Yueyu Jiang

This paper introduces C-DEPP, a method that scales deep phylogenetic embedding to large reference trees by using an ensemble approach, enabling efficient placement of 20 million 16S fragments on the GG2 tree in 41 hours.

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

DEPP extends species trees using single genes by learning to place them without pre-specified models, enabling integration of 16S and metagenomic data.

This paper introduces APPLES-2, a distance-based phylogenetic placement method that is more accurate and scalable than existing methods, enabling efficient placement of microbial genomes on large trees.