CaMP - cancer metabolic pathway viewer

Serves as the backend code for https://www.curatemetabolicpathways.com

leADS: improved metabolic pathway inference based on active dataset subsampling

CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)

Web application of metabolics pathway visualisation, for the Gencovery business (https://gencovery.com/), created during the PDP project during the M1 of the Master of Bioinformatics, in Bordeaux.

Code and data repository for Modeling Metabolic Fluxes Using Deep Learning Based on Enzyme Variations

This repository collects my project for the Applied Genomics course. It includes the presentation on the chromosome-scale reference genome of the Alpine marmot, integrating multi-omics to study hibernation and high-altitude adaptation. Teaching materials (notes, transcripts, slides) used during the course are also provided for study purposes.

reMap: relabeling metabolic pathway data with groups to improve prediction outcomes

Knowledge graph construction for pharmacogenomic data integration. Semantic modeling of drug-gene interactions, metabolic pathways, and clinical phenotypes using graph databases and ontology frameworks for precision medicine applications.

prepBioCyc: Preprocess BioCyc files

Metabolic pathway inference using non-negative matrix factorization with community detection

PathVisio plugin to find relevant metabolic reactions from Rhea

MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

A basic network of human metabolism, including key enzymes, intermediates, and hormonal influences

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc

Library to perform metabolic engineering tasks

Identifying reprogrammed metabolic routes given omics data.

Diversity-based enumeration of optimal context-specific metabolic networks

Ⓜ️ Metabolic network completion