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Revisiting microbe-metabolite interactions: doing better than random
(2019)bioRxivRecently, Quinn and Erb et al [1] made the case that when used correctly, correlation and proportionality can outperform MMvec when identifying microbe-metabolite interactions. We revisit this comparison and show that the proposed correlation and proportionality are outperformed by MMvec on real data due to their inability to deal with sparsity commonly observed in microbiome and metabolome datasets.Working Paper -
Lack of evidence that ursodeoxycholic acids effects on the gut microbiome influence colorectal adenoma risk
(2017)bioRxivObjective We previously reported that Ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduces risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colon cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Design Using banked stool samples collected as part of a phase III randomized clinical ...Working Paper -
Protocol: Genome-Scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening
(2016)bioRxivForward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial immune system CRISPR (clustered regularly interspaced short palindromic repeats) has been adapted for genome-scale screening by combining Cas9 with guide RNA libraries. Here we describe a protocol for ...Working Paper