Published in bioRxiv, 2020
Recommended citation: Gene exchange networks define species-like units in marine prokaryotes R. Stepanauskas, J.M. Brown, U. Mai, O. Bezuidt, M. Pachiadaki, J. Brown, S.J. Biller, P.M. Berube, N.R. Record, S. Mirarab bioRxiv 2020.09.10.291518; doi: https://doi.org/10.1101/2020.09.10.291518
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
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
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
Published in BMC Genomics, 2018
TreeShrink is an algorithm for detecting abnormally long branches in one or a collection of phylogenetic trees.
Recommended citation: Mai, U., Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics 19, 272 (2018). https://doi.org/10.1186/s12864-018-4620-2.
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.