Good morning β Here are today's papers!
Preprints:π
βοΈ Beyond a binary view of cystic fibrosis: systemic immunity and inflammation across the spectrum of CFTR dysfunction
βοΈ scMagnifier: resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering
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Papers:π
ποΈ Cancer-Associated Fibroblasts Functions as Multifunctional Architects of the Tumor Stroma and Represent Emerging Therapeutic Vulnerabilities.
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Preprints:π
βοΈ Beyond a binary view of cystic fibrosis: systemic immunity and inflammation across the spectrum of CFTR dysfunction
βοΈ scMagnifier: resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering
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Papers:π
ποΈ Cancer-Associated Fibroblasts Functions as Multifunctional Architects of the Tumor Stroma and Represent Emerging Therapeutic Vulnerabilities.
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Good morning β Here are today's papers!
Preprints:π
βοΈ Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of "prime-and-kill" synNotch-CAR-T cells
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Papers:π
ποΈ IGSF9 drives malignant transformation and predicts early-stage lung adenocarcinoma in integrated transcriptomic analyses.
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Preprints:π
βοΈ Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of "prime-and-kill" synNotch-CAR-T cells
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Papers:π
ποΈ IGSF9 drives malignant transformation and predicts early-stage lung adenocarcinoma in integrated transcriptomic analyses.
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Good morning β Here are today's papers!
Preprints:π
βοΈ Intercellular communication is a heritable dimension of human tissue architecture
βοΈ Cell type composition drives patient stratification in single-cell RNA-seq cohorts
βοΈ CoLa-VAE: Cell-Cell Communication-aware Variational Autoencoder with Dynamic Graph Laplacian Constraints
βοΈ GraphBG: Fast Bayesian Domain Detection via Spectral Graph Convolutions for Multi-slice and Multi-modal Spatial Transcriptomics
βοΈ scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data
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Papers:π
ποΈ Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment.
ποΈ Gut Commensal Klebsiella pneumoniae Extracellular Vesicles Shape a Liver Microenvironment Conducive to Gut-Liver Bacterial Translocation and Pro-Tumorigenic Processes.
ποΈ ZFP36L1 promotes non-small cell lung cancer progression under hypoxia by modulating CXCL9:SPP1 polarity: A single-cell transcriptomic study.
ποΈ Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning.
ποΈ ECM-Stiffness Mediated Persistent Fibroblast Activation Requires Integrin and Formin Dependent Chromatin Remodeling.
ποΈ Single-cell spatial atlas of the aging human breast.
ποΈ Kernel-DMD for multiome data integration and control.
ποΈ Complementary multi-omics profiling of chronic thromboembolic pulmonary hypertension reveals immune cell alterations, epigenetic changes, and genetically supported candidate genes.
ποΈ Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.
ποΈ scDenorm: a denormalisation tool for integrating single-cell transcriptomics data.
ποΈ Benchmarking single-cell tumor immune atlases and application for uncovering cell states related to immunotherapy response.
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Preprints:π
βοΈ Intercellular communication is a heritable dimension of human tissue architecture
βοΈ Cell type composition drives patient stratification in single-cell RNA-seq cohorts
βοΈ CoLa-VAE: Cell-Cell Communication-aware Variational Autoencoder with Dynamic Graph Laplacian Constraints
βοΈ GraphBG: Fast Bayesian Domain Detection via Spectral Graph Convolutions for Multi-slice and Multi-modal Spatial Transcriptomics
βοΈ scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data
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Papers:π
ποΈ Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment.
ποΈ Gut Commensal Klebsiella pneumoniae Extracellular Vesicles Shape a Liver Microenvironment Conducive to Gut-Liver Bacterial Translocation and Pro-Tumorigenic Processes.
ποΈ ZFP36L1 promotes non-small cell lung cancer progression under hypoxia by modulating CXCL9:SPP1 polarity: A single-cell transcriptomic study.
ποΈ Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning.
ποΈ ECM-Stiffness Mediated Persistent Fibroblast Activation Requires Integrin and Formin Dependent Chromatin Remodeling.
ποΈ Single-cell spatial atlas of the aging human breast.
ποΈ Kernel-DMD for multiome data integration and control.
ποΈ Complementary multi-omics profiling of chronic thromboembolic pulmonary hypertension reveals immune cell alterations, epigenetic changes, and genetically supported candidate genes.
ποΈ Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.
ποΈ scDenorm: a denormalisation tool for integrating single-cell transcriptomics data.
ποΈ Benchmarking single-cell tumor immune atlases and application for uncovering cell states related to immunotherapy response.
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Good morning β Here are today's papers!
Preprints:π
No preprints found today.
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Papers:π
ποΈ Single nucleus RNA sequencing and functional in vivo studies reveal TCF21 as a protective regulator in cardiac fibrosis.
ποΈ Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.
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Preprints:π
No preprints found today.
