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Bioinformatics (Oxford, England)|June 13, 2024
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approachYueyu Jiang, Daniel McDonald, Daniela Perry, et al.Nature Biotechnology|July 27, 2023
Generation of accurate, expandable phylogenomic trees with uDanceMetin Balaban, Yueyu Jiang, Qiyun Zhu, et al.Biology|September 23, 2022
Learning Hyperbolic Embedding for Phylogenetic Tree Placement and UpdatesYueyu Jiang, Puoya Tabaghi, Siavash MirarabMolecular Ecology Resources|October 13, 2025
Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer FrequenciesEleonora Rachtman, Yueyu Jiang, Siavash MirarabSystematic Biology|April 29, 2022
DEPP: Deep Learning Enables Extending Species Trees using Single GenesYueyu Jiang, Metin Balaban, Qiyun Zhu, et al.Molecular Ecology Resources|October 13, 2021
Fast and accurate distance-based phylogenetic placement using divide and conquerMetin Balaban, Yueyu Jiang, Daniel Roush, et al.Microbiome|November 5, 2015
Context and the human microbiomeDaniel McDonald, Amanda Birmingham, Rob KnightCurrent Opinion in Critical Care|June 22, 2016
Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illnessPaul E Wischmeyer, Daniel McDonald, Rob KnightMsystems|May 3, 2018
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical InformationStefan Janssen, Daniel McDonald, Antonio Gonzalez, et al.Bioinformatics (Oxford, England)|January 3, 2022
Completing gene trees without species trees in sub-quadratic timeUyen Mai, Siavash MirarabPageof 102