CITE-seq

DextraDemixer enables accurate identification of antigen-specific T cells from pMHC multimer experiments

DextraDemixer improves identification of antigen-specific T cells from pMHC multimer data by using a Bayesian model and dynamic thresholding to reduce false discoveries.

The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors

The paper introduces a data portal and open-source tools for single-cell transcriptomics of pediatric tumors, providing uniformly processed RNA-seq data and metadata from over 700 samples across 55 cancer types.

Antigen Stimulation Reactivates HIV-1 Proviruses Despite Integration in Repressive Chromatin

This study shows antigen stimulation can reactivate HIV-1 proviruses integrated in repressive chromatin, suggesting deeper latency may contribute to viral rebound.

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

HoloCell is a generative foundation model that integrates epigenomics, transcriptomics, and proteomics data across single-cell multi-omics modalities, demonstrating superior performance in representation learning and cross-modal generation.

A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

CRAFT, a transformer model, learns a generative grammar of healthy TCR repertoires to detect cancer-associated immune remodeling through structured deviations in sequence space.

Characterisation of Peripheral Blood B Cell Receptor Repertoire in Severe Eosinophilic Asthma and EGPA

This study characterizes B cell receptor repertoires in severe eosinophilic asthma and EGPA, finding increased IgG4 and other subclasses, shared clones, and treatment-related changes.

Sensory neurons encode long-term inflammatory memory that promotes gastric regeneration and tumorigenesis

This paper shows that sensory neurons form long-term inflammatory memory, enhancing gastric regeneration and tumor susceptibility after injury.

Maintenance of immune tolerance during aging requires competitive expansion of memory phenotype regulatory T cells

Reinforcement learning-driven unified generative framework for multi-objective RNA codon design

RNARL is a reinforcement learning framework for RNA codon design that generates high-performance sequences across multiple species and RNA types.

Aquaporin-4-Specific T Cell Responses in NMOSD Revealed by mRNA-Engineered Dendritic Cells

The paper uses mRNA-engineered dendritic cells to detect AQP4-specific T cell responses in NMOSD patients, showing strong activation in a patient with recent disease activity.

A Reproducible and Extensible Benchmark of Supervised Cell Type Annotation Tools for Cytometry Data

This paper benchmarks supervised cell type annotation tools for cytometry data using a reproducible framework, showing performance varies across datasets and populations, with rare populations being a challenge.

Directing fratricide within T cell products using an anti-uPAR chimeric antigen receptor to drive the production of potent therapeutic cells

This paper introduces a method to enhance T cell therapy by using a CAR targeting uPAR to eliminate dysfunctional T cells through directed fratricide.

Antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation bias

This study identifies antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination using single-cell RNA and TCR sequencing, revealing phenotypic differences between stimulated and unstimulated states.

Monju: Multi-criteria clustering in single-cell omics

Monju performs multi-criteria clustering on single-cell omics data by integrating multiple clustering solutions to assess cluster stability.

Jump-starting the T cell response in established tumors

This study shows that entinostat enhances CD8+ T cell responses in tumors but only when administered during a specific window after T cell activation, and this effect can be restored by prior oncolytic virus treatment.

Personalized multi-assay profiling of respiratory motile ciliopathies and mRNA therapy

This study develops a personalized multi-assay platform using nasal epithelial cells to assess ciliary function and therapeutic response in primary ciliary dyskinesia.

Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses

This study shows dendritic cells enhance CAR T cell persistence in irradiated tumors by antigen-dressing and stimulating CAR T cells through chimeric receptors.

AbSolution: interactive exploration of sequence-derived features in AIRR-seq repertoires

AbSolution enables integrated analysis of sequence-derived features in immune repertoires across datasets and conditions.

scDIG: An R Shiny Application for Interactive Density-Based Gating of Single-Cell Proteomic and Transcriptomic Data

scDIG is an R Shiny tool for interactive density-based gating of single-cell proteomic and transcriptomic data, resolving CD4+ T cell subpopulations in CITE-seq data.

Age-dependent PD-1 induction restricts IL-2-driven effector T cell responses during La Crosse virus infection in mice

This study shows that age-dependent PD-1 induction limits IL-2-driven effector T cell responses during La Crosse virus infection in mice, leading to impaired viral control.

Reprogramming tumour-associated macrophages from immune suppressive to inflammatory state by Checkpoint kinase 1 inhibitor combination treatment

This study shows that CHK1i+LDHU reprograms tumour-associated macrophages to an inflammatory state while preserving immunosuppressive features, enhancing CD8 T cell activation and therapeutic efficacy.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

Activation-dependent lentiviruses enable antigen-specific T cell expansion and transduction

This paper develops 4-1BB-targeting lentiviral vectors to selectively expand and transduce antigen-specific T cells, enhancing their function in cancer immunotherapy.

SRSA-VAE: Self-Attention-Based Feature Learning for Single-Cell Multimodal Clustering

SRSA-VAE improves single-cell clustering by using self-attention and residual connections, outperforming existing methods on scRNA-seq and CITE-seq data.

Dynamic dorsal body morphology encodes engineering design principles of fish propulsion and hydrodynamics

The paper introduces a data-driven framework to connect fish body shape dynamics to hydrodynamic performance using CFD simulations and reduced-order modeling.

Cell Type Weighted Dimensionality Reduction

This paper introduces CWDR, a dimensionality reduction method that improves visualization of cell types by incorporating lineage information, reducing overlap between clusters in high-dimensional data.

CD4+ T cells promote fibrosis during metabolic dysfunction-associated steatohepatitis

This study identifies CD4+ T cells as drivers of fibrosis in MASH by showing their proinflammatory activity and the therapeutic potential of targeting the OX40L-OX40 axis.

Allogeneic CRISPR-Engineered CAR-T Cells Drive Potent Antitumor Activity in Solid Tumors

This study develops allogeneic CRISPR-engineered CAR-T cells targeting GPC2 and GPC3, showing potent antitumor activity in solid tumors with repeated dosing and no toxicity.

Extracellular Vesicles Enable CircRNA Delivery via in situ Biogenesis and Sorting

This paper develops an EV-based platform for efficient circRNA delivery, enabling sustained protein expression and therapeutic applications in dendritic cell targeting and myocardial fibrosis.

Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES

CANDIES denoises and integrates spatial multi-omics data using a conditional diffusion model and contrastive learning, improving downstream analysis tasks.