Siavash Mirarab

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

6.0Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Greengenes2 unifies microbial data in a single reference tree

Nature Biotechnology(2023)10.1038/s41587-023-01845-1

Top 5%

4.4DataRank

Top 5%629 citations

Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio González +20 more

Papers

Driven by 30 papers — median percentile 91. Top paper: “Greengenes2 unifies microbial data in a single reference tree”.

Greengenes2 unifies microbial data in a single reference tree

Nature Biotechnology(2023)10.1038/s41587-023-01845-1

Top 5%

4.4DataRank

Top 5%629 citations

Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio González +20 more

Greengenes2 enables a shared data universe for microbiome studies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.19.520774

Top 13%

1.6DataRank

Top 13%44 citations

Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio González +20 more

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Nature Communications(2020)10.1038/s41467-020-16366-7

N/A

1.0DataRank · unranked

917 citations

Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi +13 more

Dense sampling of bird diversity increases power of comparative genomics

Nature(2020)10.1038/s41586-020-2873-9

N/A

0.946DataRank · unranked

549 citations

Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve +95 more

Phylogenomics: Constrained gene tree inference

Nature Ecology & Evolution(2017)10.1038/s41559-016-0056

N/A

0.667DataRank · unranked

10 citations

Siavash Mirarab

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

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009449

N/A

0.550DataRank · unranked

38 citations

Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna +1 more

Generation of accurate, expandable phylogenomic trees with uDance

Nature Biotechnology(2023)10.1038/s41587-023-01868-8

N/A

0.470DataRank · unranked

22 citations

Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab +1 more

Author Correction: Greengenes2 unifies microbial data in a single reference tree

Nature Biotechnology(2023)10.1038/s41587-023-02026-w

N/A

0.470DataRank · unranked

22 citations

Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio González +20 more

A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods

Frontiers in Immunology(2022)10.3389/fimmu.2022.1014439

N/A

0.373DataRank · unranked

11 citations

Andrey V. Bzikadze, Yana Safonova, Siavash Mirarab, Chao Zhang

CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing

Bioinformatics(2024)10.1093/bioinformatics/btae150

N/A

0.360DataRank · unranked

10 citations

Eleonora Rachtman, Siavash Mirarab, Ali Osman Berk Şapcı

Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model

Systematic Biology(2024)10.1093/sysbio/syae034

N/A

0.275DataRank · unranked

5 citations

Eduardo Charvel, Siavash Mirarab, Uyen Mai

Median quartet tree search algorithms using optimal subtree prune and regraft

Algorithms for Molecular Biology(2024)10.1186/s13015-024-00257-3

N/A

0.208DataRank · unranked

3 citations

Siavash Mirarab, Shayesteh Arasti

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

Bioinformatics(2024)10.1093/bioinformatics/btae361

N/A

0.165DataRank · unranked

2 citations

Daniel McDonald, Daniela S. Perry, Rob Knight, Siavash Mirarab, Yueyu Jiang

DEPP: Deep Learning Enables Extending Species Trees using Single Genes

Systematic Biology(2022)10.1093/sysbio/syac031

N/A

0DataRank · unranked

36 citations

Metin Balaban, Qiyun Zhu, Siavash Mirarab, Yueyu Jiang

Branch Length Transforms using Optimal Tree Metric Matching

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.13.566962

N/A

0DataRank · unranked

4 citations

Puoya Tabaghi, Yasamin Tabatabaee, Alan K. Mayer, Siavash Mirarab, Shayesteh Arasti

Author Correction: Generation of accurate, expandable phylogenomic trees with uDance

Nature Biotechnology(2023)10.1038/s41587-023-02027-9

N/A

0DataRank · unranked

0 citations

Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab +1 more

Principal Component Analysis in Space Forms

IEEE Transactions on Signal Processing(2024)10.1109/tsp.2024.3457529

N/A

0DataRank · unranked

5 citations

Michael Khanzadeh, Yusu Wang, Siavash Mirarab, Puoya Tabaghi

Memory-bound k -mer selection for large and evolutionarily diverse reference libraries

Genome Research(2024)10.1101/gr.279339.124

N/A

0DataRank · unranked

4 citations

Siavash Mirarab, Ali Osman Berk Şapcı

ASTER: A Package for Large-Scale Phylogenomic Reconstructions

Molecular Biology and Evolution(2025)10.1093/molbev/msaf172

N/A

0DataRank · unranked

50 citations

Rasmus Nielsen, Siavash Mirarab, Chao Zhang

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2500553122

N/A

0DataRank · unranked

12 citations

Siavash Mirarab, Yatish Turakhia, Anshu Gupta

Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss

Genome Biology and Evolution(2025)10.1093/gbe/evaf200

N/A

0DataRank · unranked

2 citations

Chao Zhang, Shayesteh Arasti, Siavash Mirarab, Yasamin Tabatabaee

Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k ‐Mer Frequencies

Molecular Ecology Resources(2025)10.1111/1755-0998.70055

N/A

0DataRank · unranked

1 citations

Yueyu Jiang, Siavash Mirarab, Eleonora Rachtman

Machine learning enables alignment-free distance calculation and phylogenetic placement using k-mer frequencies

(2025)10.22541/au.174539883.30231226/v1

N/A

0DataRank · unranked

1 citations

Yueyu Jiang, Siavash Mirarab, Eleonora Rachtman

krepp v0.6.0

Zenodo (CERN European Organization for Nuclear Research)(2025)10.5281/zenodo.18048160

N/A

0DataRank · unranked

0 citations

Siavash Mirarab, Ali Osman Berk Şapcı

krepp v0.7.0

Zenodo (CERN European Organization for Nuclear Research)(2025)10.5281/zenodo.18584430

N/A

0DataRank · unranked

0 citations

Siavash Mirarab, Ali Osman Berk Şapcı

krepp v0.7.2

Zenodo (CERN European Organization for Nuclear Research)(2025)10.5281/zenodo.19644249

N/A

0DataRank · unranked

0 citations

Siavash Mirarab, Ali Osman Berk Şapcı

Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model

Bioinformatics Advances(2022)10.1093/bioadv/vbac055

N/A

0DataRank · unranked

4 citations

Nishat Anjum Bristy, Ahnaf Faisal, Md. Shamsuzzoha Bayzid, Siavash Mirarab, Metin Balaban

Log Transformation Improves Dating of Phylogenies

Molecular Biology and Evolution(2020)10.1093/molbev/msaa222

N/A

0DataRank · unranked

16 citations

Siavash Mirarab, Uyen Mai

Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling

Cell Systems(2022)10.1016/j.cels.2022.06.007

N/A

0DataRank · unranked

12 citations

Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab, Eleonora Rachtman

Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates

Biology(2022)10.3390/biology11091256

N/A

0DataRank · unranked

16 citations

Puoya Tabaghi, Siavash Mirarab, Yueyu Jiang

Siavash Mirarab

Indexed papers

Top data-sharing exemplar

Papers