Good morning ☕ Here are today's papers!
Preprints:👇
✏️ singIST: an R/Bioconductor library and Quarto dashboard for automated single-cell comparative transcriptomics analysis ofdisease models and humans
✏️ Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq data with SPAE
✏️ High-throughput Single-cell Proteomics Enabled by Integrating nPOP-workflow with Quantitative Hyperplexing
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Preprints:👇
✏️ singIST: an R/Bioconductor library and Quarto dashboard for automated single-cell comparative transcriptomics analysis ofdisease models and humans
✏️ Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq data with SPAE
✏️ High-throughput Single-cell Proteomics Enabled by Integrating nPOP-workflow with Quantitative Hyperplexing
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies
✏️ Classification with Missing Data - A NIFty Pipeline for Single-Cell Proteomics
✏️ Performance of the 10X Genomics Flex Single-Cell Sequencing Assay and its Application to Overcome Challenges in Clinical Trial Samples
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Preprints:👇
✏️ MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies
✏️ Classification with Missing Data - A NIFty Pipeline for Single-Cell Proteomics
✏️ Performance of the 10X Genomics Flex Single-Cell Sequencing Assay and its Application to Overcome Challenges in Clinical Trial Samples
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Reconstructing biologically coherent cellular profiles from imaging-based spatial transcriptomics
✏️ Inferring large networks with matrix factorisation to capture non-linear dependencies among genes using sparse single-cell profiles
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Papers:👇
🗞️ LoHi-SSL: a Multi-Level Synergistic Learning Model for Integrating Single-Cell Multi-Omics Data via Low- and High-Order Information Fusion.
🗞️ Spatial single-cell proteotyping reveals immunotherapy-resistant features within the complex tumor microenvironment of metastatic NSCLC.
🗞️ scCMA: A Contrastive Masked Autoencoder Framework for Robust Representation Learning of scRNA-seq Data.
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Preprints:👇
✏️ Reconstructing biologically coherent cellular profiles from imaging-based spatial transcriptomics
✏️ Inferring large networks with matrix factorisation to capture non-linear dependencies among genes using sparse single-cell profiles
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Papers:👇
🗞️ LoHi-SSL: a Multi-Level Synergistic Learning Model for Integrating Single-Cell Multi-Omics Data via Low- and High-Order Information Fusion.
🗞️ Spatial single-cell proteotyping reveals immunotherapy-resistant features within the complex tumor microenvironment of metastatic NSCLC.
🗞️ scCMA: A Contrastive Masked Autoencoder Framework for Robust Representation Learning of scRNA-seq Data.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Decoupling Lineage and Intrinsic Information in Single-Cell Lineage Tracing Data with Deep Disentangled Representation Learning
✏️ scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq
✏️ Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq
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Papers:👇
🗞️ The SDC1-ENO1 Axis in Cancer-Associated Fibroblasts Generates a Lactate-Rich Microenvironment that Drives Tumor Radioresistance.
🗞️ The Human Organ Atlas.
🗞️ Type 2 lymphocytes restrict type 3 lymphocytes during liver fibrosis and colocalize in fibroblast niches.
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Preprints:👇
✏️ Decoupling Lineage and Intrinsic Information in Single-Cell Lineage Tracing Data with Deep Disentangled Representation Learning
✏️ scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq
✏️ Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq
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Papers:👇
🗞️ The SDC1-ENO1 Axis in Cancer-Associated Fibroblasts Generates a Lactate-Rich Microenvironment that Drives Tumor Radioresistance.
🗞️ The Human Organ Atlas.
🗞️ Type 2 lymphocytes restrict type 3 lymphocytes during liver fibrosis and colocalize in fibroblast niches.
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Good morning ☕ Here are today's papers!
