Trajectory Inference of clinical data via Multi-commodity Flow
End-to-end 16S microbiome analysis (FASTQ to PCoA) of Crohn's Disease. Implements a QIIME 2 & Docker pipeline to identify significant phylogenetic dysbiosis (p=0.0007).
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.
A non-profit app designed to help those with colitis and crohns identify sugar alcohols
Multi-agent system for biomedical research. BioAgentics uses coordinated AI agents to identify research opportunities, build computational tools, analyze genomic data, screen drug candidates, and advance our understanding of disease biology.
Collection of personal stories and scientific evidence about people who have been able to bring their Crohn's disease to sustained remission without using western medicine
Some examples of the animations I created for activity reminders with a Vector robot that's part of a home robotics project for managing life with a chronic illness
A curated list of apps, tools, food databases, diets, research, and communities for IBD, IBS, and elimination diets.
The directory of Crohn's and Colitis events.
A multivariable MbWAS pipeline identifying taxonomic biomarkers of gut dysbiosis in Crohn's Disease. Implements zero-replaced Centered Log-Ratio (CLR) transformations and two-part hurdle regression models integrated via the Cauchy combination test to contrast the HMP2 / IBDMDB cohort.
All QC, annotation, and analyses for IBD exomes
A computational metataxonomics pipeline for 16S rRNA-seq, quantifying mucosal dysbiosis, differential microbial abundance, and co-occurrence network topologies to identify keystone taxa in Crohn's Disease.
Streamlit web-app for calculating the updated Lémann Index, measures cumulative bowel-damage in Crohn’s disease (strictures + fistulae + surgery). Research/education use only.
Network based analysis of NOD2 signaling in inflammatory bowel disease.
Open-source amenities navigator for IBD patients in Ireland
Simultaneous analysis of genes and transposable elements (TEs) from 10X scRNAseq datasets derived from CD and NIBD samples using Alevin.
Unified CT and MR enterography foundation-model pipeline for Crohn's disease. Code for the npj Digital Medicine paper.
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