CITE-seq

UMINT: Unsupervised Neural Network For Single Cell Multi-Omics Integration

UMINT is a novel unsupervised neural network for integrating single-cell multi-omics data, achieving better performance than existing methods on CITE-seq datasets.

Noncanonical TRAIL Signaling Promotes Myeloid-Derived Suppressor Cell Abundance and Tumor Progression in Cholangiocarcinoma

This study shows that TRAIL+ cancer cells use noncanonical TRAIL signaling in MDSCs to promote their abundance and tumor progression in cholangiocarcinoma.

Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet

The paper introduces CrossmodalNet, an interpretable model that predicts surface protein expression from scRNA-seq data and incorporates temporal information to uncover gene-protein relationships.

Apposed networks of interacting TCRs and BCRs exhibiting mosaicked CDR3 sequences made of fixed junctional motifs

The paper identifies two networks of TCRβ and IGH clonotypes with conserved CDR3 sequences associated with over 63 diseases, suggesting evolutionary-conserved primordial antigen receptors.

Quantitative Annotations of T-Cell Repertoire Specificity

This paper introduces TCRanno, a tool to quantify TCR repertoire specificity, revealing insights into infections, autoimmunity, and cancer through analysis of 4,195 repertoires.

Integrated Spatial Transcriptomic and Proteomic Analysis of Fresh Frozen Tissue Based on Stereo-seq

Stereo-CITE-seq combines CITE-seq with Stereo-seq to simultaneously profile whole transcriptomes and protein markers on the same fresh-frozen tissue section.

Sex biased human thymic architecture guides T cell development through spatially defined niches

The paper maps sex differences in thymic niches using spatial multi-omics to reveal how sex influences T cell development and immune function.

Peripersonal encoding of forelimb proprioception in the mouse somatosensory cortex

This study identifies the rodent proprioceptive cortex using calcium imaging and optogenetics, showing that limb movements are encoded as spatial direction vectors in somatosensory and motor areas.

Interspecies generation of functional muscle stem cells

This study generates functional muscle stem cells across species by injecting corrected iPSCs into blastocysts, restoring dystrophin expression in DMD mice.

Non-equilibrium antigen recognition in acute infections

This paper models B-cell antigen recognition during acute infections, showing it follows a generalized Luria-Delbruck process with power-law statistics and highlights the impact of aging on immune response.

Host-cell Interactions of Engineered T cell Micropharmacies

This study demonstrates that SEAKER cells, engineered T cells with prodrug-activating functions, effectively target solid tumors in immunocompetent hosts despite immune responses.

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

This paper benchmarks 21 dimension reduction methods on CyTOF data, finding SAUCIE, SQuaD-MDS, and scvis as top performers with different strengths.

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.

ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intra-clonal diversities: application to human B-cell tumors

Memory Th1 cells modulate heterologous diseases through innate function

This study identifies memory Th1 cells that can respond rapidly to unrelated pathogens or diseases through TCR-independent IFN-γ production, influencing susceptibility to heterologous challenges.

Embryonic type 3 innate lymphoid cells sense maternal dietary cholesterol to control local Peyer's patch development

The paper identifies how maternal dietary cholesterol influences Peyer's patch development through LTi cell GPR183 sensing of 7,25-HC.

Titering of Chimeric Antigen Receptors on CAR T Cells enabled by a Microfluidic-based Dosage-Controlled Intracellular mRNA Delivery Platform

This paper introduces a microfluidic platform for controlled delivery of CAR gene mRNA to T cells, enabling titering of CAR expression on their surface.

InClust+: the multimodal version of inClust for multimodal data integration, imputation, and cross modal generation

InClust+ extends the inClust framework to handle multimodal data integration, imputation, and cross-modal generation, showing performance comparable to existing tools.

A subset of CD4+ effector memory T cells limit immunity to pulmonary viral infection and prevent tissue pathology via activation of latent TGFβ

The paper identifies a subset of CD4+ effector memory T cells that limit secondary immune responses to viral re-infection and prevent lung pathology by activating latent TGFβ.

Fixation Before Dissociation Using a Deep Eutectic Solvent Preserves In Vivo States and Phospho-Signaling in Single-Cell Sequencing

This study introduces a deep eutectic solvent fixation method that preserves in vivo cellular states and phospho-signaling for scRNA-seq, enabling the identification of hyperactivated Th17 T cells.

A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding Using Lossless String Compression

The paper introduces a lossless string compression method based on LZ-76 to encode T-cell receptor beta chain repertoires, enabling applications like diversity estimation and sequence generation.

The memory of pathogenic IgE is contained within CD23+IgG1+ memory B cells poised to switch to IgE in food allergy

The paper identifies CD23+IgG1+ memory B cells in peanut allergy that can switch to IgE and contain high affinity allergen-specific clones.

Increased TCR signaling in regulatory T cells is disengaged from TCR affinity

The paper compares TCR repertoires of regulatory and effector T cells in non-obese diabetic mice, showing similar reactivity but differing suppressive capacity linked to TCR affinity.

Defining T cell receptor repertoires using nanovial-based affinity and functional screening

This study uses nanovials to screen antigen-specific T cells based on affinity and function, identifying a more specific functional TCR repertoire than standard techniques.

Robust Single-cell Matching and Multi-modalAnalysis Using Shared and Distinct FeaturesReveals Orchestrated Immune Responses

The paper introduces MARIO, a cell matching algorithm that integrates single-cell proteomic and multi-modal data, revealing orchestrated immune responses in lung tissue.

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

The paper introduces a new V allele naming scheme and genotype inference method for adaptive immune receptor sequencing, validated with genomic long read data and implemented in an R package.

Combining mutation and recombination statistics to infer clonal families in antibody repertoires

The paper introduces HILARy, a method to identify clonal families in antibody repertoires by combining mutation and recombination statistics, finding evolutionary properties are independent of junction length and revealing broad selection pressures.

Rapid recall and de novo T cell responses during SARS-CoV-2 breakthrough infection

This study examines T cell responses during SARS-CoV-2 breakthrough infections, showing rapid recall of memory T cells and a correlation between CD8+ T cell activation and viral clearance.

HBM-CITEseq: a uniform CITE-seq processing pipeline for the HuBMAP Consortium

The paper introduces HBM-CITEseq, a CITE-seq processing pipeline for the HuBMAP Consortium that aligns with existing RNA-seq pipelines and is available on GitHub.

High-dimensional single-cell definition of CLL T cells identifies Galectin-9 as novel immunotherapy target

The paper defines CLL T cell subtypes and identifies Galectin-9 as a novel immunotherapy target through single-cell and multi-omics analyses.