Data and analysis code for the Indian gut microbiota study

agp data to understand gut microbiome and childhood obesity.

Vectorization and Unsupervised Learning of Mouse Operation Taxonomic Units to determine which species of bacteria form distinct groups in a dataset.