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Papers:π
ποΈ Single nucleus RNA sequencing and functional in vivo studies reveal TCF21 as a protective regulator in cardiac fibrosis.
ποΈ Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.
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OUP Academic
Single nucleus RNA sequencing and functional in vivo studies reveal TCF21 as a protective regulator in cardiac fibrosis
AbstractAims. Cardiac fibrosis remains a significant and currently untreatable contributor to mortality in chronic heart disease. This study aimed to compr
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Papers:π
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Preprints:π
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Papers:π
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Good morning β Here are today's papers!
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Papers:π
ποΈ Single-cell and spatial profiling in cancer biology and clinical oncology.
ποΈ Benchmarking alignment methods for spatial transcriptomics data.
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Preprints:π
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Papers:π
ποΈ Single-cell and spatial profiling in cancer biology and clinical oncology.
ποΈ Benchmarking alignment methods for spatial transcriptomics data.
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Nature
Single-cell and spatial profiling in cancer biology and clinical oncology
Nature Cancer - Izar and colleagues review the insights into cancer biology gained via single-cell analyses and spatial profiling and overview the challenges and opportunities associated with the...
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Preprints:π
βοΈ DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated Genes from Spatial Transcriptomics
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No papers found today.
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Preprints:π
βοΈ DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated Genes from Spatial Transcriptomics
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Papers:π
No papers found today.
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Good morning β Here are today's papers!
Preprints:π
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Papers:π
No papers found today.
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Preprints:π
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Papers:π
No papers found today.
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Good morning β Here are today's papers!
Preprints:π
βοΈ Dysplastic Epithelial Repair Propagates Chronic Pathology Through the Paracrine Transformation of Pulmonary Fibroblasts
βοΈ Transcriptomic Integration Reveals a Conserved InflammatoryβProliferative Paradox in Acquired Resistance to Immune Checkpoint Blockade
βοΈ Preservation of Human Colonic Stem Cells Requires an ERK Dynamics Checkpoint Mediated by AKT
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Papers:π
ποΈ An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.
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Preprints:π
βοΈ Dysplastic Epithelial Repair Propagates Chronic Pathology Through the Paracrine Transformation of Pulmonary Fibroblasts
βοΈ Transcriptomic Integration Reveals a Conserved InflammatoryβProliferative Paradox in Acquired Resistance to Immune Checkpoint Blockade
βοΈ Preservation of Human Colonic Stem Cells Requires an ERK Dynamics Checkpoint Mediated by AKT
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Papers:π
ποΈ An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.
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Good morning β Here are today's papers!
Preprints:π
βοΈ Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches
βοΈ Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics
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Papers:π
ποΈ Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.
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Preprints:π
βοΈ Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches
βοΈ Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics
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Papers:π
ποΈ Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.
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Good morning β Here are today's papers!
Preprints:π
βοΈ STDrug enables spatially informed personalized drug repurposing from spatial transcriptomics
βοΈ CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation
βοΈ Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics
βοΈ Longitudinal Single-Cell RNA-seq Profiling of Lung Cell Phenotypes, Signaling, and Cross-talk During Fibrosis Resolution
βοΈ Distinct Spatial Programs of Response versus Resistance in Non-Small Cell Lung Cancer after Neoadjuvant Chemoimmunotherapy
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Papers:π
ποΈ Img2Gene: Debiased Spatially Resolved Transcriptomics with Biological Context from Pathology Images.
ποΈ Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease.
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Preprints:π
βοΈ STDrug enables spatially informed personalized drug repurposing from spatial transcriptomics
βοΈ CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation
βοΈ Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics
βοΈ Longitudinal Single-Cell RNA-seq Profiling of Lung Cell Phenotypes, Signaling, and Cross-talk During Fibrosis Resolution
βοΈ Distinct Spatial Programs of Response versus Resistance in Non-Small Cell Lung Cancer after Neoadjuvant Chemoimmunotherapy
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Papers:π
ποΈ Img2Gene: Debiased Spatially Resolved Transcriptomics with Biological Context from Pathology Images.
ποΈ Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease.
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Good morning β Here are today's papers!
Preprints:π
βοΈ Geometry-aware ligand-receptor analysis distinguishes interface association from spatial localization and reveals a continuum of tumor communication
βοΈ Counterfactual Modeling of Directional Cell Cell Influence in Spatial Transcriptomics
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Papers:π
ποΈ GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis.
ποΈ CIPHER-seq enables intracellular multimodal profiling of cytokine responses in single immune cells.
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Preprints:π
βοΈ Geometry-aware ligand-receptor analysis distinguishes interface association from spatial localization and reveals a continuum of tumor communication
βοΈ Counterfactual Modeling of Directional Cell Cell Influence in Spatial Transcriptomics
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Papers:π
ποΈ GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis.
ποΈ CIPHER-seq enables intracellular multimodal profiling of cytokine responses in single immune cells.
