Evidence map›Paper›PMID 31121116›Full record

ArticleCell systems2019

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.

Genevieve L Stein-O'Brien, Brian S Clark, Thomas Sherman, Cristina Zibetti, Qiwen Hu, Rachel Sealfon, Sheng Liu, Jiang Qian, Carlo Colantuoni, Seth Blackshaw and 2 more

Erratum issuedOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 101 papers.

0numbers the graph read from it
0cells of the map it votes in
101citing papers in PubMed
9.9field-weighted citation impact, top 1% of its field
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

101 citing papers in PubMed, 183 citations in OpenAlex.

  1. Article
  2. A Gene-Program Architecture of Mouse T cells.bioRxiv : the preprint server for biology · 2026
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  10. Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026
    Review
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  12. Article
  13. The long noncoding RNAbioRxiv : the preprint server for biology · 2025
    Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Review
  19. Article
  20. Review

41 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors at 4 institutions in 1 country.

Genevieve L Stein-O'BrienDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA.
Brian S ClarkSolomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
Thomas ShermanDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
Cristina ZibettiSolomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
Qiwen HuDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
Rachel SealfonFlatiron Institute, New York, NY, USA.
Sheng LiuDepartment of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA.
Jiang QianDepartment of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA.
Carlo ColantuoniSolomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA.
Seth BlackshawSolomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA; Center for Human Systems Biology, Johns Hopkins University, Baltimore, MD, USA.
Loyal A GoffSolomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
Elana J FertigDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering and Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA. Electronic address: ejfertig@jhmi.edu.
Johns Hopkins University · USSidney Kimmel Comprehensive Cancer Center · USFlatiron Health (United States) · USTranslational Therapeutics (United States) · US

Funding

Translational Research Central ServicesP30CA006973 · NCI · JOHNS HOPKINS UNIVERSITY · PI Rosalie Wollett · 1985 to 2026
$208.6M
Multidiciplinary Integrative Genomic Approach to Distinguish Lethal from Indolent Prostate Cancer in Men of Europena and African AncestryU01CA196390 · NCI · JOHNS HOPKINS UNIVERSITY · PI DE MARZO, ANGELO MICHAEL, PIENTA, KENNETH J. · 2015 to 2020
$5.8M
Transcriptional regulation of retinal cell differentiation and functionR01EY020560 · NEI · JOHNS HOPKINS UNIVERSITY · PI BLACKSHAW, SETH · 2011 to 2021
$4.4M
Integrating bioinformatics into multiscale models for hepatocellular carcinomaU01CA212007 · NCI · JOHNS HOPKINS UNIVERSITY · PI EWALD, ANDREW JOSEF, FERTIG, ELANA · 2018 to 2022
$3.2M
Comparative transcriptomic and epigenomic analyses of Muller glia reprogrammingU01EY027267 · NEI · UNIVERSITY OF NOTRE DAME · PI BLACKSHAW, SETH, HYDE, DAVID R · 2016 to 2019
$3.0M
Dynamical Models of Cetuximab Resistance in HNSCC Based on Serial Genomics DataR01CA177669 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2014 to 2019
$1.8M
Identification of the molecular mechanisms mediating intrinsic control of retinal progenitor competenceR00EY027844 · NEI · WASHINGTON UNIVERSITY · PI CLARK, BRIAN S · 2019 to 2021
$739k
Identification of the molecular mechanisms mediating intrinsic control of retinal progenitor competenceK99EY027844 · NEI · JOHNS HOPKINS UNIVERSITY · PI CLARK, BRIAN S · 2017 to 2018
$205k
Regulation of Retinal Progenitor Cell Competence by Long noncoding RNAsF32EY024201 · NEI · JOHNS HOPKINS UNIVERSITY · PI CLARK, BRIAN S · 2014 to 2016
$164k
NCI NIH HHS P30 CA006973NCI NIH HHS R01 CA177669NCI NIH HHS U01 CA196390NCI NIH HHS U01 CA212007NEI NIH HHS F32 EY024201NEI NIH HHS K99 EY027844NEI NIH HHS R00 EY027844NEI NIH HHS R01 EY020560NEI NIH HHS U01 EY027267
6 · The paper itself

Abstract

Analysis of gene expression in single cells allows for decomposition of cellular states as low-dimensional latent spaces. However, the interpretation and validation of these spaces remains a challenge. Here, we present scCoGAPS, which defines latent spaces from a source single-cell RNA-sequencing (scRNA-seq) dataset, and projectR, which evaluates these latent spaces in independent target datasets via transfer learning. Application of developing mouse retina to scRNA-Seq reveals intrinsic relationships across biological contexts and assays while avoiding batch effects and other technical features. We compare the dimensions learned in this source dataset to adult mouse retina, a time-course of human retinal development, select scRNA-seq datasets from developing brain, chromatin accessibility data, and a murine-cell type atlas to identify shared biological features. These tools lay the groundwork for exploratory analysis of scRNA-seq data via latent space representations, enabling a shift in how we compare and identify cells beyond reliance on marker genes or ensemble molecular identity.

Indexed as

AlgorithmsAnimalsDatabases, GeneticExome SequencingFemaleGene Expression ProfilingHumansMachine LearningMaleMiceMice, TransgenicRetinaSequence Analysis, RNASingle-Cell AnalysisSoftwareTranscriptomedevelopmental biologydimension reductionintegrated analysislatent spacesNMFretinascRNA-seqsingle cellstransfer learning

Identifiers

PMID31121116
PMCPMC6588402
OpenAlexW2951232102

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.