Evidence map›Paper›PMID 41053815›Full record

ArticleGenome biology2025

Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution.

Luzhang Ji, Qihang Zou, Ke Tang, Chenfei Wang

Abstract read
PubMed Full text at PMC Publisher
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. Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026
    Review
  3. Article
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

4 authors.

Luzhang Ji *Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Qihang Zou *Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Ke TangKey Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Chenfei WangKey Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. 08chenfeiwang@tongji.edu.cn.

Funding

National Natural Science Foundation of China 32222026
6 · The paper itself

Abstract

Single-cell multiomic technologies enable the joint analysis of different modalities, but face challenges due to experimental complexity. Current computational methods for single-cell cross-modality translation lack biological interpretability. Here, we present Cisformer, a cross-attention-based generative model tailored for cross-modality generation between gene expression and chromatin accessibility at single-cell resolution. Systematic benchmarking demonstrates the superior accuracy and generalization of Cisformer against existing methods. Cisformer leverages its inherent interpretability to precisely link cis-regulatory elements to target genes, facilitating the identification of functional transcription factors associated with tumorigenesis and aging. Overall, Cisformer is a powerful tool for single-cell multiomic data analysis.

Indexed as

Gene Expression RegulationSingle-Cell AnalysisSoftwareTranscription, GeneticAnimalsChromatinHumansTranscription FactorsChromatinTranscription FactorsCis-regulatory elementCross-modality generationModel interpretabilitySingle-cell multiomicsTranscriptional regulationTranscription factorTransformer

Identifiers

PMID41053815
PMCPMC12498472

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.