ArticleNature2023
Spatial epigenome-transcriptome co-profiling of mammalian tissues.
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Article in Nature, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 308 papers.
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308citing papers in PubMed
57.6field-weighted citation impact, top 1% of its field
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Who cites it
308 citing papers in PubMed, 377 citations in OpenAlex.
- Flexible Integration of Structurally Diverse Spatial Multi-Omics With AgaeSMO.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026Review
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- The dual-enhanced graph learning framework DePass allows paired data integration in single-cell and spatial multiomics.Nature cell biology · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- Deep Learning-Assisted Prioritization of Candidate Drug Targets in Tumors Using Spatial Multi-Omics.Biology · 2026Review
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- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Scalable, generalizable and uncertainty-aware integration of spatial multiomics across diverse modalities and platforms with SCIGMA.Nature genetics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- SpaHDSRL: hierarchical dual-graph self-supervised representation learning for integrating spatially resolved multi-omics data.Briefings in bioinformatics · 2026Article
- CRISPR-Cas9 and precision editing technologies linking functional genomics to clinical translation in genetic diseases.Clinical and translational medicine · 2026Review
- SpaMOAL is a deep learning method that enables accurate spatial domain identification from multi-omics data.PLoS biology · 2026Article
- Unified representation learning for spatial multi-omics.Bioinformatics (Oxford, England) · 2026Article
- MultiSpaceNet: graph-based joint representation learning for paired spatial transcriptome-proteome data.Bioinformatics (Oxford, England) · 2026Article
- Article
- CoxFormer enables spatial omics inference with multimodal generative modeling.Nature communications · 2026Article
248 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
23 authors at 10 institutions in 4 countries.
Di Zhang *Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
Yanxiang Deng *Department of Biomedical Engineering, Yale University, New Haven, CT, USA. yanxiang.deng@pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0002-9975-8086
Petra KukanjaLaboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0003-1228-5923
Eneritz AgirreLaboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-5012-0305
Marek BartosovicLaboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Mingze DongDepartment of Pathology, Yale University School of Medicine, New Haven, CT, USA.
Cong MaDepartment of Computer Science, Princeton University, Princeton, NJ, USA.
Sai MaKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9785-7929
Graham SuDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
Shuozhen BaoDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-9301-9952
Yang LiuDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-1830-948X
Yang XiaoDepartment of Biomedical Engineering, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0001-7878-4923
Gorazd B RosoklijaDepartment of Psychiatry, Columbia University, New York, NY, USA.
Andrew J DworkDepartment of Psychiatry, Columbia University, New York, NY, USA.
J John MannDepartment of Psychiatry, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0002-0265-6586
Kam W LeongDepartment of Biomedical Engineering, Columbia University, New York, NY, USA.
Maura BoldriniDepartment of Psychiatry, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0003-3574-7641
Liya WangAtlasXomics, Inc., New Haven, CT, USA.ORCID http://orcid.org/0000-0001-6810-1332
Maximilian HaeusslerGenomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
Benjamin J RaphaelDepartment of Computer Science, Princeton University, Princeton, NJ, USA.ORCID http://orcid.org/0000-0003-1274-048X
Yuval KlugerDepartment of Pathology, Yale University School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-3035-071X
Gonçalo Castelo-BrancoLaboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. goncalo.castelo-branco@ki.se.ORCID http://orcid.org/0000-0003-2247-9393
Rong FanDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA. rong.fan@yale.edu.ORCID http://orcid.org/0000-0001-7805-8059
Karolinska Institutet · SEYale Cancer Center · USYale University · USMacedonian Academy of Sciences and Arts · MKNew York Psychoanalytic Society and Institute · USPrinceton University · USBroad Institute · USColumbia University · USColumbia University Irving Medical Center · USUniversity of California, Santa Cruz · US
Funding
Spatiotemporal Tumor Analytics for Guiding Sequential Targeted-Inhibitor: Immunotherapy Combinations (ST-Analytics)U54CA274509 · NCI · INSTITUTE FOR SYSTEMS BIOLOGY · PI James R. Heath · 2022 to 2026
$15.6MYale Cooperative Hematology Specialized Core CenterU54DK106857 · NIDDK · YALE UNIVERSITY · PI JOHN HWA, Diane S Krause · 2015 to 2026
$9.7MYale TMC for Cellular Senescence in Lymphoid OrgansU54AG076043 · NIA · YALE UNIVERSITY · PI FAN, RONG, HALENE, STEPHANIE · 2021 to 2025
$7.0MYale Murine-TMC on Immune Cell Senescence Derived InflammationU54AG079759 · NIA · YALE UNIVERSITY · PI DIXIT, VISHWA DEEP, MONTGOMERY, RUTH R · 2022 to 2025
$6.5MHigh-throughput in vivo and in vitro functional and multi-omics screens of neuropsychiatric and neurodevelopmental disorder risk genesRM1MH132648 · NIMH · YALE UNIVERSITY · PI Kristen Jennifer Brennand, Rong Fan · 2023 to 2026
$5.6MCenter for Human Lymphoma Spatiotemporal Atlas (HuLymSTA)U01CA294514 · NCI · YALE UNIVERSITY · PI FAN, RONG, HALENE, STEPHANIE · 2024 to 2025
$5.1MComprehensive and Robust Tools for Analysis of Tumor Heterogeneity and EvolutionU24CA248453 · NCI · PRINCETON UNIVERSITY · PI Benjamin Raphael · 2020 to 2026
$4.7MHighly scalable and sensitive spatial transcriptomic and epigenomic sequencing of brain tissues from human and non-human primateRF1MH128876 · NIMH · YALE UNIVERSITY · PI FAN, RONG, SESTAN, NENAD · 2021 to 2021
$2.9MEx vivo analysis of human brain tumor cells in a microvascular niche modelR01CA245313 · NCI · YALE UNIVERSITY · PI FAN, RONG, ZHOU, JIANGBING · 2020 to 2024
$2.6MHigh-spatial-resolution ECM-inclusive multi-omics sequencing of human PFA and FFPE tissue slidesUH3CA257393 · NCI · YALE UNIVERSITY · PI FAN, RONG · 2022 to 2023
$1.2MHigh-spatial-resolution ECM-inclusive multi-omics sequencing of human PFA and FFPE tissue slidesUG3CA257393 · NCI · YALE UNIVERSITY · PI FAN, RONG · 2020 to 2021
$800kNCI NIH HHS R01 CA245313NCI NIH HHS R01CA245313NCI NIH HHS U01 CA294514NCI NIH HHS U24 CA248453NCI NIH HHS U54 CA274509NCI NIH HHS U54CA274509NCI NIH HHS UG3 CA257393NCI NIH HHS UG3CA257393NCI NIH HHS UH3 CA257393NIA NIH HHS U54 AG076043NIA NIH HHS U54AG076043NIA NIH HHS U54 AG079759NIA NIH HHS U54AG079759NIDDK NIH HHS U54 DK106857NIMH NIH HHS RF1 MH128876NIMH NIH HHS RF1MH128876NIMH NIH HHS RM1 MH132648
Abstract
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context
Indexed as
ChromatinEpigenomeMammalsTranscriptomeAgingAnimalsBrainEpigenesis, GeneticEpigenomicsGene Expression ProfilingGene Expression RegulationHistonesHumansMiceOrgan SpecificitySingle-Cell AnalysisChromatinHistones
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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.