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1. Full Text INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores
by Rabiee, Maryam and Mirarab, Siavash
Systematic Biology, ISSN 1063-5157, 07/2019
Phylogenomic analyses have increasingly adopted species tree reconstruction using methods that account for gene tree discordance using pipelines that require... 
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2. Full Text ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
by Mirarab, Siavash and Warnow, Tandy
Bioinformatics, ISSN 1367-4803, 06/2015, Volume 31, Issue 12, pp. i44 - i52
Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting,... 
ANGIOSPERMS | ROOT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PHYLOGENETIC ANALYSIS | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Data Interpretation, Statistical | Algorithms | Plants - genetics | Genes, Plant | Computer Simulation | Genetic Speciation | Genomics | Phylogeny | Plants - classification | Index Medicus | Ismb | Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland
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3. Full Text A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition
by Moshiri, Niema and Mirarab, Siavash
Systematic Biology, ISSN 1063-5157, 05/2018, Volume 67, Issue 3, pp. 475 - 489
Abstract Models of tree evolution have mostly focused on capturing the cladogenesis processes behind speciation. Processes that derive the evolution of genomic... 
Model | Evolution | Alu | Retrotransposition | Models, Biological | Humans | Classification - methods | Phylogeny | Alu Elements - genetics | Genome, Human - genetics | Evolution, Molecular | Index Medicus | model | evolution | Regular | retrotransposition
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4. Full Text Evaluating summarymethods for multilocus species tree estimation in the presence of incomplete lineage sorting
by Mirarab, Siavash and Bayzid, Md Shamsuzzoha and Warnow, Tandy
Systematic Biology, ISSN 1063-5157, 2016, Volume 65, Issue 3, pp. 366 - 380
Multilocus Bootstrapping | Incomplete Lineage Sorting | Concatenation | MRL | Species Tree Estimation | Consensus Methods | MRP | Supertree Methods | Gene Tree Discordance | MP-EST
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5. Full Text Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
by Sayyari, Erfan and Mirarab, Siavash
Molecular biology and evolution, ISSN 0737-4038, 07/2016, Volume 33, Issue 7, pp. 1654 - 1668
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there... 
branch length estimation | local support | quartet-based methods | multi-species coalescent | posterior probability | Incomplete lineage sorting | ASTRAL | PHYLOGENOMICS | MAXIMUM-LIKELIHOOD | PHYLOGENETIC ANALYSIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESTIMATING SPECIES TREES | INFERENCE | CONCORDANCE | GENE TREES | EVOLUTIONARY BIOLOGY | BOOTSTRAP | GENETICS & HEREDITY | BAYESIAN-ESTIMATION | DISCORDANCE | Computational Biology - methods | Algorithms | Computer Simulation | Genetic Speciation | Bayes Theorem | Probability | Models, Genetic | Phylogeny | Genomics - methods | Index Medicus | Fast Track
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6. Full Text Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
by Mirarab, Siavash and Bayzid, Md Shamsuzzoha and Warnow, Tandy
Systematic Biology, ISSN 1063-5157, 05/2016, Volume 65, Issue 3, pp. 366 - 380
Abstract Species tree estimation is complicated by processes, such as gene duplication and loss and incomplete lineage sorting (ILS), that cause discordance... 
MAXIMUM-LIKELIHOOD | incomplete lineage sorting | TIMES | MRL | MRP | ALGORITHMS | SIMULATION | consensus methods | multilocus bootstrapping | SISTER GROUP | gene tree discordance | supertree methods | GENE TREES | CHOICE | EVOLUTIONARY BIOLOGY | concatenation | PHYLOGENY INFERENCE | species tree estimation | TURTLES | MP-EST | Gene Duplication | Probability | Classification - methods | Phylogeny | Computer Simulation | Genetics | Accuracy | Genealogy | Estimating techniques | Maximum likelihood method | Index Medicus
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7. Full Text ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees
by Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash
BMC Bioinformatics, ISSN 1471-2105, 05/2018, Volume 19, Issue Suppl 6, pp. 153 - 153
Background: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny.... 
Incomplete lineage sorting | ASTRAL | Phylogenomics | SUPPORT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PHYLOGENETIC ANALYSIS | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | INFERENCE | TOOL | Algorithms | Animals | Species Specificity | Time Factors | Computer Simulation | Databases, Genetic | Birds - classification | Models, Genetic | Phylogeny | Birds - genetics | Index Medicus
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8. Full Text Statistical binning enables an accurate coalescent-based estimation of the avian tree
by Mirarab, Siavash and Bayzid, Md. Shamsuzzoha and Boussau, Bastien and Warnow, Tandy
Science, ISSN 0036-8075, 12/2014, Volume 346, Issue 6215, pp. 1337 - 1337
Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although... 