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Good morning β Here are today's papers!
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Papers:π
ποΈ RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.
ποΈ The rise of spatial TCR profiling: Emerging technologies and open challenges.
ποΈ Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success.
ποΈ An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and Ξ³Ξ΄ T cells in cholangitis.
ποΈ Defining the tumor microenvironment of non-small cell lung cancer.
ποΈ SenSet defines cell-type specific senescence signatures in the aged human lung.
ποΈ Single-cell TCR mapping reveals spatially coordinated T cell states in head and neck cancer.
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Preprints:π
No preprints found today.
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Papers:π
ποΈ RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.
ποΈ The rise of spatial TCR profiling: Emerging technologies and open challenges.
ποΈ Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success.
ποΈ An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and Ξ³Ξ΄ T cells in cholangitis.
ποΈ Defining the tumor microenvironment of non-small cell lung cancer.
ποΈ SenSet defines cell-type specific senescence signatures in the aged human lung.
ποΈ Single-cell TCR mapping reveals spatially coordinated T cell states in head and neck cancer.
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Nature
RESCUE: recovery of unattributed expression patterns in spatial transcriptomics
Nature Communications - Spatial transcriptomics analyses often lose a substantial fraction of molecular signals because standard cell segmentation and deconvolution methods fail to capture...
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Papers:π
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Preprints:π
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Good morning β Here are today's papers!
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Papers:π
ποΈ Senescence Programs Shape the Chronic Wound Microenvironment.
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Papers:π
ποΈ Senescence Programs Shape the Chronic Wound Microenvironment.
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SAGE Journals
Senescence Programs Shape the Chronic Wound Microenvironment
Significance: Chronic wounds such as diabetic foot ulcers, venous leg ulcers, and pressure ulcers are characterized by impaired healing and persistent inflammat...
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Good morning β Here are today's papers!
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Papers:π
ποΈ Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.
ποΈ Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities.
ποΈ + + Single-cell and spatial transcriptomics reveal that the CXCL12-CXCR4 axis drives the immune-desert phenotype in small cell lung cancer by recruiting immunosuppressive CXCR4 neutrophils and S100A8 monocytes.
ποΈ Spatially Resolved Heterogeneity of Lymphatic Vasculature in the Adult Lung.
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Papers:π
ποΈ Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.
ποΈ Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities.
ποΈ + + Single-cell and spatial transcriptomics reveal that the CXCL12-CXCR4 axis drives the immune-desert phenotype in small cell lung cancer by recruiting immunosuppressive CXCR4 neutrophils and S100A8 monocytes.
ποΈ Spatially Resolved Heterogeneity of Lymphatic Vasculature in the Adult Lung.
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Nature
Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance
Nature Communications - Poly(A) tails are critical to gene regulation, yet their organism-wide patterns remain unmapped. Here, the authors provide an 18-organ mouse atlas, revealing that poly(A)...
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Good morning β Here are today's papers!
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Good morning β Here are today's papers!
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ποΈ Integrating bulk and single-cell transcriptomic data to construct a risk model for histidine metabolism-related epithelial cell features in lung adenocarcinoma, predicting prognosis and immune landscape.
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ποΈ Integrating bulk and single-cell transcriptomic data to construct a risk model for histidine metabolism-related epithelial cell features in lung adenocarcinoma, predicting prognosis and immune landscape.
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Taylor & Francis
Integrating bulk and single-cell transcriptomic data to construct a risk model for histidine metabolism-related epithelial cellβ¦
The rising incidence and mortality of lung adenocarcinoma (LUAD) present a significant public health challenge. Histidine, an essential amino acid, plays a pivotal role in metabolic processes, yet ...
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ποΈ A velocity-informed framework for resolving functional stratification in rare human stem cells.
ποΈ scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.
ποΈ CD163 and Tim-4 identify resident intestinal macrophages that are spatially regulated by TGF-Ξ².
ποΈ Single-Cell Profiling Identifies CLEC5A+ Macrophages as Key Drivers of Thoracic Aortic Aneurysm Via CCL5-Mediated M1 Polarization.
ποΈ The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.
ποΈ Beyond the Transcriptome: Leveraging Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) for Deeper Cellular Insights.
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Papers:π
ποΈ A velocity-informed framework for resolving functional stratification in rare human stem cells.
ποΈ scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.
ποΈ CD163 and Tim-4 identify resident intestinal macrophages that are spatially regulated by TGF-Ξ².
ποΈ Single-Cell Profiling Identifies CLEC5A+ Macrophages as Key Drivers of Thoracic Aortic Aneurysm Via CCL5-Mediated M1 Polarization.
ποΈ The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.
ποΈ Beyond the Transcriptome: Leveraging Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) for Deeper Cellular Insights.
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Nature
A velocity-informed framework for resolving functional stratification in rare human stem cells
Leukemia - A velocity-informed framework for resolving functional stratification in rare human stem cells