Evidence map›Paper›PMID 41566400›Full record

ArticleGenome biology2026

Harmonizing single-cell 3D genome data with STARK and scNucleome.

Wen-Jie Jiang, KangWen Cai, YuanChen Sun, An Liu, HanWen Zhu, RuiXiang Gao, Chunge Zhong, Nana Wei, Futing Lai, Teng Fei and 4 more

Abstract read
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In one paragraph

Article in Genome biology, 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

14 authors.

Wen-Jie Jiang *Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University Third Hospital, Peking University, Beijing, 100191, China.
KangWen Cai *Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
YuanChen Sun *Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
An LiuKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
HanWen ZhuDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
RuiXiang GaoKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
Chunge ZhongKey Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China.
Nana WeiKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
Futing LaiDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
Teng FeiKey Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China.
Yu-Juan WangKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
Xiaoqi ZhengCenter for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. xqzheng@shsmu.edu.cn.
Ming XuDepartment of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University Third Hospital, Peking University, Beijing, 100191, China. xuminghi@bjmu.edu.cn.
Hua-Jun WuKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China. hjwu@pku.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, quality control, and analysis of diverse sc3DG-seq data. Utilizing STARK, we benchmark 15 technologies, quantitatively comparing their strengths and limitations. We also develop EmptyCells to filter empty barcodes and introduce Spatial Structure Capture Efficiency (SSCE) to assess chromatin structure capture quality. Additionally, we establish scNucleome, a uniformly processed repository of sc3DG-seq datasets, to serve as a foundational resource for future 3D genome research.

Indexed as

GenomeGenomicsSingle-Cell AnalysisSoftwareAnimalsChromatinHumansSequence Analysis, DNAChromatinBenchmarkScNucleomeSingle cell 3D genomeSingle cell Hi-CSTARK

Identifiers

PMID41566400
PMCPMC12983743

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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.