INFERRING SPECIES TREES | SCALE COESTIMATION | PHYLUM | GENE TREES | TIMES | CLOSEST LIVING RELATIVES | MULTIDISCIPLINARY SCIENCES | INCONGRUENCE | INFERENCE | GENOME | REVEALS | Mammals - genetics | Mammals - classification | Vertebrates - genetics | Computational Biology | Birds - classification | Phylogeny | Yeasts - genetics | Likelihood Functions | Sequence Alignment | Animals | Vertebrates - classification | Birds - genetics | Genome | Phylogenetics | Birds | Statistical analysis | Decision trees | Index Medicus | Trees | Production methods | Pipelines | Genes | Error detection | Graph theory | Estimates | Optimization
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9. Full Text TreeShrink: Fast and accurate detection of outlier long branches in collections of phylogenetic trees
by Mai, Uyen and Mirarab, Siavash
BMC Genomics, ISSN 1471-2164, 05/2018, Volume 19, Issue Suppl 5, pp. 272 - 272
Background: Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level,... 
Gene tree discordance | Rogue taxon removal | Tree diameter | PHYLOGENOMICS | XENOTURBELLA | SIMULATION | XENACOELOMORPHA | ALIGNMENTS | TAXA | SUPPORT | ORIGIN | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | SELECTION | Mammals - genetics | Computational Biology - methods | Mammals - classification | Datasets as Topic | Species Specificity | Genes | Humans | Phylogeny | Plants - classification | Algorithms | Animals | Plants - genetics | Models, Genetic | Software | Phylogenetic trees | Research | Analysis | Index Medicus
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10. Full Text ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
by Yin, John and Zhang, Chao and Mirarab, Siavash
Bioinformatics (Oxford, England), ISSN 1367-4803, 03/2019
Evolutionary histories can change from one part of the genome to another. The potential for discordance between the gene trees has motivated the development of... 
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11. Full Text Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?
by Shekhar, Shubhanshu and Roch, Sebastien and Mirarab, Siavash
IEEE/ACM Transactions on Computational Biology and Bioinformatics, ISSN 1545-5963, 09/2018, Volume 15, Issue 5, pp. 1738 - 1747
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete... 
incomplete lineage sorting | Sociology | species tree estimation | Estimation | Genomics | Vegetation | Phylogenetics | Topology | Complexity theory | Statistics | sample complexity | ASTRAL | PHYLOGENOMICS | DIVERSIFICATION | TIMES | RESOLUTION | BIOCHEMICAL RESEARCH METHODS | STATISTICS & PROBABILITY | INFERENCE | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICS, INTERDISCIPLINARY APPLICATIONS | EVOLUTION | DISCORDANCE | Computational Biology - methods | Algorithms | Computer Simulation | Genetic Speciation | Models, Genetic | Software | Phylogeny | Trees | Reconstruction | Species | Genes | Discordance
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12. Full Text Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction
by Sayyari, Erfan and Mirarab, Siavash
BMC Genomics, ISSN 1471-2164, 11/2016, Volume 17, Issue Suppl 10, pp. 783 - 783
Background: Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and... 
Quartet methods | Species tree | Multi-species coalescent | Incomplete lineage sorting | PHYLOGENOMICS | SEQUENCES | TIMES | PERFORMANCE | INFERENCE | GENE TREES | SUPPORT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | Genetic research | Origin of species | Genetic aspects | Phylogeny | Analysis | Index Medicus
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13. Full Text Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
by Mai, Uyen and Sayyari, Erfan and Mirarab, Siavash
PLoS ONE, ISSN 1932-6203, 08/2017, Volume 12, Issue 8, pp. e0182238 - e0182238
Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream... 
