Siavash Mirarab

According to our database, Siavash Mirarab authored at least 44 papers between 2007 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Median quartet tree search algorithms using optimal subtree prune and regraft.

Shayesteh Arasti, Siavash Mirarab

Algorithms Mol. Biol., December, 2024

2023

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using <i>Mycobacterium tuberculosis</i> isolates.

Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar

Bioinform., January, 2023

Principal Component Analysis in Space Forms.

Puoya Tabaghi, Michael Khanzadeh, Yusu Wang, Siavash Mirarab

CoRR, 2023

Phylogenomic branch length estimation using quartets.

Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab

Bioinform., 2023

Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time.

Shayesteh Arasti, Siavash Mirarab

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing.

Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab

Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022

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

Chao Zhang, Siavash Mirarab

Bioinform., October, 2022

Completing gene trees without species trees in sub-quadratic time.

Uyen Mai, Siavash Mirarab

Bioinform., 2022

Quantifying Hierarchical Conflicts in Homology Statements.

Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Phylogenetic Placement Problem: A Hyperbolic Embedding Approach.

Yueyu Jiang, Puoya Tabaghi, Siavash Mirarab

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements.

Navid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab, Md. Shamsuzzoha Bayzid

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships.

Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2022

2021

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

Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna

PLoS Comput. Biol., 2021

SODA: multi-locus species delimitation using quartet frequencies.

Maryam Rabiee, Siavash Mirarab

Bioinform., 2021

2020

Phylogenetic double placement of mixed samples.

Metin Balaban, Siavash Mirarab

Bioinform., 2020

Log Transformation Improves Dating of Phylogenies.

Uyen Mai, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2020

2019

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

John Yin, Chao Zhang, Siavash Mirarab

Bioinform., 2019

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.

Erfan Sayyari, Ban Kawas, Siavash Mirarab

Bioinform., 2019

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

Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab

Bioinform., 2019

APPLES: Fast Distance-Based Phylogenetic Placement.

Metin Balaban, Shahab Sarmashghi, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2019

2018

Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?

Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

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

Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab

BMC Bioinform., 2018

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims.

Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2018

2017

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

Chao Zhang, Erfan Sayyari, Siavash Mirarab

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

TreeShrink: Efficient Detection of Outlier Tree Leaves.

Uyen Mai, Siavash Mirarab

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

2015

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

Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow

J. Comput. Biol., 2015

Ultra-large alignments using Phylogeny-aware Profiles.

Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow

CoRR, 2015

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

Siavash Mirarab, Tandy J. Warnow

Bioinform., 2015

Ultra-Large Alignments Using Ensembles of Hidden Markov Models.

Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow

Proceedings of the Research in Computational Molecular Biology, 2015

2014

TIPP: taxonomic identification and phylogenetic profiling.

Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow

Bioinform., 2014

ASTRAL: genome-scale coalescent-based species tree estimation.

Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow

Bioinform., 2014

PASTA: Ultra-Large Multiple Sequence Alignment.

Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow

Proceedings of the Research in Computational Molecular Biology, 2014

2013

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

Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Meg Pirrung, Brian C. O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan

BMC Bioinform., 2013

Inferring Optimal Species Trees Under Gene Duplication and Loss.

Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012

Size-Constrained Regression Test Case Selection Using Multicriteria Optimization.

Siavash Mirarab, Soroush Akhlaghi, Ladan Tahvildari

IEEE Trans. Software Eng., 2012

MRL and SuperFine+MRL: new supertree methods.

Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow

Algorithms Mol. Biol., 2012

SEPP: SATe -Enabled Phylogenetic Placement.

Siavash Mirarab, Nam Nguyen, Tandy J. Warnow

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011

FASTSP: linear time calculation of alignment accuracy.

Siavash Mirarab, Tandy J. Warnow

Bioinform., 2011

2010

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

Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel

IEEE Trans. Software Eng., 2010

2008

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

Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel

Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of Software Engineering, 2008

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

Siavash Mirarab, Ladan Tahvildari

Proceedings of the First International Conference on Software Testing, 2008

Adaptive Action Selection in Autonomic Software Using Reinforcement Learning.

Mehdi Amoui, Mazeiar Salehie, Siavash Mirarab, Ladan Tahvildari

Proceedings of the Fourth International Conference on Autonomic and Autonomous Systems, 2008

2007

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems.

Siavash Mirarab, Alaa Hassouna, Ladan Tahvildari

Proceedings of the 15th International Conference on Program Comprehension (ICPC 2007), 2007

A Prioritization Approach for Software Test Cases Based on Bayesian Networks.

Siavash Mirarab, Ladan Tahvildari

Proceedings of the Fundamental Approaches to Software Engineering, 2007