Evidence map›Paper›PMID 40611203›Full record

ArticleGenome biology2025

Ensemblex: an accuracy-weighted ensemble genetic demultiplexing framework for population-scale scRNAseq sample pooling.

Michael R Fiorini, Saeid Amiri, Allison A Dilliott, Cristine M Yde Ohki, Lukasz Smigielski, Susanne Walitza, Edward A Fon, Edna Grünblatt, Rhalena A Thomas, Sali M K Farhan

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In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
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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

10 authors.

Michael R FioriniDepartment of Human Genetics, McGill University, Montreal, QC, H3A 2B4, Canada.
Saeid AmiriThe Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada.
Allison A DilliottThe Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada.
Cristine M Yde OhkiDepartment of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
Lukasz SmigielskiDepartment of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
Susanne WalitzaDepartment of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
Edward A FonThe Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada.
Edna GrünblattDepartment of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
Rhalena A Thomas *The Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada. rhalena.thomas@mcgill.ca.
Sali M K Farhan *Department of Human Genetics, McGill University, Montreal, QC, H3A 2B4, Canada. Sali.farhan@mcgill.ca.

Funding

Michael J. Fox Foundation for Parkinson's Research MJFF-021629Universität Zürich FK-22-044
6 · The paper itself

Abstract

Multiplexing samples from distinct individuals prior to sequencing is a promising step towards achieving population-scale single-cell RNA sequencing by reducing the restrictive costs of the technology. Individual genetic demultiplexing tools resolve the donor-of-origin identity of pooled cells using natural genetic variation but present diminished accuracy on highly multiplexed experiments, impeding the analytic potential of the dataset. In response, we introduce Ensemblex: an accuracy-weighted, ensemble genetic demultiplexing framework that integrates four distinct algorithms to identify the most probable subject labels. Using computationally and experimentally pooled samples, we demonstrate Ensemblex's superior accuracy and illustrate the implications of robust demultiplexing on biological analyses.

Indexed as

Sequence Analysis, RNASingle-Cell AnalysisSoftwareAlgorithmsHumansSingle-Cell Gene Expression AnalysisAccuracy-weighted probabilityDifferential gene expressionDopaminergic neuronsDoublet detectionGenetic demultiplexingHigh-throughput sequencingInduced pluripotent stem cellsMultiplexingSample poolingSingle-cell RNA sequencing

Identifiers

PMID40611203
PMCPMC12224856

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Registered trials

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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.