Siavash Mirarab

Algorithms Mol. Biol., December, 2024

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.

[BibT_eX]

[DOI]

Bioinform., 2024

Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries.

[BibT_eX]

[DOI]

Ali Osman Berk Sapci

Proceedings of the Research in Computational Molecular Biology, 2024

Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using <i>Mycobacterium tuberculosis</i> isolates.

[BibT_eX]

[DOI]

Bioinform., January, 2023

Principal Component Analysis in Space Forms.

[BibT_eX]

[DOI]

CoRR, 2023

Phylogenomic branch length estimation using quartets.

[BibT_eX]

[DOI]

Bioinform., 2023

Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time.

[BibT_eX]

[DOI]

Shayesteh Arasti

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing.

[BibT_eX]

[DOI]

Ali Osman Berk Sapci

Eleonora Rachtman

Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022

ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees.

[BibT_eX]

[DOI]

Chao Zhang

Bioinform., October, 2022

QuCo: quartet-based co-estimation of species trees and gene trees.

[BibT_eX]

[DOI]

Maryam Rabiee

Bioinform., 2022

Completing gene trees without species trees in sub-quadratic time.

[BibT_eX]

[DOI]

Uyen Mai

Bioinform., 2022

Quantifying Hierarchical Conflicts in Homology Statements.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Phylogenetic Placement Problem: A Hyperbolic Embedding Approach.

[BibT_eX]

[DOI]

Yueyu Jiang

Puoya Tabaghi

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements.

[BibT_eX]

[DOI]

Md. Shamsuzzoha Bayzid

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2022

2021

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2021

SODA: multi-locus species delimitation using quartet frequencies.

[BibT_eX]

[DOI]

Maryam Rabiee

Bioinform., 2021

2020

Phylogenetic double placement of mixed samples.

[BibT_eX]

[DOI]

Metin Balaban

Bioinform., 2020

Log Transformation Improves Dating of Phylogenies.

[BibT_eX]

[DOI]

Uyen Mai

Proceedings of the Research in Computational Molecular Biology, 2020

2019

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization.

[BibT_eX]

[DOI]

John Yin

Chao Zhang

Bioinform., 2019

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.

[BibT_eX]

[DOI]

Erfan Sayyari

Ban Kawas

Bioinform., 2019

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.

[BibT_eX]

[DOI]

Niema Moshiri

Manon Ragonnet-Cronin

Joel O. Wertheim

Bioinform., 2019

APPLES: Fast Distance-Based Phylogenetic Placement.

[BibT_eX]

[DOI]

Metin Balaban

Shahab Sarmashghi

Proceedings of the Research in Computational Molecular Biology, 2019

2018

Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?

[BibT_eX]

[DOI]

Shubhanshu Shekhar

Sebastien Roch

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.

[BibT_eX]

[DOI]

BMC Bioinform., 2018

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2018

2017

ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches.

[BibT_eX]

[DOI]

Chao Zhang

Erfan Sayyari

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

TreeShrink: Efficient Detection of Outlier Tree Leaves.

[BibT_eX]

[DOI]

Uyen Mai

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

2015

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

[BibT_eX]

[DOI]

J. Comput. Biol., 2015

Ultra-large alignments using Phylogeny-aware Profiles.

[BibT_eX]

[DOI]

CoRR, 2015

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

[BibT_eX]

[DOI]

Bioinform., 2015

Ultra-Large Alignments Using Ensembles of Hidden Markov Models.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2015

2014

TIPP: taxonomic identification and phylogenetic profiling.

[BibT_eX]

[DOI]

Bioinform., 2014

ASTRAL: genome-scale coalescent-based species tree estimation.

[BibT_eX]

[DOI]

Rezwana Reaz

Md. Shamsuzzoha Bayzid

Théo Zimmermann

M. Shel Swenson

Bioinform., 2014

PASTA: Ultra-Large Multiple Sequence Alignment.

[BibT_eX]

[DOI]

Nam-phuong Nguyen

Proceedings of the Research in Computational Molecular Biology, 2014

2013

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Inferring Optimal Species Trees Under Gene Duplication and Loss.

[BibT_eX]

[DOI]

Md. Shamsuzzoha Bayzid

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012

Size-Constrained Regression Test Case Selection Using Multicriteria Optimization.

[BibT_eX]

[DOI]

Soroush Akhlaghi

IEEE Trans. Software Eng., 2012

MRL and SuperFine+MRL: new supertree methods.

[BibT_eX]

[DOI]

Nam-phuong Nguyen

Algorithms Mol. Biol., 2012

SEPP: SATe -Enabled Phylogenetic Placement.

[BibT_eX]

[DOI]

Nam Nguyen

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011

FASTSP: linear time calculation of alignment accuracy.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments.

[BibT_eX]

[DOI]

IEEE Trans. Software Eng., 2010

2008

An empirical study of the effect of time constraints on the cost-benefits of regression testing.

[BibT_eX]

[DOI]

Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of Software Engineering, 2008

An Empirical Study on Bayesian Network-based Approach for Test Case Prioritization.

[BibT_eX]

[DOI]

Proceedings of the First International Conference on Software Testing, 2008

Adaptive Action Selection in Autonomic Software Using Reinforcement Learning.

[BibT_eX]

[DOI]

Proceedings of the Fourth International Conference on Autonomic and Autonomous Systems, 2008

2007

Using Bayesian Belief Networks to Predict Change Propagation in Software Systems.

[BibT_eX]

[DOI]

Alaa Hassouna

Proceedings of the 15th International Conference on Program Comprehension (ICPC 2007), 2007

A Prioritization Approach for Software Test Cases Based on Bayesian Networks.

[BibT_eX]

[DOI]