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No preprints found today.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Cell type-specific gene regulatory network inference from single cell transcriptomics with ctOTVelo
✏️ stMCP: Spatial Transcriptomics with a Model Context Protocol Server
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Preprints:👇
✏️ Cell type-specific gene regulatory network inference from single cell transcriptomics with ctOTVelo
✏️ stMCP: Spatial Transcriptomics with a Model Context Protocol Server
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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:👇
✏️ UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction
✏️ SpotGraphs: Graph-based analysis of spatially resolved transcriptional data in R
✏️ An explanatory benchmark of spatial domain detection reveals key drivers of method performance
✏️ Frequency-domain kernels enable atlas-scale detection of spatially variable genes
✏️ A systematic analysis of brain tissue response to microelectrode material and size with single-cell spatial transcriptomics
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Papers:👇
🗞️ Integrated single-cell and spatial analysis reveals context-dependent myeloid-T cell interactions in response to immune checkpoint blockade in head and neck cancer.
🗞️ A benchmark of semi-supervised scRNA-seq integration methods in real-world scenarios.
🗞️ SAD: Sparse-Aware Diffusion Model for Single-Cell Gene Expression Completion.
🗞️ singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.
🗞️ From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.
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Preprints:👇
✏️ UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction
✏️ SpotGraphs: Graph-based analysis of spatially resolved transcriptional data in R
✏️ An explanatory benchmark of spatial domain detection reveals key drivers of method performance
✏️ Frequency-domain kernels enable atlas-scale detection of spatially variable genes
✏️ A systematic analysis of brain tissue response to microelectrode material and size with single-cell spatial transcriptomics
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Papers:👇
🗞️ Integrated single-cell and spatial analysis reveals context-dependent myeloid-T cell interactions in response to immune checkpoint blockade in head and neck cancer.
🗞️ A benchmark of semi-supervised scRNA-seq integration methods in real-world scenarios.
🗞️ SAD: Sparse-Aware Diffusion Model for Single-Cell Gene Expression Completion.
🗞️ singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.
🗞️ From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.
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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:👇
✏️ Epithelial MHC II antigen presentation dynamically informs intestinal homeostasis and injury
✏️ Mapping spatial cell-cell communication programs by tailoring chains of cells for transformer neural networks
✏️ Decomap-seq enables efficient and reliable retrieval of spatial transcripts
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Papers:👇
🗞️ + The roles and heterogeneity of CD8 T cells in inflammatory bowel disease: A narrative review of insights from single‑cell transcriptomics (Review).
🗞️ Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.
🗞️ Prior-guided factorization for reliable imputation of scRNA-seq data.
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Preprints:👇
✏️ Epithelial MHC II antigen presentation dynamically informs intestinal homeostasis and injury
✏️ Mapping spatial cell-cell communication programs by tailoring chains of cells for transformer neural networks
✏️ Decomap-seq enables efficient and reliable retrieval of spatial transcripts
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Papers:👇
🗞️ + The roles and heterogeneity of CD8 T cells in inflammatory bowel disease: A narrative review of insights from single‑cell transcriptomics (Review).
🗞️ Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.
🗞️ Prior-guided factorization for reliable imputation of scRNA-seq data.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Advancing Nuclei Isolation from Frozen Human Heart for Single-Nucleus RNA Sequencing Applications
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Preprints:👇
✏️ Advancing Nuclei Isolation from Frozen Human Heart for Single-Nucleus RNA Sequencing Applications
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Good morning ☕ Here are today's papers!
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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🗞️ Single-cell dissection of pleural and systemic immunity uncovers pathogen-specific immune reprogramming in tuberculosis versus lung adenocarcinoma.
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Preprints:👇
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Papers:👇
🗞️ Single-cell dissection of pleural and systemic immunity uncovers pathogen-specific immune reprogramming in tuberculosis versus lung adenocarcinoma.
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SpringerLink
Single-cell dissection of pleural and systemic immunity uncovers pathogen-specific immune reprogramming in tuberculosis versus…
Inflammation Research - To dissect how malignant versus infectious pleural disease reshapes local and systemic immunity, we compared lung adenocarcinoma with tuberculosis using matched pleural...
Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Single-cell Landscape of T Cell Heterogeneity in Kawasaki Disease: STAT3/JAK Axis Regulates the Lineage Differentiation Bias of Th17 Cells
✏️ Fibroblast-derived Collagen VI shapes the structure and function of the tumor-immune microenvironment in clear cell renal cell carcinoma
✏️ Spatial transcriptomics identifies dysregulated programs across neural and non-neural tissues in spinal muscular atrophy
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Papers:👇
🗞️ AutoGERN: Single-Cell RNA-Seq Gene Regulatory Network Inference via Explicit Link Modeling and Adaptive Architectures.
🗞️ Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.
🗞️ spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model.
🗞️ Macrophages expressing macrophage receptor with collagen structure attenuate liver fibrosis through a tissue restoration phenotype.
🗞️ DyGFormer:Transformer With Resistance-Distance Bias for Semi-Supervised Cell-Type Identification.
🗞️ scResponse: A Rank-Based Method for Identifying Cell States That Contribute to Immunotherapy Response by Single-Cell Data.
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Preprints:👇
✏️ Single-cell Landscape of T Cell Heterogeneity in Kawasaki Disease: STAT3/JAK Axis Regulates the Lineage Differentiation Bias of Th17 Cells
✏️ Fibroblast-derived Collagen VI shapes the structure and function of the tumor-immune microenvironment in clear cell renal cell carcinoma
✏️ Spatial transcriptomics identifies dysregulated programs across neural and non-neural tissues in spinal muscular atrophy
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Papers:👇
🗞️ AutoGERN: Single-Cell RNA-Seq Gene Regulatory Network Inference via Explicit Link Modeling and Adaptive Architectures.
🗞️ Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.
🗞️ spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model.
🗞️ Macrophages expressing macrophage receptor with collagen structure attenuate liver fibrosis through a tissue restoration phenotype.
🗞️ DyGFormer:Transformer With Resistance-Distance Bias for Semi-Supervised Cell-Type Identification.
🗞️ scResponse: A Rank-Based Method for Identifying Cell States That Contribute to Immunotherapy Response by Single-Cell Data.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Spatial multi-omics of multiple myeloma uncovers niche-dependent pro-myeloma and immunosuppressive signaling in the bone marrow and extramedullary lesions
✏️ Spatially-resolved single cell atlas of liposarcoma reveals lineage hierarchies, immune niches, and regulatory circuits
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Papers:👇
🗞️ Targeting the epithelium in pulmonary fibrosis.
🗞️ Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy-Naïve Localized Prostate Cancer.
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Preprints:👇
✏️ Spatial multi-omics of multiple myeloma uncovers niche-dependent pro-myeloma and immunosuppressive signaling in the bone marrow and extramedullary lesions
✏️ Spatially-resolved single cell atlas of liposarcoma reveals lineage hierarchies, immune niches, and regulatory circuits
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Papers:👇
🗞️ Targeting the epithelium in pulmonary fibrosis.
🗞️ Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy-Naïve Localized Prostate Cancer.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis
✏️ Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology
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Preprints:👇
✏️ A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis
✏️ Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Beyond a binary view of cystic fibrosis: systemic immunity and inflammation across the spectrum of CFTR dysfunction
✏️ scMagnifier: resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering
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Papers:👇
🗞️ Cancer-Associated Fibroblasts Functions as Multifunctional Architects of the Tumor Stroma and Represent Emerging Therapeutic Vulnerabilities.
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Preprints:👇
✏️ Beyond a binary view of cystic fibrosis: systemic immunity and inflammation across the spectrum of CFTR dysfunction
✏️ scMagnifier: resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering
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Papers:👇
🗞️ Cancer-Associated Fibroblasts Functions as Multifunctional Architects of the Tumor Stroma and Represent Emerging Therapeutic Vulnerabilities.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ 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:👇
🗞️ IGSF9 drives malignant transformation and predicts early-stage lung adenocarcinoma in integrated transcriptomic analyses.
