CITE-seq

Probabilistic modeling of ambient noise in single-cell omics data

The paper develops scAR, a machine learning model to remove ambient noise from single-cell omics data across multiple technologies, showing high denoising accuracy.

Systematic analysis of human antibody response to ebolavirus glycoprotein reveals high prevalence of neutralizing public clonotypes

The paper analyzes the human antibody response to ebolavirus glycoprotein, identifying public clonotypes with neutralizing activity and implications for vaccine design.

Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence

This study identifies Sema4A as a critical niche factor required for myeloid-biased HSC self-renewal and long-term persistence under stress.

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

The paper develops a statistical model to predict B- and T-cell receptor repertoire overlap in healthy and SARS-CoV-2 infected individuals, identifying COVID-associated receptors and designing a diagnostic tool.

Divergent clonal differentiation trajectories of T cell exhaustion

This study identifies divergent clonal differentiation trajectories of T cell exhaustion during chronic viral infection, showing that TCR signal strength determines terminal or KLR Tex fates.

A third vaccination with a single T cell epitope protects against SARS-CoV-2 infection in the absence of neutralizing antibodies

A third dose of a single T cell epitope vaccine protects mice from SARS-CoV-2 infection without neutralizing antibodies by enhancing effector-memory and tissue-resident memory T cells.

DALI (Diversity AnaLysis Interface): a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling.

DALI is a software tool that integrates multimodal single-cell RNA-seq and immune receptor data to analyze T and B cell diversity, supporting both bioinformaticians and immunologists.

Combinatorial T cell engineering eliminates on-target off-tumor toxicity of CD229 CAR T cells while maintaining anti-tumor activity.

The paper engineers low-affinity CD229 CAR T cells with CJUN overexpression to reduce on-target off-tumor toxicity while preserving anti-tumor activity.

Low-affinity CAR T cells exhibit reduced trogocytosis, preventing fratricide and antigen-negative tumor escape while preserving anti-tumor activity

T cell receptor repertoire signatures associated with COVID-19 severity

The paper analyzes T cell receptor repertoires from COVID-19 patients and healthy donors to identify signatures associated with disease severity and develops machine learning models to predict severity based on TCR features.

Seven chain adaptive immune receptor repertoire analysis in rheumatoid arthritis: association to disease and clinically relevant phenotypes

This study analyzes the seven-chain adaptive immune receptor repertoire in rheumatoid arthritis, identifying disease associations and treatment response markers through immunosequencing and HLA integration.

Plasmodium-encoded murine IL-6 impairs liver stage infection and elicits long-lasting sterilizing immunity

This study shows that Plasmodium parasites engineered to express murine IL-6 fail to progress to blood stage infection and induce long-lasting CD8+ T cell-mediated immunity.

Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection

The paper identifies Ly6A+CCR9+CD4+ T cells in the intestinal epithelium that protect against enteric viral infections through IFN-gamma-dependent mechanisms.

Phospho-RNA sequencing with CircAID-p-seq

The paper introduces circAID-p-seq, a PCR-free method for phospho-RNA sequencing, and demonstrates its application in ribosome profiling to study RNA-protein interactions.

DeepMAPS: Single-cell biological network inference using heterogeneous graph transformer

DeepMAPS infers biological networks from single-cell multi-omics data using a heterogeneous graph transformer, outperforming existing tools in cell clustering and pathway prediction.

New interpretable machine learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy

FAUST is a new interpretable machine learning method for single-cell cytometry that discovers and validates T cell correlates of response to anti-PD-1 immunotherapy.

Antigen experience relaxes the organisational structure of the T cell receptor repertoire

The paper examines how antigen exposure affects the structural organization of T cell receptor repertoires in mice across different life stages and infection states.

A Systematic Comparison of Differential Analysis Methods for CyTOF Data

The paper compares differential expression analysis methods for CyTOF data, finding that median-based methods are reliable for non-zero-inflated data while methods using full distributions handle zero-inflation better but may overpredict.

SunCatcher: Clonal Barcoding with qPCR-Based Detection Enables Functional Analysis of Live Cells and Generation of Custom Combinations of Cells for Research and Discovery

Probiotic-guided CAR-T cells for universal solid tumor targeting

This paper develops probiotic-guided CAR-T cells (ProCARs) that use synthetic antigens produced by tumor-colonizing bacteria to enhance T cell activation and tumor lysis in xenograft models.

Efficient and precise single-cell reference atlas mapping with Symphony

Symphony maps query cells to large reference atlases efficiently, enabling rapid identification of cell states and phenotypes across diverse datasets.

Simultaneous single cell measurements of intranuclear proteins and gene expression

The paper introduces inCITE-seq, a method for simultaneous measurement of intranuclear proteins and gene expression in single cells, and demonstrates its application in analyzing neuronal activity in mouse brain tissue.

CAR T cell therapy drives endogenous locoregional T cell dynamics in a responding patient with glioblastoma

This study tracks T cell dynamics in a glioblastoma patient undergoing CAR T cell therapy, showing endogenous T cells are activated and contribute to treatment response.

Spike independent infection of human coronavirus 229E in bat cells

This study shows that human coronavirus 229E can infect bat cells without using its spike protein, revealing a spike-independent infection mechanism in bats.

Monocyte-derived transcriptome signature indicates antibody-dependent cellular 1 phagocytosis as the primary mechanism of vaccine-induced protection against HIV-1

The paper identifies a monocyte-derived transcriptome signature linked to antibody-dependent cellular phagocytosis as a correlate of vaccine-induced protection against HIV-1 in clinical trials.

Naive and in vitro-activated primary mouse CD8+ T cells retain in vivo immune responsiveness after electroporation-based CRISPR/Cas9 genetic engineering

This study shows that nucleofection-based CRISPR/Cas9 editing preserves in vivo immune function of naive CD8+ T cells but slightly impairs in vitro-activated cells, with varying gene product decay rates.

SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

SPaRTAN links cell-surface receptors to transcription factors using CITE-seq data and cis-regulatory information, revealing novel receptor-TF relationships in immune and tumor cells.

Clustering single cell CITE-seq data with a canonical correlation based deep learning method

This paper introduces scCTClust, a deep learning method for clustering CITE-seq data that integrates RNA and protein information, achieving better clustering results than existing methods.

Microenvironmental correlates of immune checkpoint inhibitor response in human melanoma brain metastases revealed by T cell receptor and single-cell RNA sequencing

Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and subsequent weight regain.

This study uses multi-omics to show that obesity-related immune cell changes in adipose tissue persist during weight loss and weight regain in mice.