Method development

Because a large component of our work is analysis of gut metagenomes, we contribute to methods development in the field. Below are recent examples.

Youngblut ND, de la Cuesta-Zuluaga J, and RE Ley. Incorporating genome-based phylogeny and trait similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. bioRxiv 2020.07.16.207845 https://www.biorxiv.org/content/10.1101/2020.07.16.207845v1 (2020)

Mineeva O, Rojas-Carulla M, Ley RE, Schoelkopf B and Youngblut ND. DeepMAsED: Evaluating the quality of metagenomics assemblies. Bioinformatics btaa124. doi: 10.1093/bioinformatics/btaa124 (2020)

de la Cuesta-Zuluaga J, Ley RE and Youngblut ND. Struo: a pipeline for building custom databases for common metagenome profilers, Bioinformatics, 36:7, 2314–2315 (2020)

McDonald D, et al. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18 (2018)

Costea PI, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology 3: 8-16 (2018)

 

See also here and check the preprint page for updates.