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ORCIDSiavash Mirarab
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2020 – today
- 2024
[j23]Shayesteh Arasti, Siavash Mirarab:
Median quartet tree search algorithms using optimal subtree prune and regraft. Algorithms Mol. Biol. 19(1): 12 (2024)- [j22]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) - [c23]Ali Osman Berk Sapci, Siavash Mirarab:
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. RECOMB 2024: 340-343 - [c22]Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab:
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. RECOMB 2024: 462-465 - 2023
- [j21]Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. Bioinform. 39(1) (2023) - [j20]Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab:
Phylogenomic branch length estimation using quartets. Bioinform. 39(Supplement-1): 185-193 (2023) - [c21]Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab:
CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing. RECOMB-CG 2023: 196-214 - [c20]Shayesteh Arasti, Siavash Mirarab:
Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. WABI 2023: 4:1-4:20 - [i3]Puoya Tabaghi, Michael Khanzadeh, Yusu Wang, Siavash Mirarab:
Principal Component Analysis in Space Forms. CoRR abs/2301.02750 (2023) - 2022
- [j19]Uyen Mai, Siavash Mirarab:
Completing gene trees without species trees in sub-quadratic time. Bioinform. 38(6): 1532-1541 (2022) - [j18]Chao Zhang, Siavash Mirarab:
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinform. 38(21): 4949-4950 (2022) - [c19]Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab:
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. RECOMB 2022: 366-368 - [c18]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: 33-51 - [c17]Yueyu Jiang, Puoya Tabaghi, Siavash Mirarab:
Phylogenetic Placement Problem: A Hyperbolic Embedding Approach. RECOMB-CG 2022: 68-85 - [c16]Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller:
Quantifying Hierarchical Conflicts in Homology Statements. RECOMB-CG 2022: 146-167 - 2021
- [j17]Maryam Rabiee, Siavash Mirarab:
SODA: multi-locus species delimitation using quartet frequencies. Bioinform. 36(24): 5623-5631 (2021) - [j16]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) - 2020
- [j15]Metin Balaban, Siavash Mirarab:
Phylogenetic double placement of mixed samples. Bioinform. 36(Supplement-1): i335-i343 (2020) - [c15]Uyen Mai, Siavash Mirarab:
Log Transformation Improves Dating of Phylogenies. RECOMB 2020: 264-265
2010 – 2019
- 2019
- [j14]Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab:
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinform. 35(11): 1852-1861 (2019) - [j13]Erfan Sayyari, Ban Kawas, Siavash Mirarab:
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. Bioinform. 35(14): i31-i40 (2019) - [j12]John Yin, Chao Zhang, Siavash Mirarab:
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinform. 35(20): 3961-3969 (2019) - [c14]Metin Balaban, Shahab Sarmashghi, Siavash Mirarab:
APPLES: Fast Distance-Based Phylogenetic Placement. RECOMB 2019: 287-288 - 2018
- [j11]Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab:
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19-S(6): 15-30 (2018) - [j10]Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab:
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1738-1747 (2018) - [c13]Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab:
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. RECOMB 2018: 276-277 - 2017
- [c12]Chao Zhang, Erfan Sayyari, Siavash Mirarab:
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. RECOMB-CG 2017: 53-75 - [c11]Uyen Mai, Siavash Mirarab:
TreeShrink: Efficient Detection of Outlier Tree Leaves. RECOMB-CG 2017: 116-140 - [c10]Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab:
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? RECOMB 2017: 393-395 - [i2]Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab:
Species tree estimation using ASTRAL: how many genes are enough? CoRR abs/1704.06831 (2017) - 2015
- [j9]Siavash Mirarab, Tandy J. Warnow:
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. 31(12): 44-52 (2015) - [j8]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): 377-386 (2015) - [c9]Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow:
Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB 2015: 259-260 - [i1]Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow:
Ultra-large alignments using Phylogeny-aware Profiles. CoRR abs/1504.01142 (2015) - 2014
- [j7]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): 541-548 (2014) - [j6]Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow:
TIPP: taxonomic identification and phylogenetic profiling. Bioinform. 30(24): 3548-3555 (2014) - [c8]Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow:
PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB 2014: 177-191 - 2013
- [j5]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:
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinform. 14: 158 (2013) - [c7]Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow:
Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing 2013: 250-261 - 2012
- [j4]Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow:
MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. 7: 3 (2012) - [j3]Siavash Mirarab, Soroush Akhlaghi, Ladan Tahvildari:
Size-Constrained Regression Test Case Selection Using Multicriteria Optimization. IEEE Trans. Software Eng. 38(4): 936-956 (2012) - [c6]Siavash Mirarab, Nam Nguyen, Tandy J. Warnow:
SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing 2012: 247-258 - 2011
- [j2]Siavash Mirarab, Tandy J. Warnow:
FASTSP: linear time calculation of alignment accuracy. Bioinform. 27(23): 3250-3258 (2011) - 2010
- [j1]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): 593-617 (2010)
2000 – 2009
- 2008
- [c5]Mehdi Amoui, Mazeiar Salehie, Siavash Mirarab, Ladan Tahvildari:
Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. ICAS 2008: 175-181 - [c4]Siavash Mirarab, Ladan Tahvildari:
An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. ICST 2008: 278-287 - [c3]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: 71-82 - 2007
- [c2]Siavash Mirarab, Ladan Tahvildari:
A Prioritization Approach for Software Test Cases Based on Bayesian Networks. FASE 2007: 276-290 - [c1]Siavash Mirarab, Alaa Hassouna, Ladan Tahvildari:
Using Bayesian Belief Networks to Predict Change Propagation in Software Systems. ICPC 2007: 177-188
Coauthor Index
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last updated on 2024-10-07 21:17 CEST by the dblp team
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