Evidence map›Paper›PMID 31110232›Full record

ArticleNature communications2019

Model-based understanding of single-cell CRISPR screening.

Bin Duan, Chi Zhou, Chengyu Zhu, Yifei Yu, Gaoyang Li, Shihua Zhang, Chao Zhang, Xiangyun Ye, Hanhui Ma, Shen Qu and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.

0numbers the graph read from it
0cells of the map it votes in
60citing 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

60 citing papers in PubMed.

  1. Review
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  11. Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Machine learning to dissect perturbations in complex cellular systems.Computational and structural biotechnology journal · 2025
    Review
  18. Review
  19. Single-cell technologies: current and near future.Science China. Life sciences · 2025
    Article
  20. Review
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

14 authors.

Bin DuanDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Chi ZhouDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Chengyu ZhuDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Yifei YuDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Gaoyang LiTongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.
Shihua ZhangInstitute of Applied Mathematics, Academy of Mathematics and Systems Science, Beijing, China.ORCID http://orcid.org/0000-0003-0192-7118
Chao ZhangDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Xiangyun YeShanghai Chest Hospital Shanghai Jiaotong University, Shanghai, China.
Hanhui MaSchool of Life Science and Technology ShanghaiTech University, Shanghai, China.
Shen QuDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China.
Zhiyuan ZhangDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Ping WangTongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China. pwangecnu@163.com.
Shuyang SunDepartment of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China. shuyangs@shsmu.edu.cn.
Qi LiuDepartment of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Bioinformatics Department, College of Life Science, Tongji University, Shanghai, China. qiliu@tongji.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The recently developed single-cell CRISPR screening techniques, independently termed Perturb-Seq, CRISP-seq, or CROP-seq, combine pooled CRISPR screening with single-cell RNA-seq to investigate functional CRISPR screening in a single-cell granularity. Here, we present MUSIC, an integrated pipeline for model-based understanding of single-cell CRISPR screening data. Comprehensive tests applied to all the publicly available data revealed that MUSIC accurately quantifies and prioritizes the individual gene perturbation effect on cell phenotypes with tolerance for the substantial noise that exists in such data analysis. MUSIC facilitates the single-cell CRISPR screening from three perspectives, i.e., prioritizing the gene perturbation effect as an overall perturbation effect, in a functional topic-specific way, and quantifying the relationships between different perturbations. In summary, MUSIC provides an effective and applicable solution to elucidate perturbation function and biologic circuits by a model-based quantitative analysis of single-cell-based CRISPR screening data.

Indexed as

Models, GeneticClustered Regularly Interspaced Short Palindromic RepeatsComputational BiologyDatasets as TopicFeasibility StudiesGene Expression ProfilingGene Knockdown TechniquesHumansJurkat CellsK562 CellsRNA, Guide, CRISPR-Cas SystemsSequence Analysis, RNASingle-Cell AnalysisRNA, Guide, CRISPR-Cas Systems

Identifiers

PMID31110232
PMCPMC6527552

What OpenQuestion holds

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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.