Lab Resources

A program to identify associations between host genetic variation and microbiome composition using machine-learning

Software, code, installation instructions, and tutorial (GitHub)
Online network visualization tool
Paper (GigaScience)

Primate Orthologous Exon Database

This database provides a catalog of unique, non-overlapping, orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. The database can be used in analysis of multi-species RNA-seq data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.

Visit online database

Note: the Primate Orthologous Exon Database is out of date and no longer being updated or supported.

SPIKE

SPIKE is a database of highly curated human signaling pathways with an associated interactive software tool. Users can view and download individual pathway maps and browse the entire database from this website, or install a stand-alone software tool that allows dynamic visualization and manipulation of the database and additional analyses.

Visit SPIKE website

Data from Morton et al. (2015) PLOS Genetics
All Supplementary Tables and Figures
Figshare

All raw sequence data (fastq files)
MG-RAST

Data from Burns et al. (2014) Genome Medicine
All Supplementary Data files, including OTU, pathway, and enzyme abundance tables
Genome Medicine

Data from Blekhman et al. (2010) Genome Research
Supplementary Table 1
Tab-delimited text file (zip)

Data from Blekhman et al. (2008) PLoS Genetics
Supplementary data
Tab-delimited text file (zip)

hOMIM data from Blekhman et al. (2008) Current Biology
A curated dataset of human mendelian disease genes.
Tab-delimited text file