Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

Along with collaborators at UCLA, we were able to detect a small, but significant amount of microbes in blood This is surprising since it's typically assumed that the immune system typically removes any microbial presence from human blood. I used a reference-free microbial community algorithm, called EMDeBruijn, to help corroborate the patterns we saw which included an increase in microbial diversity in schizophrenia patients. EMDeBruijn is a metric based on the Wasserstein metric (aka the Earth Mover's Distance) and a de Bruijn graph induced by the k-mers in a metagenomic DNA sample.

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

In a very reproducible fashion, we assess a wide variety of computational techniques in metagenomics, including assembly (putting together pieces of genomes, called contigs, from short reads), binning (figuring out where the contigs came from), and taxonomic profiling (determining which organisms are present in a sample and at what relative amount).