Megascale microbiome analysis with DartUniFrac.

Jianshu Zhao, Daniel McDonald, Igor Sfiligoi, Manuel E Lladser, Lucas Patel, Yuhan Weng, Lora Khatib, Samuel Degregori, Antonio Gonzalez, Catherine A Lozupone and 1 more

Abstract read

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In one paragraph

Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Jianshu ZhaoDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2586-3852

Daniel McDonaldDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Igor SfiligoiSan Diego Supercomputing Center, University of California San Diego, La Jolla, CA, USA.

Manuel E LladserDepartment of Applied Mathematics, University of Colorado, Boulder, CO, USA.

Lucas PatelDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8607-2782

Yuhan WengDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Lora KhatibDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Samuel DegregoriDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Antonio GonzalezDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Catherine A LozuponeDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID http://orcid.org/0000-0003-4786-7202

Rob KnightDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.ORCID http://orcid.org/0000-0002-0975-9019

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

UniFrac measures phylogeny-aware differences between microbiome samples but scales poorly with modern dataset sizes. We introduce an algorithm, DartUniFrac, and a near-optimal implementation with graphics processing unit acceleration that is up to three orders of magnitude faster than UniFrac and scales to millions of samples (pairwise) and billions of taxa. DartUniFrac connects UniFrac with weighted Jaccard similarity and exploits sketching algorithms for fast computation.

Identifiers

PMID42665683

DOI10.1038/s41592-019-0686-2

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.