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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
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Posts
Future Blog Post
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Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
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.
TreeShrink: Fast and accurate detection of outlier long branches in collections of phylogenetic trees.
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.
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
Gene exchange networks define species-like units in marine prokaryotes
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
talks
Great Lakes Bioinformatics Consortium (GLBIO) 2017
Published:
- Talk title: Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
- Won 1 of the 2 best-paper awards.
Evolution 2018
Published:
- Talk title: Minimum Variance Rooting and TreeShrink as new components in a phylogenetic reconstruction pipeline
SSB 2020 - Systematics in the Swamp
Published:
- Talk title: Finding Errors in Phylogenomic Data Using TreeShrink
- Part of the 2020 Phylogenomics Symposium and Software School
- An overview of the TreeShrink method and a tutorial on the software
RECOMB 2020
Published:
- Talk title: Log Transformation Improves Dating of Phylogenies
- Extended abstract appeared in RECOMB 2020 conference proceedings
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.
Summer Research Internship Program 2020
Mentor, UCSD, ECE Department, 2020
Research mentor
- Mentee: Merve Kilic
- Project title: A Fast Implementation of Root-to-Tip Rooting for Virus Phylogenies