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References from Dual Host–Pathogen Screening of the Lung During Severe Influenza Using Spatial Transcriptomics. Local targets link to admitted publications; unresolved targets remain external evidence.
Highly Sensitive Spatial Transcriptomics at Near‐Cellular Resolution With Slide‐seqV2
10.1038/s41587-020-0739-1 · 2021 · External reference
Plasmodium Infection Induces Phenotypic, Clonal, and Spatial Diversity Among Differentiating CD4(+) T Cells
10.1016/j.celrep.2024.114317 · 2024 · External reference
A Spatial Sequencing Atlas of Age‐Induced Changes in the Lung During Influenza Infection
10.1038/s41467-023-42021-y · 2023 · External reference
Spatiotemporal Analysis of Lung Immune Dynamics in Lethal Coccidioides Posadasii Infection
10.1128/mbio.02562-24 · 2025 · External reference
The Cervicovaginal Microbiome Associates With Spatially Restricted Host Transcriptional Signatures Throughout the Human Ectocervical Epithelium and Submucosa
10.1371/journal.ppat.1013677 · 2025 · External reference
Paired Single‐Cell and Spatial Transcriptional Profiling Reveals a Central Osteopontin Macrophage Response Mediating Tuberculous Granuloma Formation
10.1128/mbio.01559-25 · 2025 · External reference
Single‐Cell and Spatial Transcriptomic Profiling Reveals Distinct Immune Landscapes in Murine Lungs Infected With H1N1 Versus H5N1 Influenza Viruses
10.1128/jvi.00746-26 · 2026 · External reference
Profiling of Lung SARS‐CoV‐2 and Influenza Virus Infection Dissects Virus‐Specific Host Responses and Gene Signatures
10.1183/13993003.01881-2021 · 2022 · External reference
Transcriptomic Profiling of Cardiac Tissues From SARS‐CoV‐2 Patients Identifies DNA Damage
10.1111/imm.13577 · 2023 · External reference
Eosinophils Enhance Granuloma‐Mediated Control of Persistent Salmonella Infection in Mice
10.1038/s41564-025-02187-1 · 2025 · External reference
BCG Vaccination Stimulates Integrated Organ Immunity by Feedback of the Adaptive Immune Response to Imprint Prolonged Innate Antiviral Resistance
10.1038/s41590-023-01700-0 · 2024 · External reference
An Aberrant Immune‐Epithelial Progenitor Niche Drives Viral Lung Sequelae
10.1038/s41586-024-07926-8 · 2024 · External reference
Damping Excessive Viral‐Induced IFN‐Gamma Rescues the Impaired Anti‐Aspergillus Host Immune Response in Influenza‐Associated Pulmonary Aspergillosis
10.1016/j.ebiom.2024.105347 · 2024 · External reference
Bcl6 Expression Is Associated With a Distinct Immune Landscape and Spatial Transcriptome in COVID‐19
10.1172/jci.insight.189134 · 2025 · External reference
FMT Promotes Type 2 Mucosal Immune Responses With Colonic Epithelium Proliferation in Recurrent CDI Patients
10.1172/jci.insight.195678 · 2025 · External reference
Dysplastic Lung Repair Fosters a Tuberculosis‐Promoting Microenvironment Through Maladaptive Macrophage Polarization
10.1371/journal.ppat.1013563 · 2025 · External reference
Spatial Mapping of SARS‐CoV‐2 and H1N1 Lung Injury Identifies Differential Transcriptional Signatures
10.1016/j.xcrm.2021.100242 · 2021 · External reference
Combination of Spatial Transcriptomics Analysis and Retrospective Study Reveals Liver Infection of SARS‐COV‐2 Is Associated With Clinical Outcomes of COVID‐19
10.1016/j.ebiom.2024.105517 · 2025 · External reference
Spatial Gene Expression Analysis Reveals Pathological Niches in Japanese Encephalitis Virus Neuroinvasion
10.1073/pnas.2515006122 · 2025 · External reference
Pathogenicity of Different PR8 Influenza A Virus Variants in Mice Is Determined by Both Viral and Host Factors
10.1016/j.virol.2010.12.047 · 2011 · External reference
