Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ STDrug enables spatially informed personalized drug repurposing from spatial transcriptomics
โ๏ธ CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation
โ๏ธ Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics
โ๏ธ Longitudinal Single-Cell RNA-seq Profiling of Lung Cell Phenotypes, Signaling, and Cross-talk During Fibrosis Resolution
โ๏ธ Distinct Spatial Programs of Response versus Resistance in Non-Small Cell Lung Cancer after Neoadjuvant Chemoimmunotherapy
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Papers:๐
๐๏ธ Img2Gene: Debiased Spatially Resolved Transcriptomics with Biological Context from Pathology Images.
๐๏ธ Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ STDrug enables spatially informed personalized drug repurposing from spatial transcriptomics
โ๏ธ CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation
โ๏ธ Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics
โ๏ธ Longitudinal Single-Cell RNA-seq Profiling of Lung Cell Phenotypes, Signaling, and Cross-talk During Fibrosis Resolution
โ๏ธ Distinct Spatial Programs of Response versus Resistance in Non-Small Cell Lung Cancer after Neoadjuvant Chemoimmunotherapy
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Papers:๐
๐๏ธ Img2Gene: Debiased Spatially Resolved Transcriptomics with Biological Context from Pathology Images.
๐๏ธ Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Geometry-aware ligand-receptor analysis distinguishes interface association from spatial localization and reveals a continuum of tumor communication
โ๏ธ Counterfactual Modeling of Directional Cell Cell Influence in Spatial Transcriptomics
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Papers:๐
๐๏ธ GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis.
๐๏ธ CIPHER-seq enables intracellular multimodal profiling of cytokine responses in single immune cells.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Geometry-aware ligand-receptor analysis distinguishes interface association from spatial localization and reveals a continuum of tumor communication
โ๏ธ Counterfactual Modeling of Directional Cell Cell Influence in Spatial Transcriptomics
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Papers:๐
๐๏ธ GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis.
๐๏ธ CIPHER-seq enables intracellular multimodal profiling of cytokine responses in single immune cells.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.
๐๏ธ The rise of spatial TCR profiling: Emerging technologies and open challenges.
๐๏ธ Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success.
๐๏ธ An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and ฮณฮด T cells in cholangitis.
๐๏ธ Defining the tumor microenvironment of non-small cell lung cancer.
๐๏ธ SenSet defines cell-type specific senescence signatures in the aged human lung.
๐๏ธ Single-cell TCR mapping reveals spatially coordinated T cell states in head and neck cancer.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.
๐๏ธ The rise of spatial TCR profiling: Emerging technologies and open challenges.
๐๏ธ Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success.
๐๏ธ An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and ฮณฮด T cells in cholangitis.
๐๏ธ Defining the tumor microenvironment of non-small cell lung cancer.
๐๏ธ SenSet defines cell-type specific senescence signatures in the aged human lung.
๐๏ธ Single-cell TCR mapping reveals spatially coordinated T cell states in head and neck cancer.
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Enjoy your reading! ๐
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...
โค1
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Senescence Programs Shape the Chronic Wound Microenvironment.
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Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Senescence Programs Shape the Chronic Wound Microenvironment.
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Enjoy your reading! ๐
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...
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.
๐๏ธ Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities.
๐๏ธ + + 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.
๐๏ธ Spatially Resolved Heterogeneity of Lymphatic Vasculature in the Adult Lung.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.
๐๏ธ Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities.
๐๏ธ + + 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.
๐๏ธ Spatially Resolved Heterogeneity of Lymphatic Vasculature in the Adult Lung.
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Enjoy your reading! ๐
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)...
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ 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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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ 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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Enjoy your reading! ๐
Taylor & Francis
Integrating bulk and single-cell transcriptomic data to construct a risk model for histidine metabolism-related epithelial cellโฆ
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 ...
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ A velocity-informed framework for resolving functional stratification in rare human stem cells.
๐๏ธ scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.
๐๏ธ CD163 and Tim-4 identify resident intestinal macrophages that are spatially regulated by TGF-ฮฒ.
๐๏ธ Single-Cell Profiling Identifies CLEC5A+ Macrophages as Key Drivers of Thoracic Aortic Aneurysm Via CCL5-Mediated M1 Polarization.
๐๏ธ The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.
๐๏ธ Beyond the Transcriptome: Leveraging Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) for Deeper Cellular Insights.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ A velocity-informed framework for resolving functional stratification in rare human stem cells.
๐๏ธ scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.
๐๏ธ CD163 and Tim-4 identify resident intestinal macrophages that are spatially regulated by TGF-ฮฒ.
๐๏ธ Single-Cell Profiling Identifies CLEC5A+ Macrophages as Key Drivers of Thoracic Aortic Aneurysm Via CCL5-Mediated M1 Polarization.
๐๏ธ The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.
๐๏ธ Beyond the Transcriptome: Leveraging Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) for Deeper Cellular Insights.
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Enjoy your reading! ๐
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
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Biomarkers of mitochondrial dynamics in idiopathic pulmonary fibrosis: Identification and validation through transcriptomic and single-cell analyses.
๐๏ธ Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.
๐๏ธ Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Biomarkers of mitochondrial dynamics in idiopathic pulmonary fibrosis: Identification and validation through transcriptomic and single-cell analyses.
