List of works by Siavash Mirarab

A Prioritization Approach for Software Test Cases Based on Bayesian Networks

scholarly article

A Two-State Model of Tree Evolution and its Applications to Alu Retrotransposition

scientific article published on 20 November 2017

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

scientific article

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

A requirement-based software testing framework: An industrial practice

A roadmap for global synthesis of the plant tree of life.

scientific article published on 30 March 2018

APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments

scientific article published on 23 September 2019

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

scientific article published on June 2015

ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.

scientific article

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization

scientific article published on 01 October 2019

ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees

scientific article published in 2022

ASTRAL: genome-scale coalescent-based species tree estimation

scientific article

Adaptive Action Selection in Autonomic Software Using Reinforcement Learning

scholarly article published March 2008

An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization

An empirical study of the effect of time constraints on the cost-benefits of regression testing

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

scientific article

Assembly-free and alignment-free sample identification using genome skims

BBCA: Improving the scalability of *BEAST using random binning

scientific article

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Data access for the 1,000 Plants (1KP) project

scientific article

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

DiscoVista: interpretable visualizations of gene tree discordance

scientific article published on 5 February 2018

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

scientific article published on 15 November 2021

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

scientific article

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences

scientific article published on 01 June 2019

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies ⬇️

scientific article published on 15 April 2016

FastSP: linear time calculation of alignment accuracy

scientific article

Fine-mapping the Favored Mutation in a Positive Selective Sweep

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

scientific article published on 4 October 2017

HIPPI: highly accurate protein family classification with ensembles of HMMs

scientific article

INFERRING OPTIMAL SPECIES TREES UNDER GENE DUPLICATION AND LOSS

article

INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores

scientific article published on 01 March 2020

Identifying the favored mutation in a positive selective sweep.

scientific article published on 19 February 2018

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

article

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

scientific article published on 21 June 2019

Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates

scientific article published in 2022

MRL and SuperFine+MRL: new supertree methods

scientific article published on 26 January 2012

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

scientific article published on 11 August 2017

Multi-allele species reconstruction using ASTRAL

article

PASTA: Ultra-Large Multiple Sequence Alignment

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

scientific article published on 30 December 2014

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

scientific article published on 17 April 2018

Phylogenetic Signal of Indels and the Neoavian Radiation

Phylogenomic analyses data of the avian phylogenomics project

scientific article

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

scientific article published on 2 October 2015

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

article

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

scientific article published on 02 December 2019

Phylogenomics: Constrained gene tree inference.

scientific article

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

scientific article (publication date: 13 May 2013)

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

scientific article published on 19 May 2020

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

scientific article published on October 2015

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

scientific article published on September 2015

SEPP: SATé-Enabled Phylogenetic Placement

scholarly article published December 2011

Size-Constrained Regression Test Case Selection Using Multicriteria Optimization

article by Siavash Mirarab et al published July 2012 in IEEE Transactions on Software Engineering

Skmer: assembly-free and alignment-free sample identification using genome skims

scientific article published on 13 February 2019

Species tree estimation using ASTRAL: how many genes are enough?

scientific article

Statistical binning enables an accurate coalescent-based estimation of the avian tree

scientific article

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

scientific article published on 01 July 2019

TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution

scientific article published in 2021

TIPP: taxonomic identification and phylogenetic profiling

scientific article

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

scientific article published on 28 February 2018

The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference ⬇️

scientific article

The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters

scientific article published on 13 January 2020

TreeCluster: Clustering biological sequences using phylogenetic trees

scientific article published on 22 August 2019

TreeShrink: Efficient Detection of Outlier Tree Leaves

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

scientific article

Ultra-Large Alignments Using Ensembles of Hidden Markov Models

Ultra-large alignments using phylogeny-aware profiles

scientific article published on 16 June 2015

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

scientific article published on 18 June 2015

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

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