Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
🗞️ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
🗞️ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
🗞️ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
🗞️ Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.
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Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Fibroblast dynamics in colorectal cancer: stability, plasticity, and novel markers.
🗞️ DiffBulk: Enhancing Spatial Transcriptomic Prediction with Diffusion-Based Training.
🗞️ + Multi-Omics reveals SPP1 + malignant and CXCR4 TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.
🗞️ Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
🗞️ 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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❤1
Good morning ☕ Here are today's papers!
Preprints:👇
✏️ SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium
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🗞️ Comprehensive Multi-Omics Profiling of Tertiary Lymphoid Structures Reveals Immunogenetic Landscapes and Prognostic Subtypes in Lung Adenocarcinoma.
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Preprints:👇
✏️ SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium
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🗞️ Comprehensive Multi-Omics Profiling of Tertiary Lymphoid Structures Reveals Immunogenetic Landscapes and Prognostic Subtypes in Lung Adenocarcinoma.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations
✏️ spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis
✏️ Robust identification of cell-cell communication heterogeneity in single cells
✏️ Clustering Strategies Improve Structure-Preserving Visualization of Single-Cell RNA-seq Data with CBMAP
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Papers:👇
🗞️ Syrah: a pipeline to maximize spatial transcriptomics data output.
🗞️ REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.
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Preprints:👇
✏️ Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations
✏️ spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis
✏️ Robust identification of cell-cell communication heterogeneity in single cells
✏️ Clustering Strategies Improve Structure-Preserving Visualization of Single-Cell RNA-seq Data with CBMAP
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Papers:👇
🗞️ Syrah: a pipeline to maximize spatial transcriptomics data output.
🗞️ REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer
✏️ MilliMap: interactive closed-loop analysis for spatial omics
✏️ STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis
✏️ Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data
✏️ Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
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Papers:👇
🗞️ Charting spatial ligand-target activity using Renoir.
🗞️ DiffuST: a Latent Diffusion Model for Spatial Transcriptomics Denoising.
🗞️ Neighborhood-informed positional information for precise cell identity specification.
🗞️ CellFuse enables Multi-modal Integration of Single-cell and Spatial Proteomics Data for Systems-level Analysis in Cancer.
🗞️ Transcriptional and ubiquitinative suppression of macrophage CST3 disrupts colonic homeostasis through defective efferocytosis.
🗞️ Extracellular vimentin promotes neutrophil-dominant granulomatous inflammation in progressive pulmonary sarcoidosis.
🗞️ RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.
🗞️ Cancer-Associated Fibroblasts Promote Epithelial-Mesenchymal Transition and Classical to Basal Subtype Shift in Pancreatic Cancer.
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Preprints:👇
✏️ Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer
✏️ MilliMap: interactive closed-loop analysis for spatial omics
✏️ STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis
✏️ Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data
✏️ Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
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Papers:👇
🗞️ Charting spatial ligand-target activity using Renoir.
🗞️ DiffuST: a Latent Diffusion Model for Spatial Transcriptomics Denoising.
🗞️ Neighborhood-informed positional information for precise cell identity specification.
🗞️ CellFuse enables Multi-modal Integration of Single-cell and Spatial Proteomics Data for Systems-level Analysis in Cancer.
🗞️ Transcriptional and ubiquitinative suppression of macrophage CST3 disrupts colonic homeostasis through defective efferocytosis.
🗞️ Extracellular vimentin promotes neutrophil-dominant granulomatous inflammation in progressive pulmonary sarcoidosis.
🗞️ RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.
🗞️ Cancer-Associated Fibroblasts Promote Epithelial-Mesenchymal Transition and Classical to Basal Subtype Shift in Pancreatic Cancer.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Sex-biased Fibroblast Subpopulations and Transcriptional Programs Reveal Mechanisms of Skin Lesion Development in Systemic Sclerosis
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No papers found today.
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Preprints:👇
✏️ Sex-biased Fibroblast Subpopulations and Transcriptional Programs Reveal Mechanisms of Skin Lesion Development in Systemic Sclerosis
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Single-Cell Atlas of Renal Cell Carcinoma Brain Metastasis Uncovers Mechanisms of Immune Dysfunction and Resistance
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🗞️ iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.
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Preprints:👇
✏️ Single-Cell Atlas of Renal Cell Carcinoma Brain Metastasis Uncovers Mechanisms of Immune Dysfunction and Resistance
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Papers:👇
🗞️ iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches
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🗞️ CXCL16 promotes macrophage-driven inflammation and vascular smooth muscle cell phenotypic switching during carotid plaque destabilization.
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Preprints:👇
✏️ IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches
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🗞️ CXCL16 promotes macrophage-driven inflammation and vascular smooth muscle cell phenotypic switching during carotid plaque destabilization.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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🗞️ Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics.
🗞️ Single-cell transcriptomics reveals anti-inflammatory effects of prednisolone on the hepatic niche in biliary atresia.
🗞️ Single-cell and spatial transcriptomics reveal an arachidonic acid-related cellular atlas in lung adenocarcinoma.
🗞️ Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL.
🗞️ Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
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Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics.
🗞️ Single-cell transcriptomics reveals anti-inflammatory effects of prednisolone on the hepatic niche in biliary atresia.
🗞️ Single-cell and spatial transcriptomics reveal an arachidonic acid-related cellular atlas in lung adenocarcinoma.
🗞️ Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL.
🗞️ Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
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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 ☕ Here are today's papers!
Preprints:👇
✏️ Integrative Single-Cell and Multi-Cohort Analysis of the Netrin-1 Signaling Pathway Reveals Divergent Prognostic Trends and Sex-Dimorphic Associations in Glioblastoma
✏️ Transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold spatial neighborhoods
✏️ Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer
✏️ The ATLAS Penalty: Auxiliary-Transformed Location-Aware Smoothing with Applications to Spatial Transcriptomics
✏️ Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation
✏️ A harmonized single-cell RNA-seq atlas of human localized and metastatic prostate cancers and benign tissues
✏️ Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models.
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Papers:👇
🗞️ Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics data.
🗞️ Tonic and early interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures.
🗞️ SIRT6-Mediated Deacetylation of ATF3 Promotes Silica-Induced Lung Fibrosis by Enhancing its Nuclear Import via Binding to Importin α.
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Preprints:👇
✏️ Integrative Single-Cell and Multi-Cohort Analysis of the Netrin-1 Signaling Pathway Reveals Divergent Prognostic Trends and Sex-Dimorphic Associations in Glioblastoma
✏️ Transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold spatial neighborhoods
✏️ Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer
✏️ The ATLAS Penalty: Auxiliary-Transformed Location-Aware Smoothing with Applications to Spatial Transcriptomics
✏️ Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation
✏️ A harmonized single-cell RNA-seq atlas of human localized and metastatic prostate cancers and benign tissues
✏️ Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models.
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Papers:👇
🗞️ Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics data.
🗞️ Tonic and early interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures.
🗞️ SIRT6-Mediated Deacetylation of ATF3 Promotes Silica-Induced Lung Fibrosis by Enhancing its Nuclear Import via Binding to Importin α.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Multi-layer transcriptomic characterization of age-related immune dynamics
✏️ 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
✏️ A workflow for combined detection of protein interactions and cell types for translational studies
✏️ Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics
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Papers:👇
🗞️ Optimized nuclei isolation and snRNA-seq reveal oligodendrocyte pathway dysregulation in MOGHE brain tissue from pediatric patients.
🗞️ Protocol for isolating cells from a single cryopreserved gastrointestinal endoscopic biopsy for single-cell RNA sequencing.
🗞️ Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.
🗞️ Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.
🗞️ Impaired mucociliary clearance in bronchiectasis: the result of a differentiation-delayed airway epithelium?
🗞️ 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! 👋
Preprints:👇
✏️ Multi-layer transcriptomic characterization of age-related immune dynamics
✏️ 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
✏️ A workflow for combined detection of protein interactions and cell types for translational studies
✏️ Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics
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Papers:👇
🗞️ Optimized nuclei isolation and snRNA-seq reveal oligodendrocyte pathway dysregulation in MOGHE brain tissue from pediatric patients.
🗞️ Protocol for isolating cells from a single cryopreserved gastrointestinal endoscopic biopsy for single-cell RNA sequencing.
🗞️ Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.
🗞️ Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.
🗞️ Impaired mucociliary clearance in bronchiectasis: the result of a differentiation-delayed airway epithelium?
🗞️ Pan-cancer analysis of single-cell profiles with polygenic signals reveals genetic influences on tumor immunity across cancers.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ scDIG: An R Shiny Application for Interactive Density-Based Gating of Single-Cell Proteomic and Transcriptomic Data
✏️ SpatialCCCbench: Standardized Metrics for the Systematic Evaluation of Spatial Cell-Cell Communication Methods
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Papers:👇
🗞️ + A Stromal-Centered Single-Cell Landscape Identifies POSTN Fibroblasts as a High-Risk Stromal Subset in Hepatocellular Carcinoma.
🗞️ The role of the RS1-NEDD4-YAP1 axis orchestrates epithelial-macrophage interplay in COPD.
🗞️ Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants.
🗞️ Lactate and Akkermansia muciniphila: Emerging Roles in Inflammatory Bowel Disease and Colorectal Cancer.
🗞️ Optimisation of Xenium automated in situ sequencing for PAXgene-fixed tissue samples.
🗞️ THBS1 SPP1 Multiregional profiling reveals - monocyte-macrophage axis drives immunosuppression and outcome in colorectal liver metastases.
🗞️ Comprehensive bioinformatics analysis of EXOSC family genes in lung adenocarcinoma.
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Preprints:👇
✏️ scDIG: An R Shiny Application for Interactive Density-Based Gating of Single-Cell Proteomic and Transcriptomic Data
✏️ SpatialCCCbench: Standardized Metrics for the Systematic Evaluation of Spatial Cell-Cell Communication Methods
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Papers:👇
🗞️ + A Stromal-Centered Single-Cell Landscape Identifies POSTN Fibroblasts as a High-Risk Stromal Subset in Hepatocellular Carcinoma.
🗞️ The role of the RS1-NEDD4-YAP1 axis orchestrates epithelial-macrophage interplay in COPD.
🗞️ Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants.
🗞️ Lactate and Akkermansia muciniphila: Emerging Roles in Inflammatory Bowel Disease and Colorectal Cancer.
🗞️ Optimisation of Xenium automated in situ sequencing for PAXgene-fixed tissue samples.
🗞️ THBS1 SPP1 Multiregional profiling reveals - monocyte-macrophage axis drives immunosuppression and outcome in colorectal liver metastases.
🗞️ Comprehensive bioinformatics analysis of EXOSC family genes in lung adenocarcinoma.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ PerturbPlan: An analytical framework for designing Perturb-seq experiments
✏️ Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME
✏️ Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics
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Papers:👇
🗞️ Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance.
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Preprints:👇
✏️ PerturbPlan: An analytical framework for designing Perturb-seq experiments
✏️ Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME
✏️ Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics
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Papers:👇
🗞️ Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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No papers found today.
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Preprints:👇
No preprints found today.
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No papers found today.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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Papers:👇
No papers found today.
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Preprints:👇
No preprints found today.
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No papers found today.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ SpatialClaw: A Memory-Augmented Autonomous Ecosystem for Spatial Omics Analysis
✏️ Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis
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Papers:👇
🗞️ Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.
🗞️ Integration of single-cell RNA-sequencing and machine learning identifies GRN and FCER1G as potential peroxisomal targets in influenza pathogenesis.
🗞️ SOFisher: reinforcement learning-guided experiment designs for spatial omics.
🗞️ Integrative single-cell RNA-seq and transcriptomic analysis uncovers cellular heterogeneity and immunotherapy resistance mechanisms in colorectal cancer.
🗞️ Benchmarking the prediction of responding cells to perturbations affecting both gene expression and cellular abundance using scRNA sequencing.
🗞️ Mechanisms and reversal strategies of liver fibrosis: from regulation of cell fate to clinical translation.
🗞️ Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.
🗞️ SDMCC: Sample-wise Debiased Multilevel Contrastive Clustering for Single-cell Gene Expression Data.
🗞️ Toward simultaneous pseudo-space reconstruction and cell-type deconvolution of single-cell spatial transcriptome using SpaDicer.
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Enjoy your reading! 👋
Preprints:👇
✏️ SpatialClaw: A Memory-Augmented Autonomous Ecosystem for Spatial Omics Analysis
✏️ Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis
────────────
Papers:👇
🗞️ Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.
🗞️ Integration of single-cell RNA-sequencing and machine learning identifies GRN and FCER1G as potential peroxisomal targets in influenza pathogenesis.
🗞️ SOFisher: reinforcement learning-guided experiment designs for spatial omics.
🗞️ Integrative single-cell RNA-seq and transcriptomic analysis uncovers cellular heterogeneity and immunotherapy resistance mechanisms in colorectal cancer.
🗞️ Benchmarking the prediction of responding cells to perturbations affecting both gene expression and cellular abundance using scRNA sequencing.
🗞️ Mechanisms and reversal strategies of liver fibrosis: from regulation of cell fate to clinical translation.
🗞️ Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.
🗞️ SDMCC: Sample-wise Debiased Multilevel Contrastive Clustering for Single-cell Gene Expression Data.
🗞️ Toward simultaneous pseudo-space reconstruction and cell-type deconvolution of single-cell spatial transcriptome using SpaDicer.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Beyond Suppression: The Plasticity, Dysfunction, and Therapeutic Reprogramming of Regulatory T Cells in Inflammatory Bowel Disease.
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Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Beyond Suppression: The Plasticity, Dysfunction, and Therapeutic Reprogramming of Regulatory T Cells in Inflammatory Bowel Disease.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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No papers found today.
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Preprints:👇
No preprints found today.
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No papers found today.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Integrative multi-omics analysis identifies LIPA as a prognostic hub and ferroptosis regulator in lung adenocarcinoma.
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Preprints:👇
No preprints found today.
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Papers:👇
🗞️ Integrative multi-omics analysis identifies LIPA as a prognostic hub and ferroptosis regulator in lung adenocarcinoma.
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SpringerLink
Integrative multi-omics analysis identifies LIPA as a prognostic hub and ferroptosis regulator in lung adenocarcinoma
Molecular and Cellular Biochemistry - Lung adenocarcinoma (LUAD) remains one of the leading causes of cancer mortality, underscoring the urgent need for biomarkers and therapeutic targets rooted in...