Siavash Mirarab
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Explore the profile of Siavash Mirarab including associated specialties, affiliations and a list of published articles.
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93
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6327
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Recent Articles
1.
Tabatabaee Y, Claramunt S, Mirarab S
bioRxiv
. 2025 Mar;
PMID: 40060389
Species trees need to be dated for many downstream applications. Typical molecular dating methods take a phylogenetic tree with branch lengths in substitution units as well as a set of...
2.
Tabatabaee Y, Zhang C, Arasti S, Mirarab S
bioRxiv
. 2025 Mar;
PMID: 40027742
Code Availability: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER . Data Availability: The datasets and scripts used in this study are available at https://github.com/ytabatabaee/CASTLES-Pro-paper .
3.
Zhang C, Nielsen R, Mirarab S
Science
. 2025 Jan;
387(6737):eadk9688.
PMID: 39847611
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. Although genome-wide data are routinely used for discordance-aware phylogenomic analyses, because of modeling and...
4.
Sapci A, Mirarab S
Genome Res
. 2024 Aug;
34(9):1455-1467.
PMID: 39209553
Using -mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these downstream applications relies on the density of the reference...
5.
Sapci A, Mirarab S
bioRxiv
. 2024 Jul;
PMID: 39026785
Using -mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these down-stream applications relies on the density of the reference...
6.
Mai U, Charvel E, Mirarab S
Syst Biol
. 2024 Jul;
73(5):823-838.
PMID: 38970346
Dating phylogenetic trees to obtain branch lengths in time units is essential for many downstream applications but has remained challenging. Dating requires inferring substitution rates that can change across the...
7.
Jiang Y, McDonald D, Perry D, Knight R, Mirarab S
Bioinformatics
. 2024 Jun;
40(6).
PMID: 38870525
Motivation: Phylogenetic placement of a query sequence on a backbone tree is increasingly used across biomedical sciences to identify the content of a sample from its DNA content. The accuracy...
8.
Gupta A, Mirarab S, Turakhia Y
bioRxiv
. 2024 Jun;
PMID: 38854139
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are...
9.
Arasti S, Tabaghi P, Tabatabaee Y, Mirarab S
bioRxiv
. 2024 May;
PMID: 38746464
Code And Data Availability: The software is available at https://github.com/shayesteh99/TCMM.git . Data is available on Github https://github.com/shayesteh99/TCMM-Data.git .
10.
Mirarab S, Bafna V
Methods Mol Biol
. 2024 Apr;
2744:247-265.
PMID: 38683324
In this protocol paper, we review a set of methods developed in recent years for analyzing nuclear reads obtained from genome skimming. As the cost of sequencing drops, genome skimming...