A Prioritization Approach for Software Test Cases Based on Bayesian Networks. - Siavash Mirarab; Ladan Tahvildari (FASE, 2007)

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems. - Siavash Mirarab; Alaa Hassouna; Ladan Tahvildari (ICPC, 2007)

Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. - Mehdi Amoui; Mazeiar Salehie; Siavash Mirarab; Ladan Tahvildari (ICAS, 2008)

An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. - Siavash Mirarab; Ladan Tahvildari (ICST, 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 (SIGSOFT FSE, 2008)

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)

FASTSP: linear time calculation of alignment accuracy. - Siavash Mirarab; Tandy J. Warnow (Bioinform., 2011)

SEPP: SATe -Enabled Phylogenetic Placement. - Siavash Mirarab; Nam Nguyen; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2012)

MRL and SuperFine+MRL: new supertree methods. - Nam-phuong Nguyen; Siavash Mirarab; Tandy J. Warnow (Algorithms Mol. Biol., 2012)

Size-Constrained Regression Test Case Selection Using Multicriteria Optimization. - Siavash Mirarab; Soroush Akhlaghi; Ladan Tahvildari (IEEE Trans. Software Eng., 2012)

Inferring Optimal Species Trees Under Gene Duplication and Loss. - Md. Shamsuzzoha Bayzid; Siavash Mirarab; Tandy J. Warnow (Pacific Symposium on Biocomputing, 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; et al. (BMC Bioinform., 2013)

PASTA: Ultra-Large Multiple Sequence Alignment. - Siavash Mirarab; Nam-phuong Nguyen; Tandy J. Warnow (RECOMB, 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)

TIPP: taxonomic identification and phylogenetic profiling. - Nam-phuong Nguyen; Siavash Mirarab; Bo Liu 021; Mihai Pop; Tandy J. Warnow (Bioinform., 2014)

Ultra-Large Alignments Using Ensembles of Hidden Markov Models. - Nam-phuong Nguyen; Siavash Mirarab; Keerthana Kumar; Tandy J. Warnow (RECOMB, 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 Phylogeny-aware Profiles. - Nam-phuong Nguyen; Siavash Mirarab; Keerthana Kumar; Tandy J. Warnow (CoRR, 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)

TreeShrink: Efficient Detection of Outlier Tree Leaves. - Uyen Mai; Siavash Mirarab (RECOMB-CG, 2017)

ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. - Chao Zhang 055; Erfan Sayyari; Siavash Mirarab (RECOMB-CG, 2017)

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. - Shahab Sarmashghi; Kristine Bohmann; M. Thomas P. Gilbert; Vineet Bafna; Siavash Mirarab (RECOMB, 2018)

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. - Chao Zhang 055; Maryam Rabiee; Erfan Sayyari; Siavash Mirarab (BMC Bioinform., 2018)

Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? - Shubhanshu Shekhar; Sebastien Roch; Siavash Mirarab (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

APPLES: Fast Distance-Based Phylogenetic Placement. - Metin Balaban; Shahab Sarmashghi; Siavash Mirarab (RECOMB, 2019)

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. - Niema Moshiri; Manon Ragonnet-Cronin; Joel O. Wertheim; Siavash Mirarab (Bioinform., 2019)

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. - Erfan Sayyari; Ban Kawas; Siavash Mirarab (Bioinform., 2019)

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. - John Yin; Chao Zhang 055; Siavash Mirarab (Bioinform., 2019)

Log Transformation Improves Dating of Phylogenies. - Uyen Mai; Siavash Mirarab (RECOMB, 2020)

Phylogenetic double placement of mixed samples. - Metin Balaban; Siavash Mirarab (Bioinform., 2020)

SODA: multi-locus species delimitation using quartet frequencies. - Maryam Rabiee; Siavash Mirarab (Bioinform., 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)

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. - Eleonora Rachtman; Shahab Sarmashghi; Vineet Bafna; Siavash Mirarab (RECOMB, 2022)

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. - Navid Bin Hasan; Avijit Biswas; Metin Balaban; Siavash Mirarab; Md. Shamsuzzoha Bayzid (RECOMB-CG, 2022)

Phylogenetic Placement Problem: A Hyperbolic Embedding Approach. - Yueyu Jiang; Puoya Tabaghi; Siavash Mirarab (RECOMB-CG, 2022)

Quantifying Hierarchical Conflicts in Homology Statements. - Krister M. Swenson; Afif Elghraoui; Faramarz Valafar; Siavash Mirarab; Mathias Weller (RECOMB-CG, 2022)

Completing gene trees without species trees in sub-quadratic time. - Uyen Mai; Siavash Mirarab (Bioinform., 2022)

QuCo: quartet-based co-estimation of species trees and gene trees. - Maryam Rabiee; Siavash Mirarab (Bioinform., 2022)

ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. - Chao Zhang 055; Siavash Mirarab (Bioinform., 2022)

CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing. - Ali Osman Berk Sapci; Eleonora Rachtman; Siavash Mirarab (RECOMB-CG, 2023)

Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. - Shayesteh Arasti; Siavash Mirarab (WABI, 2023)

Phylogenomic branch length estimation using quartets. - Yasamin Tabatabaee; Chao Zhang 055; Tandy J. Warnow; Siavash Mirarab (Bioinform., 2023)

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. - Afif Elghraoui; Siavash Mirarab; Krister M. Swenson; Faramarz Valafar (Bioinform., 2023)

Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. - Shayesteh Arasti; Puoya Tabaghi; Yasamin Tabatabaee; Siavash Mirarab (RECOMB, 2024)

Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. - Ali Osman Berk Sapci; Siavash Mirarab (RECOMB, 2024)

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. - Yueyu Jiang; Daniel McDonald; Daniela Perry; Rob Knight 001; Siavash Mirarab (Bioinform., 2024)

Principal Component Analysis in Space Forms. - Puoya Tabaghi; Michael Khanzadeh; Yusu Wang 001; Siavash Mirarab (IEEE Trans. Signal Process., 2024)

Median quartet tree search algorithms using optimal subtree prune and regraft. - Shayesteh Arasti; Siavash Mirarab (Algorithms Mol. Biol., 2024)

Alignment-Free Estimation of Read to Genome Distances and Its Applications. - Ali Osman Berk Sapci; Siavash Mirarab (RECOMB, 2025)