Uyen Mai

Uyen Mai

PhD student - Department of Computer Science & Engineering, UCSD. Research in computational & evolutionary biology

Posts by Collection

publications

Minimum Variance Rooting of Phylogenetic Trees and Implications for Species Tree Reconstruction

Published in PLOS ONE, 2017

This paper introduces MinVar-Rooting, a method to root the tree at the point that minimizes the variance of the root to tip distances, and a linear-time algorithm to find the MinVar point.

Recommended citation: Mai, Uyen, Erfan Sayyari, and Siavash Mirarab. Minimum Variance Rooting of Phylogenetic Trees and Implications for Species Tree Reconstruction. Edited by Gabriel Moreno-Hagelsieb. PLOS ONE 12, no. 8 (2017): e0182238.

TreeCluster: Clustering biological sequences using phylogenetic trees

Published in PLOS ONE, 2019

TreeCluster is a tool that, given a tree T (Newick format) and a distance threshold t, finds the minimum number of clusters of the leaves of T such that some user-specified constraint is met in each cluster.

Recommended citation: Balaban M, Moshiri N, Mai U, Jia X, Mirarab S (2019) TreeCluster: Clustering biological sequences using phylogenetic trees. PLOS ONE 14(8): e0221068. https://doi.org/10.1371/journal.pone.0221068

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Published in Nature Communications, 2019

A Reference Phylogeny for Bacterial and Archaeal Genomes. Including 10,575 genomes of Bacteria and Archaea using 381 marker genes.

Recommended citation: Zhu, Q., Mai, U., Pfeiffer, W. et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun 10, 5477 (2019). https://doi.org/10.1038/s41467-019-13443-4

Log Transformation Improves Dating of Phylogenies

Published in MBE, 2020

This paper introduces wLogDate, a method for dating phylogenetic trees. wLogDate infers time tree following molecular clock principle: it minimizes the variance of the mutation rates in log scale (hence the term logDate).

Recommended citation: Uyen Mai, Siavash Mirarab, Log Transformation Improves Dating of Phylogenies, Molecular Biology and Evolution, msaa222, https://doi.org/10.1093/molbev/msaa222

talks

Evolution 2018

Published:

  • Talk title: Minimum Variance Rooting and TreeShrink as new components in a phylogenetic reconstruction pipeline

teaching

ECE 208, Computational Evolutionary Biology

Graduate course, UCSD, ECE Department, 2020

Teaching Assistant

  • This course introduces a series of general algorithmic techniques but uses computational evolutionary biology as the context. The course motivates each algorithmic concept using a specific biological application related to evolution and focuses the discussion on specific types of (big) data available in modern biological studies.