MULTISPECIES COALESCENT MODEL | PHYLOGENOMICS | NUCLEOTIDE | GENERAL MARKOV MODEL | EVOLUTION | MULTIDISCIPLINARY SCIENCES | UNIVERSAL TREE | COMPUTATION | INFERENCE | DISTANT OUTGROUPS | LIFE | Algorithms | Phylogeny | Species Specificity | Computer Simulation | Genes | Databases as Topic | Physiological aspects | Phylogenetic trees | Plant cuttings | Research | Methods | Trees | Computer simulation | Taxonomy | Biological evolution | Variance (statistics) | Genomics | Systematic biology | Discordance | Computer engineering | Genomes | Phylogenetics | Evolution | Mutation | Rooting | Molecular biology | Bioinformatics | Index Medicus
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14. Full Text Phylotranscriptomic analysis of the origin and early diversification of land plants
by Norman J. Wickett and Siavash Mirarab and Nam Nguyen and Tandy Warnow and Eric Carpenter and Naim Matasci and Saravanaraj Ayyampalayam and Michael S. Barker and J. Gordon Burleigh and Matthew A. Gitzendanner and Brad R. Ruhfel and Eric Wafula and Joshua P. Der and Sean W. Graham and Sarah Mathews and Michael Melkonian and Douglas E. Soltis and Pamela S. Soltis and Nicholas W. Miles and Carl J. Rothfels and Lisa Pokorny and A. Jonathan Shaw and Lisa DeGironimo and Dennis W. Stevenson and Barbara Surek and Juan Carlos Villarreal and Béatrice Roure and Hervé Philippe and Claude W. dePamphilis and Tao Chen and Michael K. Deyholos and Regina S. Baucom and Toni M. Kutchan and Megan M. Augustin and Jun Wang and Yong Zhang and Zhijian Tian and Zhixiang Yan and Xiaolei Wu and Xiao Sun and Gane Ka-Shu Wong and James Leebens-Mack
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 11/2014, Volume 111, Issue 45, pp. E4859 - E4868
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for... 
Land plants | Phylogeny | Streptophyta | Transcriptome | Phylogenomics | PHYLOGENY GROUP CLASSIFICATION | CHLOROPLAST GENOME SEQUENCE | PLASTID GENOMES | MULTIGENE PHYLOGENY | transcriptome | CLOSEST LIVING RELATIVES | MULTIDISCIPLINARY SCIENCES | land plants | GREEN-ALGA MOUGEOTIA | phylogeny | FLOWERING PLANTS | EARLIEST ANGIOSPERMS | SEED PLANTS | phylogenomics | EXTANT GYMNOSPERMS | Streptophyta - classification | Sequence Alignment | Streptophyta - physiology | Quantitative Trait, Heritable | Gene Expression Profiling | Genome, Plant - physiology | DNA, Plant - metabolism | Transcriptome - physiology | DNA, Plant - genetics | Evolution, Molecular | Phylogenetics | Evolution | Flowers & plants | Maximum likelihood method | Algae | Index Medicus | Biological Sciences | PNAS Plus
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15. Full Text The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments
by Hyunsook Do and Mirarab, S and Tahvildari, L and Rothermel, G
IEEE Transactions on Software Engineering, ISSN 0098-5589, 09/2010, Volume 36, Issue 5, pp. 593 - 617
Regression testing is an expensive process used to validate modified software. Test case prioritization techniques improve the cost-effectiveness of regression... 
Software testing | System testing | cost-benefits | test case prioritization | Maintenance engineering | Programming | Regression testing | Computer Society | empirical studies | Automatic testing | Bayesian methods | Software quality | Software systems | Bayesian networks | Time factors | SUITE | COST-EFFECTIVENESS | ENGINEERING, ELECTRICAL & ELECTRONIC | COMPUTER SCIENCE, SOFTWARE ENGINEERING | REGRESSION TEST SELECTION | SYSTEM MODELS | MUTATION | FAULTS | Usage | Software | Regression analysis | Cost benefit analysis | Analysis | Studies | Bayesian analysis | Software engineering | Faults | Software development | Tradeoffs | Regression | Maintenance | Order disorder | Computer programs
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16. Full Text Weighted statistical binning: Enabling statistically consistent genome-scale phylogenetic analyses
by Bayzid, Md Shamsuzzoha and Mirarab, Siavash and Boussau, Bastien and Warnow, Tandy
PLoS ONE, ISSN 1932-6203, 06/2015, Volume 10, Issue 6, pp. e0129183 - e0129183
Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across... 
INFERRING SPECIES TREES | PHYLOGENOMICS | GENE TREES | MAXIMUM-LIKELIHOOD | MULTIDISCIPLINARY SCIENCES | SEQUENCE ALIGNMENTS | BAYESIAN-INFERENCE | Models, Theoretical | Statistics as Topic | Phylogeny | Genomics - methods | Genomes | Analysis | Genomics | Trees | Statistical analysis | Genes | Heuristic methods | Biological evolution | Probability | Statistical methods | Empirical analysis | Loci | Biological activity | Computer science | Studies | Accuracy | Biological effects | Phylogenetics | Mathematical models | Bioinformatics | Species | Methods | Information theory | Index Medicus
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