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Siavash 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
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. RECOMB 2024: 462-465 - 2023
- [j21]Afif Elghraoui
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. Bioinform. 39(1) (2023) - [j20]Yasamin Tabatabaee
Phylogenomic branch length estimation using quartets. Bioinform. 39(Supplement-1): 185-193 (2023) - [c21]Ali Osman Berk Sapci
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
Completing gene trees without species trees in sub-quadratic time. Bioinform. 38(6): 1532-1541 (2022) - [j18]Chao Zhang
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
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
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
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
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
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
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19-S(6): 15-30 (2018) - [j10]Shubhanshu Shekhar
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
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
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
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. 22(5): 377-386 (2015) - [c9]Nam-phuong Nguyen
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
ASTRAL: genome-scale coalescent-based species tree estimation. Bioinform. 30(17): 541-548 (2014) - [j6]Nam-phuong Nguyen
TIPP: taxonomic identification and phylogenetic profiling. Bioinform. 30(24): 3548-3555 (2014) - [c8]Siavash Mirarab
PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB 2014: 177-191 - 2013
- [j5]Arlin Stoltzfus
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
MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. 7: 3 (2012) - [j3]Siavash Mirarab
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
FASTSP: linear time calculation of alignment accuracy. Bioinform. 27(23): 3250-3258 (2011) - 2010
- [j1]Hyunsook Do, Siavash Mirarab
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
Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. ICAS 2008: 175-181 - [c4]Siavash Mirarab
An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization. ICST 2008: 278-287 - [c3]Hyunsook Do, Siavash Mirarab
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
A Prioritization Approach for Software Test Cases Based on Bayesian Networks. FASE 2007: 276-290 - [c1]Siavash Mirarab
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 22:09 CEST by the dblp team
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