๐๏ธ Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.
๐๏ธ Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ ProPER: Programmable, multiplexed detection of molecular proximities and RNA life-cycle stages in situ
โ๏ธ SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection
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Papers:๐
๐๏ธ + A macrophage MHC-I axis links intratumoral heterogeneity to terminal CD8 T cell exhaustion in lung adenocarcinoma.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ ProPER: Programmable, multiplexed detection of molecular proximities and RNA life-cycle stages in situ
โ๏ธ SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection
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Papers:๐
๐๏ธ + A macrophage MHC-I axis links intratumoral heterogeneity to terminal CD8 T cell exhaustion in lung adenocarcinoma.
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Enjoy your reading! ๐
โค1
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
๐๏ธ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
๐๏ธ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
๐๏ธ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
๐๏ธ Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
๐๏ธ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
๐๏ธ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
๐๏ธ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
๐๏ธ Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.
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Enjoy your reading! ๐
Nature
Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers
Oncogene - Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers
Good morning โ Here are today's papers!
Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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Preprints:๐
No preprints found today.
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Papers:๐
No papers found today.
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โค1
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium
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Papers:๐
๐๏ธ Comprehensive Multi-Omics Profiling of Tertiary Lymphoid Structures Reveals Immunogenetic Landscapes and Prognostic Subtypes in Lung Adenocarcinoma.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium
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Papers:๐
๐๏ธ Comprehensive Multi-Omics Profiling of Tertiary Lymphoid Structures Reveals Immunogenetic Landscapes and Prognostic Subtypes in Lung Adenocarcinoma.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations
โ๏ธ spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis
โ๏ธ Robust identification of cell-cell communication heterogeneity in single cells
โ๏ธ Clustering Strategies Improve Structure-Preserving Visualization of Single-Cell RNA-seq Data with CBMAP
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Papers:๐
๐๏ธ Syrah: a pipeline to maximize spatial transcriptomics data output.
๐๏ธ REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations
โ๏ธ spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis
โ๏ธ Robust identification of cell-cell communication heterogeneity in single cells
โ๏ธ Clustering Strategies Improve Structure-Preserving Visualization of Single-Cell RNA-seq Data with CBMAP
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Papers:๐
๐๏ธ Syrah: a pipeline to maximize spatial transcriptomics data output.
๐๏ธ REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer
โ๏ธ MilliMap: interactive closed-loop analysis for spatial omics
โ๏ธ STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis
โ๏ธ Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data
โ๏ธ Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
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Papers:๐
๐๏ธ Charting spatial ligand-target activity using Renoir.
๐๏ธ DiffuST: a Latent Diffusion Model for Spatial Transcriptomics Denoising.
๐๏ธ Neighborhood-informed positional information for precise cell identity specification.
๐๏ธ CellFuse enables Multi-modal Integration of Single-cell and Spatial Proteomics Data for Systems-level Analysis in Cancer.
๐๏ธ Transcriptional and ubiquitinative suppression of macrophage CST3 disrupts colonic homeostasis through defective efferocytosis.
๐๏ธ Extracellular vimentin promotes neutrophil-dominant granulomatous inflammation in progressive pulmonary sarcoidosis.
๐๏ธ RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.
๐๏ธ Cancer-Associated Fibroblasts Promote Epithelial-Mesenchymal Transition and Classical to Basal Subtype Shift in Pancreatic Cancer.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer
โ๏ธ MilliMap: interactive closed-loop analysis for spatial omics
โ๏ธ STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis
โ๏ธ Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data
โ๏ธ Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
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Papers:๐
๐๏ธ Charting spatial ligand-target activity using Renoir.
๐๏ธ DiffuST: a Latent Diffusion Model for Spatial Transcriptomics Denoising.
๐๏ธ Neighborhood-informed positional information for precise cell identity specification.
๐๏ธ CellFuse enables Multi-modal Integration of Single-cell and Spatial Proteomics Data for Systems-level Analysis in Cancer.
๐๏ธ Transcriptional and ubiquitinative suppression of macrophage CST3 disrupts colonic homeostasis through defective efferocytosis.
๐๏ธ Extracellular vimentin promotes neutrophil-dominant granulomatous inflammation in progressive pulmonary sarcoidosis.
๐๏ธ RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.
๐๏ธ Cancer-Associated Fibroblasts Promote Epithelial-Mesenchymal Transition and Classical to Basal Subtype Shift in Pancreatic Cancer.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Sex-biased Fibroblast Subpopulations and Transcriptional Programs Reveal Mechanisms of Skin Lesion Development in Systemic Sclerosis
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Papers:๐
No papers found today.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Sex-biased Fibroblast Subpopulations and Transcriptional Programs Reveal Mechanisms of Skin Lesion Development in Systemic Sclerosis
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Papers:๐
No papers found today.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Single-Cell Atlas of Renal Cell Carcinoma Brain Metastasis Uncovers Mechanisms of Immune Dysfunction and Resistance
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Papers:๐
๐๏ธ iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Single-Cell Atlas of Renal Cell Carcinoma Brain Metastasis Uncovers Mechanisms of Immune Dysfunction and Resistance
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Papers:๐
๐๏ธ iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.
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Enjoy your reading! ๐