Siavash Mirarab

UC San Diego Health System — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

53h-index24.0kcitations211works14.22yr avg
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Research Topics

Genomics and Phylogenetic Studies(154), Genetic diversity and population structure(89), Chromosomal and Genetic Variations(24), Gene expression and cancer classification(20), Evolution and Paleontology Studies(19)

Publications203 total

dairabel92/spruce: Version 0.2.0
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
dairabel92/spruce: Version 0.2.0
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation
2025Open Access
Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss
Genome Biology and Evolution·2025Open Access
Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using <i>k</i> ‐Mer Frequencies
Molecular Ecology Resources·2025· 1 citedOpen Access
ASTER: A Package for Large-Scale Phylogenomic Reconstructions
Molecular Biology and Evolution·2025· 18 citedOpen Access
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES
Proceedings of the National Academy of Sciences·2025· 7 citedOpen Access
Machine learning enables alignment-free distance calculation and phylogenetic placement using k-mer frequencies
2025Open Access
Coalescent-based branch length estimation improves dating of species trees
2025· 1 citedOpen Access
Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss
2025· 4 citedOpen Access
A <i>k</i> -mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement
2025· 2 citedOpen Access
CASTER: Direct species tree inference from whole-genome alignments
Science·2025· 28 citedOpen Access
Net rate of lateral gene transfer in marine prokaryoplankton
The ISME Journal·2025· 3 citedOpen Access
Alignment-Free Estimation of Read to Genome Distances and Its Applications
Lecture notes in computer science·2025· 1 cited
Memory-bound <i>k</i> -mer selection for large and evolutionarily diverse reference libraries
Genome Research·2024· 4 citedOpen Access
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model
Systematic Biology·2024· 5 citedOpen Access
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES
2024· 1 citedOpen Access
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach
Bioinformatics·2024· 2 citedOpen Access
Complexity of avian evolution revealed by family-level genomes
Nature·2024· 245 citedOpen Access
A region of suppressed recombination misleads neoavian phylogenomics
Proceedings of the National Academy of Sciences·2024· 32 citedOpen Access
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Frequent Co-authors

Tandy Warnow(19), Erfan Sayyari(8), Nam Nguyen(8), Chao Zhang(6), M. Thomas P. Gilbert(6), Rob Knight(5), Rute R. da Fonseca(5), Md. Shamsuzzoha Bayzid(5), Uyen Mai(5), Daniel McDonald(4), Qiyun Zhu(4), Brant C. Faircloth(4), Bent Petersen(4), Joël Cracraft(4), Pamela S. Soltis(4), Metin Balaban(4), Ladan Tahvildari(4), Jon G. Sanders(3), Stefan Janssen(3), Evguenia Kopylova(3)