Good morning โ Here are today's papers!
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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!
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No preprints found today.
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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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No papers found today.
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No preprints found today.
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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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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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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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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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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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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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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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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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โค1
Good morning โ Here are today's papers!
Preprints:๐
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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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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
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Preprints:๐
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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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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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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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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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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
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
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches
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Papers:๐
๐๏ธ CXCL16 promotes macrophage-driven inflammation and vascular smooth muscle cell phenotypic switching during carotid plaque destabilization.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches
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Papers:๐
๐๏ธ CXCL16 promotes macrophage-driven inflammation and vascular smooth muscle cell phenotypic switching during carotid plaque destabilization.
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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 Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics.
๐๏ธ Single-cell transcriptomics reveals anti-inflammatory effects of prednisolone on the hepatic niche in biliary atresia.
๐๏ธ Single-cell and spatial transcriptomics reveal an arachidonic acid-related cellular atlas in lung adenocarcinoma.
๐๏ธ Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL.
๐๏ธ Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
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Enjoy your reading! ๐
Preprints:๐
No preprints found today.
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Papers:๐
๐๏ธ Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics.
๐๏ธ Single-cell transcriptomics reveals anti-inflammatory effects of prednisolone on the hepatic niche in biliary atresia.
๐๏ธ Single-cell and spatial transcriptomics reveal an arachidonic acid-related cellular atlas in lung adenocarcinoma.
๐๏ธ Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL.
๐๏ธ Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
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Enjoy your reading! ๐
Nature
Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics
Nature Communications - Dou and colleagues present DynNet, a biophysically informed deep learning framework that reconstructs continuous cellular dynamics from time-resolved single-cell data....
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Integrative Single-Cell and Multi-Cohort Analysis of the Netrin-1 Signaling Pathway Reveals Divergent Prognostic Trends and Sex-Dimorphic Associations in Glioblastoma
โ๏ธ Transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold spatial neighborhoods
โ๏ธ Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer
โ๏ธ The ATLAS Penalty: Auxiliary-Transformed Location-Aware Smoothing with Applications to Spatial Transcriptomics
โ๏ธ Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation
โ๏ธ A harmonized single-cell RNA-seq atlas of human localized and metastatic prostate cancers and benign tissues
โ๏ธ Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models.
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Papers:๐
๐๏ธ Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics data.
๐๏ธ Tonic and early interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures.
๐๏ธ SIRT6-Mediated Deacetylation of ATF3 Promotes Silica-Induced Lung Fibrosis by Enhancing its Nuclear Import via Binding to Importin ฮฑ.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Integrative Single-Cell and Multi-Cohort Analysis of the Netrin-1 Signaling Pathway Reveals Divergent Prognostic Trends and Sex-Dimorphic Associations in Glioblastoma
โ๏ธ Transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold spatial neighborhoods
โ๏ธ Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer
โ๏ธ The ATLAS Penalty: Auxiliary-Transformed Location-Aware Smoothing with Applications to Spatial Transcriptomics
โ๏ธ Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation
โ๏ธ A harmonized single-cell RNA-seq atlas of human localized and metastatic prostate cancers and benign tissues
โ๏ธ Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models.
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Papers:๐
๐๏ธ Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics data.
๐๏ธ Tonic and early interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures.
๐๏ธ SIRT6-Mediated Deacetylation of ATF3 Promotes Silica-Induced Lung Fibrosis by Enhancing its Nuclear Import via Binding to Importin ฮฑ.
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Enjoy your reading! ๐
Good morning โ Here are today's papers!
Preprints:๐
โ๏ธ Multi-layer transcriptomic characterization of age-related immune dynamics
โ๏ธ Spectral Prompting: Unsupervised Recovery of Human Hair Follicle Cell-Type and Multiscale Systems Architecture from Bulk and Single-Cell RNA-Seq Datasets via Single-Gene Seeded Spectral Unfolding
โ๏ธ A workflow for combined detection of protein interactions and cell types for translational studies
โ๏ธ Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics
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Papers:๐
๐๏ธ Optimized nuclei isolation and snRNA-seq reveal oligodendrocyte pathway dysregulation in MOGHE brain tissue from pediatric patients.
๐๏ธ Protocol for isolating cells from a single cryopreserved gastrointestinal endoscopic biopsy for single-cell RNA sequencing.
๐๏ธ Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.
๐๏ธ Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.
๐๏ธ Impaired mucociliary clearance in bronchiectasis: the result of a differentiation-delayed airway epithelium?
๐๏ธ Pan-cancer analysis of single-cell profiles with polygenic signals reveals genetic influences on tumor immunity across cancers.
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Enjoy your reading! ๐
Preprints:๐
โ๏ธ Multi-layer transcriptomic characterization of age-related immune dynamics
โ๏ธ Spectral Prompting: Unsupervised Recovery of Human Hair Follicle Cell-Type and Multiscale Systems Architecture from Bulk and Single-Cell RNA-Seq Datasets via Single-Gene Seeded Spectral Unfolding
โ๏ธ A workflow for combined detection of protein interactions and cell types for translational studies
โ๏ธ Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics
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Papers:๐
๐๏ธ Optimized nuclei isolation and snRNA-seq reveal oligodendrocyte pathway dysregulation in MOGHE brain tissue from pediatric patients.
๐๏ธ Protocol for isolating cells from a single cryopreserved gastrointestinal endoscopic biopsy for single-cell RNA sequencing.
๐๏ธ Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.
๐๏ธ Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.
๐๏ธ Impaired mucociliary clearance in bronchiectasis: the result of a differentiation-delayed airway epithelium?
๐๏ธ Pan-cancer analysis of single-cell profiles with polygenic signals reveals genetic influences on tumor immunity across cancers.
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Enjoy your reading! ๐