Lista de obras - Siavash Mirarab - Dominio Público Uruguay

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

artículo científico publicado en 2017

A communal catalogue reveals Earth's multiscale microbial diversity

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

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

artículo científico publicado en 2015

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

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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

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

artículo científico publicado en 2022

ASTRAL: genome-scale coalescent-based species tree estimation

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

BBCA: Improving the scalability of *BEAST using random binning

artículo científico publicado en 2014

Complexity of avian evolution revealed by family-level genomes

artículo científico publicado en 2024

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

artículo científico publicado en 2014

Dense sampling of bird diversity increases power of comparative genomics

artículo científico publicado en 2020

DiscoVista: interpretable visualizations of gene tree discordance

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2011

Fine-mapping the Favored Mutation in a Positive Selective Sweep

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

artículo científico publicado en 2017

HIPPI: highly accurate protein family classification with ensembles of HMMs

artículo científico publicado en 2016

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.

artículo científico publicado en 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

artículo científico publicado en 2019

Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates

artículo científico publicado en 2022

MRL and SuperFine+MRL: new supertree methods

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2018

Phylogenetic Signal of Indels and the Neoavian Radiation

Phylogenomic analyses data of the avian phylogenomics project

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2019

Phylogenomics: Constrained gene tree inference

artículo científico publicado en 2017

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

artículo científico publicado en 2013

Phylotranscriptomic analysis of the origin and early diversification of land plants

artículo científico publicado en 2014

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".

artículo científico publicado en 2015

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

artículo científico publicado en 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?

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

artículo científico publicado en 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 ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 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.

artículo científico publicado en 2018

Ultra-Large Alignments Using Ensembles of Hidden Markov Models

Ultra-large alignments using phylogeny-aware profiles

artículo científico publicado en 2015

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

Lista de obras de Siavash Mirarab

A Prioritization Approach for Software Test Cases Based on Bayesian Networks

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

A communal catalogue reveals Earth's multiscale microbial diversity

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

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

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

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

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

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

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

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

ASTRAL: genome-scale coalescent-based species tree estimation

Adaptive Action Selection in Autonomic Software Using Reinforcement Learning

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

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

BBCA: Improving the scalability of *BEAST using random binning

Complexity of avian evolution revealed by family-level genomes

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

Dense sampling of bird diversity increases power of comparative genomics

DiscoVista: interpretable visualizations of gene tree discordance

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

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

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

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

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

FastSP: linear time calculation of alignment accuracy

Fine-mapping the Favored Mutation in a Positive Selective Sweep

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

HIPPI: highly accurate protein family classification with ensembles of HMMs

INFERRING OPTIMAL SPECIES TREES UNDER GENE DUPLICATION AND LOSS

INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores

Identifying the favored mutation in a positive selective sweep.

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

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

Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates

MRL and SuperFine+MRL: new supertree methods

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

Multi-allele species reconstruction using ASTRAL

PASTA: Ultra-Large Multiple Sequence Alignment

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

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

Phylogenetic Signal of Indels and the Neoavian Radiation

Phylogenomic analyses data of the avian phylogenomics project

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

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

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

Phylogenomics: Constrained gene tree inference

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

Phylotranscriptomic analysis of the origin and early diversification of land plants

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

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

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

SEPP: SATé-Enabled Phylogenetic Placement

Size-Constrained Regression Test Case Selection Using Multicriteria Optimization

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

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

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

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

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

TIPP: taxonomic identification and phylogenetic profiling

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

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 ⬇️

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

TreeCluster: Clustering biological sequences using phylogenetic trees

TreeShrink: Efficient Detection of Outlier Tree Leaves

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

Ultra-Large Alignments Using Ensembles of Hidden Markov Models

Ultra-large alignments using phylogeny-aware profiles

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems

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

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