| 2025 | RECOMB | Alignment-Free Estimation of Read to Genome Distances and Its Applications. | Ali Osman Berk Sapci, Siavash Mirarab |
| 2024 | RECOMB | Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. | Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab |
| 2024 | RECOMB | Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. | Ali Osman Berk Sapci, Siavash Mirarab |
| 2023 | WABI | Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. | Shayesteh Arasti, Siavash Mirarab |
| 2022 | RECOMB | Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. | Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab |
| 2020 | RECOMB | Log Transformation Improves Dating of Phylogenies. | Uyen Mai, Siavash Mirarab |
| 2019 | RECOMB | APPLES: Fast Distance-Based Phylogenetic Placement. | Metin Balaban, Shahab Sarmashghi, Siavash Mirarab |
| 2018 | RECOMB | Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. | Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab |
| 2017 | RECOMB | TreeShrink: Efficient Detection of Outlier Tree Leaves. | Uyen Mai, Siavash Mirarab |
| 2017 | RECOMB | Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? | Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab |
| 2017 | RECOMB | ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. | Chao Zhang, Erfan Sayyari, Siavash Mirarab |
| 2015 | RECOMB | Ultra-Large Alignments Using Ensembles of Hidden Markov Models. | Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow |
| 2014 | RECOMB | PASTA: Ultra-Large Multiple Sequence Alignment. | Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow |
| 2013 | PSB | Inferring Optimal Species Trees Under Gene Duplication and Loss. | Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow |
| 2012 | PSB | SEPP: SATe -Enabled Phylogenetic Placement. | Siavash Mirarab, Nam Nguyen, Tandy J. Warnow |
| 2008 | ICST | An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. | Siavash Mirarab, Ladan Tahvildari |
| 2007 | FASE | A Prioritization Approach for Software Test Cases Based on Bayesian Networks. | Siavash Mirarab, Ladan Tahvildari |