Highly Pathological Influenza A Virus Infection Is Associated With Augmented Expression of PD‐1 by Functionally Compromised Virus‐Specific CD8+ T Cells
10.1128/jvi.02851-13 · 2014 · External reference
Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling Following Respiratory Viral Infection
10.1038/s41467-023-41387-3 · 2023 · External reference
SpatialDE: Identification of Spatially Variable Genes
10.1038/nmeth.4636 · 2018 · External reference
A Temporal Map of B Cell Diversification Mechanisms in Mice
10.1038/s41590-026-02563-x · 2026 · External reference
Partial Alignment of Multislice Spatially Resolved Transcriptomics Data
2023 · External reference
Spatiotemporal Modeling of Molecular Holograms
10.1016/j.cell.2024.10.011 · 2024 · External reference
Stereo‐Seq V2: Spatial Mapping of Total RNA on FFPE Sections With High Resolution
10.1016/j.cell.2025.08.008 · 2025 · External reference
An Introduction to Spatial Transcriptomics for Biomedical Research
10.1186/s13073-022-01075-1 · 2022 · External reference
Transcriptome Analysis of Infected and Bystander Type 2 Alveolar Epithelial Cells During Influenza A Virus Infection Reveals in Vivo Wnt Pathway Downregulation
10.1128/jvi.01325-18 · 2018 · External reference
Integrated Pathogen Load and Dual Transcriptome Analysis of Systemic Host‐Pathogen Interactions in Severe Malaria
2018 · External reference
Dissection of Influenza Infection in Vivo by Single‐Cell RNA Sequencing
10.1016/j.cels.2018.05.008 · 2018 · External reference
Systematic Benchmarking of High‐Throughput Subcellular Spatial Transcriptomics Platforms Across Human Tumors
10.1038/s41467-025-64292-3 · 2025 · External reference
Slide‐Seq: A Scalable Technology for Measuring Genome‐Wide Expression at High Spatial Resolution
10.1126/science.aaw1219 · 2019 · External reference
Exosomes Released by Influenza‐Virus‐Infected Cells Carry Factors Capable of Suppressing Immune Defense Genes in Naive Cells
10.3390/v14122690 · 2022 · External reference
Incomplete Forms of Influenza Virus
10.1016/s0065-3527(08)60529-1 · 1954 · External reference
The Fate of Influenza A Virus After Infection of Human Macrophages and Dendritic Cells
10.1099/vir.0.045021-0 · 2012 · External reference
Infection of Mouse Macrophages by Seasonal Influenza Viruses Can be Restricted at the Level of Virus Entry and at a Late Stage in the Virus Life Cycle
10.1128/jvi.01455-15 · 2015 · External reference
Role of Inducible Bronchus Associated Lymphoid Tissue (iBALT) in Respiratory Immunity
10.1038/nm1091 · 2004 · External reference
Regulatory T Cells Interfere With the Development of Bronchus‐Associated Lymphoid Tissue
10.1084/jem.20061424 · 2007 · External reference
Type I Interferon Induces CXCL13 to Support Ectopic Germinal Center Formation
10.1084/jem.20181216 · 2019 · External reference
Inducible Bronchus‐Associated Lymphoid Tissues (iBALT) Serve as Sites of B Cell Selection and Maturation Following Influenza Infection in Mice
10.3389/fimmu.2019.00611 · 2019 · External reference
Protocol for Acquiring High‐Quality Fresh Mouse Lung Spatial Transcriptomics Data
10.1016/j.xpro.2023.102825 · 2024 · External reference
QuPath: Open Source Software for Digital Pathology Image Analysis
10.1038/s41598-017-17204-5 · 2017 · External reference
Fast, Sensitive and Accurate Integration of Single‐Cell Data With Harmony
10.1038/s41592-019-0619-0 · 2019 · External reference
Robust Decomposition of Cell Type Mixtures in Spatial Transcriptomics
10.1038/s41587-021-00830-w · 2022 · External reference
Differences in Alveolar Size in Inbred Mouse Strains
10.1016/j.resp.2004.02.003 · 2004 · External reference
GOrilla: A Tool for Discovery and Visualization of Enriched GO Terms in Ranked Gene Lists
10.1186/1471-2105-10-48 · 2009 · External reference