1k citations · 1.2k across the 7 of their papers we have counts for
8 papers
Principal Component Analysis in Space Forms
Puoya Tabaghi, Michael Khanzadeh, Yusu Wang +1
Principal Component Analysis (PCA) is a workhorse of modern data science. While PCA assumes the data conforms to Euclidean geometry, for specific data types, such as hierarchical a…
Species Tree Estimation Using ASTRAL: Practical Considerations
Siavash Mirarab
ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the…
DiscoVista: interpretable visualizations of gene tree discordance
Erfan Sayyari, James B. Whitfield, Siavash Mirarab
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between sp…
Testing for polytomies in phylogenetic species trees using quartet frequencies
Erfan Sayyari, Siavash Mirarab
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creatin…
Species tree estimation using ASTRAL: how many genes are enough?
Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popu…
Fast coalescent-based computation of local branch support from quartet frequencies
Erfan Sayyari, Siavash Mirarab
Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial…
Ultra-large alignments using Phylogeny-aware Profiles
Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar +1
Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence align…
Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses
Md. Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau +1
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many proces…