Alexandra Zhernakova

Oct 17, 2024 | biorxiv.org | Nataliia Kuzub |Alexander Kurilshikov |Alexandra Zhernakova |Sanzhima Garmaeva

AbstractEnvironmental contamination complicates the study of low-biomass microbial communities like the human gut virome. In 1,321 early-life gut viromes and 55 negative controls (NCs) from four datasets, we identified viral contaminants and their prevalence across studies.

Jan 22, 2024 | genomebiology.biomedcentral.com | Martijn Vochteloo |Patrick Deelen |Ellen A. Tsai |Heiko Runz |Sergio Andreu-Sánchez |Jingyuan Fu | +4 more

PICALO is an EM-based algorithm for the identification of known and unknown contexts that influence the regulatory effect of genetic variants on gene expression. PICALO takes as input a set of eQTLs and their corresponding expression and genotype data, as well as a set of starting positions (e.g., potential context components). Optional arguments allow for the correction of technical covariates both with and without an interaction term.

Feb 13, 2023 | nature.com | Victòria Pascal Andreu |Hannah E. Augustijn |Lianmin Chen |Alexandra Zhernakova |Jingyuan Fu |Michael Fischbach | +1 more

AbstractThe gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites.