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ποΈ Single-cell and spatial profiling in cancer biology and clinical oncology.
ποΈ Benchmarking alignment methods for spatial transcriptomics data.
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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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βοΈ DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated Genes from Spatial Transcriptomics
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βοΈ DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated Genes from Spatial Transcriptomics
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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ποΈ Senescence Programs Shape the Chronic Wound Microenvironment.
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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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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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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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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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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
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ποΈ Biomarkers of mitochondrial dynamics in idiopathic pulmonary fibrosis: Identification and validation through transcriptomic and single-cell analyses.
ποΈ Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.
ποΈ Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.
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ποΈ Biomarkers of mitochondrial dynamics in idiopathic pulmonary fibrosis: Identification and validation through transcriptomic and single-cell analyses.
ποΈ Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.
ποΈ Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.
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βοΈ ProPER: Programmable, multiplexed detection of molecular proximities and RNA life-cycle stages in situ
βοΈ SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection
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ποΈ + A macrophage MHC-I axis links intratumoral heterogeneity to terminal CD8 T cell exhaustion in lung adenocarcinoma.
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βοΈ ProPER: Programmable, multiplexed detection of molecular proximities and RNA life-cycle stages in situ
βοΈ SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection
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ποΈ + A macrophage MHC-I axis links intratumoral heterogeneity to terminal CD8 T cell exhaustion in lung adenocarcinoma.
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Good morning β Here are today's papers!
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ποΈ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
ποΈ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
ποΈ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
ποΈ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
ποΈ Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.
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ποΈ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
ποΈ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
ποΈ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
ποΈ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
ποΈ Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.
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Nature
Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers
Oncogene - Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers
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