Siavash Mirarab

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 30

Top Topics

Sequenced Genomes

Maximum Parsimony

Top Venues

Publications

Shayesteh Arasti, Siavash Mirarab
Median quartet tree search algorithms using optimal subtree prune and regraft. Algorithms Mol. Biol. 19 (1) (2024)
Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinform. 40 (6) (2024)
Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. RECOMB (2024)
Ali Osman Berk Sapci, Siavash Mirarab
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. RECOMB (2024)
Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar
isolates. Bioinform. 39 (1) (2023)
Shayesteh Arasti, Siavash Mirarab
Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. WABI (2023)
Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab
Phylogenomic branch length estimation using quartets. Bioinform. 39 (Supplement-1) (2023)
Puoya Tabaghi, Michael Khanzadeh, Yusu Wang, Siavash Mirarab
Principal Component Analysis in Space Forms. CoRR (2023)
Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab
CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing. RECOMB-CG (2023)
Chao Zhang, Siavash Mirarab
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinform. 38 (21) (2022)
Uyen Mai, Siavash Mirarab
Completing gene trees without species trees in sub-quadratic time. Bioinform. 38 (6) (2022)
Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller
Quantifying Hierarchical Conflicts in Homology Statements. RECOMB-CG (2022)
Yueyu Jiang, Puoya Tabaghi, Siavash Mirarab
Phylogenetic Placement Problem: A Hyperbolic Embedding Approach. RECOMB-CG (2022)
Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. RECOMB (2022)
Navid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab, Md. Shamsuzzoha Bayzid
Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. RECOMB-CG (2022)
Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput. Biol. 17 (11) (2021)
Maryam Rabiee, Siavash Mirarab
SODA: multi-locus species delimitation using quartet frequencies. Bioinform. 36 (24) (2021)
Uyen Mai, Siavash Mirarab
Log Transformation Improves Dating of Phylogenies. RECOMB (2020)
Metin Balaban, Siavash Mirarab
Phylogenetic double placement of mixed samples. Bioinform. 36 (Supplement-1) (2020)
Erfan Sayyari, Ban Kawas, Siavash Mirarab
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. Bioinform. 35 (14) (2019)
John Yin, Chao Zhang, Siavash Mirarab
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinform. 35 (20) (2019)
Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinform. 35 (11) (2019)
Metin Balaban, Shahab Sarmashghi, Siavash Mirarab
APPLES: Fast Distance-Based Phylogenetic Placement. RECOMB (2019)
Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. RECOMB (2018)
Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. (6) (2018)
Chao Zhang, Erfan Sayyari, Siavash Mirarab
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. RECOMB-CG (2017)
Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? RECOMB (2017)
Uyen Mai, Siavash Mirarab
TreeShrink: Efficient Detection of Outlier Tree Leaves. RECOMB-CG (2017)
Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
Species tree estimation using ASTRAL: how many genes are enough? CoRR (2017)
Siavash Mirarab, Tandy J. Warnow
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. 31 (12) (2015)
Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
Ultra-large alignments using Phylogeny-aware Profiles. CoRR (2015)
Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. 22 (5) (2015)
Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB (2015)
Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow
PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB (2014)
Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow
ASTRAL: genome-scale coalescent-based species tree estimation. Bioinform. 30 (17) (2014)
Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow
TIPP: taxonomic identification and phylogenetic profiling. Bioinform. 30 (24) (2014)
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, Megan 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
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinform. 14 (2013)
Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow
Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing (2013)
Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow
MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. 7 (2012)
Siavash Mirarab, Soroush Akhlaghi, Ladan Tahvildari
Size-Constrained Regression Test Case Selection Using Multicriteria Optimization. IEEE Trans. Software Eng. 38 (4) (2012)
Siavash Mirarab, Nam Nguyen, Tandy J. Warnow
SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing (2012)
Siavash Mirarab, Tandy J. Warnow
FASTSP: linear time calculation of alignment accuracy. Bioinform. 27 (23) (2011)
Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel
The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments. IEEE Trans. Software Eng. 36 (5) (2010)
Mehdi Amoui, Mazeiar Salehie, Siavash Mirarab, Ladan Tahvildari
Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. ICAS (2008)
Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel
An empirical study of the effect of time constraints on the cost-benefits of regression testing. SIGSOFT FSE (2008)
Siavash Mirarab, Ladan Tahvildari
An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. ICST (2008)
Siavash Mirarab, Ladan Tahvildari
A Prioritization Approach for Software Test Cases Based on Bayesian Networks. FASE (2007)
Siavash Mirarab, Alaa Hassouna, Ladan Tahvildari
Using Bayesian Belief Networks to Predict Change Propagation in Software Systems. ICPC (2007)