ArticleNature biotechnology2024
Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology.
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Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
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132citing papers in PubMed
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132 citing papers in PubMed.
- Improving Image Quality in 10× Visium Spatial Transcriptomics Using Vispro.Methods in molecular biology (Clifton, N.J.) · 2027Article
- 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
- Insights into Microbiota-Vaccine Crosstalk in Humans: Mechanisms, Modulators, and Translational Horizons.Vaccines · 2026Review
- All-optical multimodal mapping of single-cell-type-specific metabolic activities via REDCAT.Nature methods · 2026Article
- Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.Nature methods · 2026Article
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Article
- HisToSpatialCNV: an interpretable deep learning method predicting spatial copy number variations from histopathology images.Nature biomedical engineering · 2026Article
- CoxFormer enables spatial omics inference with multimodal generative modeling.Nature communications · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Image-guided spatial omics enhancement reveals hidden spatial microstructures.Bioinformatics (Oxford, England) · 2026Article
- Leveraging multi-modal foundation models for analysing spatial multi-omic and histopathology data.Nature biomedical engineering · 2026Article
- STAID: A Self-Refining Deep Learning Framework for Spatial Cell-Type Deconvolution with Biologically Informed Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spatially resolved tissue architecture and computational pathology in pancreatic cancer.Experimental & molecular medicine · 2026Review
- Prediction of single cell expression from low-plex immunofluorescence images for guiding precision oncology.NPJ precision oncology · 2026Article
- A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell dysfunction in human lymph nodes.Cell press blue · 2026Article
- ViMST: vision transformer-based dual modality multi-task graph contrastive network for spatial transcriptomics microenvironments investigation.BMC biology · 2026Article
- Trimodal, uncertainty-guided whole-slide framework for genome-scale spatial expression and image-only virtual perturbation in cancer cohorts.Genome medicine · 2026Article
- CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images.Nature protocols · 2026Review
72 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Daiwei ZhangStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Daiwei.Zhang@Pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0002-5019-622X
Amelia SchroederStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Hanying YanStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-9227-1742
Haochen YangStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0009-0004-9523-800X
Jian HuDepartment of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA.ORCID http://orcid.org/0000-0003-2852-7675
Michelle Y Y LeeStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Kyung S ChoDepartment of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Katalin SusztakRenal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-1005-3726
George X XuDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-4098-7690
Michael D FeldmanDepartment of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA.
Edward B LeeDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-4589-1180
Emma E FurthDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Linghua WangDepartment of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9380-0266
Mingyao LiStatistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. mingyao@pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0003-2422-9494
Funding
Clinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0MTumor Microenvironment and Metastasis ProgramP30CA082709 · NCI · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI Sara K Quinney · 1999 to 2026
$59.3MUnderstanding Environmental Contributions to Heterogeneity in bvFTD.P01AG066597 · NIA · UNIVERSITY OF PENNSYLVANIA · PI David John Irwin, Corey T McMillan · 2020 to 2026
$18.8MTumor cell lineage diversity and composition in gastric cancer progression and therapy resistanceR01CA266280 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Pawel K. Mazur, Linghua Wang · 2022 to 2026
$3.2MComputational and functional strategies to decipher lncRNAs in human atherosclerosisR01HL150359 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LI, MINGYAO, REILLY, MUREDACH P · 2020 to 2023
$2.7MSingle-Cell Transcriptomic Analysis of Human RetinaR01EY030192 · NEI · UNIVERSITY OF PENNSYLVANIA · PI LI, MINGYAO · 2019 to 2022
$2.6MIntegrative analysis of spatial transcriptomics with histology images and single cellsR01HG013185 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI Mingyao Li · 2023 to 2026
$2.2MSpatial and temporal tumor-immune co-evolution and interactions that model lung adenocarcinoma developmentU01CA264583 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Humam Kadara, Linghua Wang · 2022 to 2026
$2.1MStatistical Methods for Single-Cell TranscriptomicsR01GM125301 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI LI, MINGYAO, ZHANG, NANCY R · 2017 to 2020
$1.5MNCATS NIH HHS UL1 TR001873NCI NIH HHS P30 CA082709NCI NIH HHS R01 CA266280NEI NIH HHS R01 EY030192NHGRI NIH HHS R01 HG013185NHLBI NIH HHS R01 HL150359NIA NIH HHS P01 AG066597NIGMS NIH HHS R01 GM125301U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA266280U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U01CA264583U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI) R01EY030192U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) R01HL150359U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG013158U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM125301U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging) P01AG066597
Abstract
Spatial transcriptomics (ST) has demonstrated enormous potential for generating intricate molecular maps of cells within tissues. Here we present iStar, a method based on hierarchical image feature extraction that integrates ST data and high-resolution histology images to predict spatial gene expression with super-resolution. Our method enhances gene expression resolution to near-single-cell levels in ST and enables gene expression prediction in tissue sections where only histology images are available.
Indexed as
Gene Expression ProfilingTranscriptomeAlgorithmsAnimalsHumansImage Processing, Computer-AssistedSingle-Cell Analysis
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