Evidence map›Paper›PMID 42426404›Full record

ArticleNature methods2026

NicheTrans: spatial-aware cross-omics translation.

Zhikang Wang, Qi Zou, Senlin Lin, Sijie Li, Yan Cui, Daoliang Zhang, Chuangyi Han, Yida Li, Jianmin Li, Yi Zhao and 3 more

Abstract read
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In one paragraph

Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

13 authors.

Zhikang Wang *Institute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-9587-1965
Qi Zou *Institute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-8662-5874
Senlin Lin *Institute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0009-0001-6593-4088
Sijie Li *Institute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0009-0005-0521-0722
Yan CuiInstitute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
Daoliang ZhangInstitute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
Chuangyi HanInstitute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0009-0005-8075-261X
Yida LiBiomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.
Jianmin LiDepartment of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
Yi ZhaoInstitute of Computing Technology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0001-6046-8420
Rui GaoCenter of Intelligent Medicine, School of Control Science and Engineering, Shandong University, Jinan, China.
Jiangning SongBiomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia. jiangning.song@monash.edu.ORCID http://orcid.org/0000-0001-8031-9086
Zhiyuan YuanInstitute of Science and Technology for Brain-Inspired Intelligence, Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China. zhiyuan@fudan.edu.cn.ORCID http://orcid.org/0000-0002-9367-4236

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

While spatial multiomics offers insights into complex biological systems, its widespread adoption is hindered by technical challenges, specialized requirements and limited accessibility. Here we present NicheTrans, a spatially aware cross-omics translation method and a flexible Transformer-based multimodal framework. Unlike existing single-cell translation methods, NicheTrans incorporates both cellular microenvironment information and multimodal data. We validated the advantage of NicheTrans across diverse biological cases. Through NicheTrans, we uncovered spatial multiomics domains that were not detectable through single-omics analysis alone. Model interpretation revealed key molecular relationships, including gene programs associated with dopamine metabolism and amyloid β-associated cell states. In addition, using translated protein markers as spatial landmarks, we quantified the spatial organization of key glial cell subtypes in the Alzheimer's disease brain. NicheTrans represents a powerful tool for generating comprehensive spatial multiomics insights from more accessible single-omics measurements, making multiomics analysis more feasible for the broader research community.

Indexed as

MultiomicsProteomicsAlzheimer DiseaseAnimalsBrainDopamineHumansNeurogliaSpatial TranscriptomicsDopamine

Identifiers

PMID42426404

What Socratic holds

Textmetadata
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 Socratic graph.