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Preprints:👇
✏️ 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:👇
🗞️ IGSF9 drives malignant transformation and predicts early-stage lung adenocarcinoma in integrated transcriptomic analyses.
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Good morning ☕ Here are today's papers!
Preprints:👇
✏️ Intercellular communication is a heritable dimension of human tissue architecture
✏️ Cell type composition drives patient stratification in single-cell RNA-seq cohorts
✏️ CoLa-VAE: Cell-Cell Communication-aware Variational Autoencoder with Dynamic Graph Laplacian Constraints
✏️ GraphBG: Fast Bayesian Domain Detection via Spectral Graph Convolutions for Multi-slice and Multi-modal Spatial Transcriptomics
✏️ scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data
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Papers:👇
🗞️ Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment.
🗞️ Gut Commensal Klebsiella pneumoniae Extracellular Vesicles Shape a Liver Microenvironment Conducive to Gut-Liver Bacterial Translocation and Pro-Tumorigenic Processes.
🗞️ ZFP36L1 promotes non-small cell lung cancer progression under hypoxia by modulating CXCL9:SPP1 polarity: A single-cell transcriptomic study.
🗞️ Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning.
🗞️ ECM-Stiffness Mediated Persistent Fibroblast Activation Requires Integrin and Formin Dependent Chromatin Remodeling.
🗞️ Single-cell spatial atlas of the aging human breast.
🗞️ Kernel-DMD for multiome data integration and control.
🗞️ Complementary multi-omics profiling of chronic thromboembolic pulmonary hypertension reveals immune cell alterations, epigenetic changes, and genetically supported candidate genes.
🗞️ Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.
🗞️ scDenorm: a denormalisation tool for integrating single-cell transcriptomics data.
🗞️ Benchmarking single-cell tumor immune atlases and application for uncovering cell states related to immunotherapy response.
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Preprints:👇
✏️ Intercellular communication is a heritable dimension of human tissue architecture
✏️ Cell type composition drives patient stratification in single-cell RNA-seq cohorts
✏️ CoLa-VAE: Cell-Cell Communication-aware Variational Autoencoder with Dynamic Graph Laplacian Constraints
✏️ GraphBG: Fast Bayesian Domain Detection via Spectral Graph Convolutions for Multi-slice and Multi-modal Spatial Transcriptomics
✏️ scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data
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Papers:👇
🗞️ Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment.
🗞️ Gut Commensal Klebsiella pneumoniae Extracellular Vesicles Shape a Liver Microenvironment Conducive to Gut-Liver Bacterial Translocation and Pro-Tumorigenic Processes.
🗞️ ZFP36L1 promotes non-small cell lung cancer progression under hypoxia by modulating CXCL9:SPP1 polarity: A single-cell transcriptomic study.
🗞️ Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning.
🗞️ ECM-Stiffness Mediated Persistent Fibroblast Activation Requires Integrin and Formin Dependent Chromatin Remodeling.
🗞️ Single-cell spatial atlas of the aging human breast.
🗞️ Kernel-DMD for multiome data integration and control.
🗞️ Complementary multi-omics profiling of chronic thromboembolic pulmonary hypertension reveals immune cell alterations, epigenetic changes, and genetically supported candidate genes.
🗞️ Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.
🗞️ scDenorm: a denormalisation tool for integrating single-cell transcriptomics data.
🗞️ Benchmarking single-cell tumor immune atlases and application for uncovering cell states related to immunotherapy response.
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Good morning ☕ Here are today's papers!
Preprints:👇
No preprints found today.
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🗞️ Single nucleus RNA sequencing and functional in vivo studies reveal TCF21 as a protective regulator in cardiac fibrosis.
🗞️ Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.
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Preprints:👇
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🗞️ Single nucleus RNA sequencing and functional in vivo studies reveal TCF21 as a protective regulator in cardiac fibrosis.
🗞️ 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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