Siavash Mirarab

53 papers A 2B 11C 1Misc 2Journal 29Unranked 8

Year	Rank	Type	Title / Venue / Authors
2025	B	`conf`	Alignment-Free Estimation of Read to Genome Distances and Its Applications. RECOMB Ali Osman Berk Sapci, Siavash Mirarab
2024	J	`jnl`	CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing. Bioinform. Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab
2024	J	`jnl`	Median quartet tree search algorithms using optimal subtree prune and regraft. Algorithms Mol. Biol. Shayesteh Arasti, Siavash Mirarab
2024	B	`conf`	Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. RECOMB Ali Osman Berk Sapci, Siavash Mirarab
2024	B	`conf`	Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. RECOMB Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab
2024	J	`jnl`	Principal Component Analysis in Space Forms. IEEE Trans. Signal Process. Puoya Tabaghi, Michael Khanzadeh, Yusu Wang, Siavash Mirarab
2024	J	`jnl`	Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinform. Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab
2023	—	`conf`	CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing. RECOMB-CG Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab
2023	J	`jnl`	Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Bioinform. Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar
2023	C	`conf`	Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. WABI Shayesteh Arasti, Siavash Mirarab
2023	J	`jnl`	Phylogenomic branch length estimation using quartets. Bioinform. Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab
2023	J	`jnl`	Principal Component Analysis in Space Forms. CoRR Puoya Tabaghi, Michael Khanzadeh, Yusu Wang, Siavash Mirarab
2022	J	`jnl`	ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinform. Chao Zhang, Siavash Mirarab
2022	J	`jnl`	Completing gene trees without species trees in sub-quadratic time. Bioinform. Uyen Mai, Siavash Mirarab
2022	—	`conf`	Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. RECOMB-CG Navid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab, Md. Shamsuzzoha Bayzid
2022	—	`conf`	Phylogenetic Placement Problem: A Hyperbolic Embedding Approach. RECOMB-CG Yueyu Jiang, Puoya Tabaghi, Siavash Mirarab
2022	J	`jnl`	QuCo: quartet-based co-estimation of species trees and gene trees. Bioinform. Maryam Rabiee, Siavash Mirarab
2022	—	`conf`	Quantifying Hierarchical Conflicts in Homology Statements. RECOMB-CG Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller
2022	B	`conf`	Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. RECOMB Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab
2021	J	`jnl`	Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput. Biol. Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna
2021	J	`jnl`	SODA: multi-locus species delimitation using quartet frequencies. Bioinform. Maryam Rabiee, Siavash Mirarab
2020	B	`conf`	Log Transformation Improves Dating of Phylogenies. RECOMB Uyen Mai, Siavash Mirarab
2020	J	`jnl`	Phylogenetic double placement of mixed samples. Bioinform. Metin Balaban, Siavash Mirarab
2019	B	`conf`	APPLES: Fast Distance-Based Phylogenetic Placement. RECOMB Metin Balaban, Shahab Sarmashghi, Siavash Mirarab
2019	J	`jnl`	ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinform. John Yin, Chao Zhang, Siavash Mirarab
2019	J	`jnl`	FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinform. Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab
2019	J	`jnl`	TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. Bioinform. Erfan Sayyari, Ban Kawas, Siavash Mirarab
2018	J	`jnl`	ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
2018	B	`conf`	Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. RECOMB Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab
2018	J	`jnl`	Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE ACM Trans. Comput. Biol. Bioinform. Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
2017	—	`conf`	ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. RECOMB-CG Chao Zhang, Erfan Sayyari, Siavash Mirarab
2017	B	`conf`	Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? RECOMB Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
2017	J	`jnl`	Species tree estimation using ASTRAL: how many genes are enough? CoRR Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab
2017	—	`conf`	TreeShrink: Efficient Detection of Outlier Tree Leaves. RECOMB-CG Uyen Mai, Siavash Mirarab
2015	J	`jnl`	ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. Siavash Mirarab, Tandy J. Warnow
2015	J	`jnl`	PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow
2015	B	`conf`	Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
2015	J	`jnl`	Ultra-large alignments using Phylogeny-aware Profiles. CoRR Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
2014	J	`jnl`	ASTRAL: genome-scale coalescent-based species tree estimation. Bioinform. Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow
2014	B	`conf`	PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow
2014	J	`jnl`	TIPP: taxonomic identification and phylogenetic profiling. Bioinform. Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow
2013	Misc	`conf`	Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow
2013	J	`jnl`	Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinform. 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
2012	J	`jnl`	MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow
2012	Misc	`conf`	SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing Siavash Mirarab, Nam Nguyen, Tandy J. Warnow
2012	J	`jnl`	Size-Constrained Regression Test Case Selection Using Multicriteria Optimization. IEEE Trans. Software Eng. Siavash Mirarab, Soroush Akhlaghi, Ladan Tahvildari
2011	J	`jnl`	FASTSP: linear time calculation of alignment accuracy. Bioinform. Siavash Mirarab, Tandy J. Warnow
2010	J	`jnl`	The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments. IEEE Trans. Software Eng. Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel
2008	—	`conf`	Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. ICAS Mehdi Amoui, Mazeiar Salehie, Siavash Mirarab, Ladan Tahvildari
2008	A	`conf`	An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. ICST Siavash Mirarab, Ladan Tahvildari
2008	—	`conf`	An empirical study of the effect of time constraints on the cost-benefits of regression testing. SIGSOFT FSE Hyunsook Do, Siavash Mirarab, Ladan Tahvildari, Gregg Rothermel
2007	B	`conf`	A Prioritization Approach for Software Test Cases Based on Bayesian Networks. FASE Siavash Mirarab, Ladan Tahvildari
2007	A	`conf`	Using Bayesian Belief Networks to Predict Change Propagation in Software Systems. ICPC Siavash Mirarab, Alaa Hassouna, Ladan Tahvildari