gut-brain-axis

A genome-resolved metagenomics pipeline replicating the Sharon et al. (2019) gut-brain axis study. Features MEGAHIT de novo co-assembly, Bowtie2 competitive read recruitment, and Anvi'o single-nucleotide variant (SNV) microdiversity profiling.

• Updated Jul 11, 2026
• Shell

Reproducible code and analyses for a follow-up household-matched case-control study of gut microbiome alterations in canine idiopathic epilepsy.

• Updated Jul 19, 2026
• HTML

PostgreSQL analytics warehouse integrating de novo viral metagenome assembly, CheckV quality control, and geNomad taxonomic/functional annotations to profile condition-associated bacteriophage populations in an ASD vs. TD fecal microbiota transplant gnotobiotic mouse model (Sharon et al. 2019).

• Updated Jul 23, 2026
• Python

An integrated computational pipeline for CRISPR-Cas13a (SHERLOCK) malaria diagnostics and trans-kingdom neuro-immune mapping, linking PfK13-driven pathogen detection to microglial homeostatic (CX3CR1/Iba1) set-points and Gut-Brain Axis (GBA) dysregulation.

• Updated Apr 5, 2026
• R

Single-nucleus transcriptomic profiling of gut and paired brain tissues from flies fed with lipid extracts.

• Updated May 4, 2025
• R

#ioneurosciencehubfootnoteIntersection=) Exploring the intersection of vitamin B12 and cognitive decline in older adults.

• Updated Feb 27, 2025

Comparative viromics pipeline designed to profile gut viral communities in neurodysbiosis and control cohorts. Implements de novo MEGAHIT assembly, geNomad prediction, CheckV quality assessment, and Bowtie2 read recruitment to characterize gut bacteriophage signatures in humanized mouse models.

• Updated Aug 23, 2026
• Shell

Kallyope — independent third-party profile of a public API surface, by API Evangelist. Kallyope, Inc. is a New York City clinical-stage biotechnology company, founded in 2015 by Columbia University scientists Charles Zuker, Tom Maniatis and Richard Axel, that translates the biology of the gut-brain axis into medicines.

• Updated Sep 4, 2026