CITE-seq

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro

The paper identifies and removes background noise in CITE-seq data using DecontPro, a Bayesian model that improves clustering specificity and reduces contamination from spongelets and ambient ADTs.

Quantifiable TCR repertoire changes in pre-diagnostic blood specimens among high-grade ovarian cancer patients

The paper analyzes TCR repertoires in blood samples of ovarian cancer patients and controls to identify early detectable immune signatures for high-grade ovarian cancer.

Thymically imprinted differential responsivity of naive CD4 T cells to IL2 results in a heterogeneity of both Treg induction and subsequent effector functioning

This study shows that thymic imprinting causes naive CD4 T cells to have different cytokine responses, leading to varied Treg induction and effector function.

Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors

The paper identifies a potent effector state among exhausted CD8 T cells in tumors using multimodal CITE-Seq, showing enhanced cytokine production and tumor-killing ability.

CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

The paper uses CITE-seq to analyze B cells from vitamin D-treated MS patients, identifying NF-kB pathway inhibition as a potential mechanism for vitamin D's protective effects.

Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status

The paper develops AIRRTM, a generative model that identifies and generates disease-associated adaptive immune receptor sequences using only repertoire-level immune status data.

RORγt+ B cells express proinflammatory cytokines and promote allo- and auto- immunity

The paper identifies TIM-4+ B cells that express proinflammatory cytokines like IL-17A and promote auto- and allo-immunity by preventing their conversion into regulatory B cells.

KSHV 3.0: A State-of-the-Art Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing

This study enhances the annotation of the KSHV transcriptome using long-read and short-read sequencing, identifying novel transcripts and improving existing annotations.

Multiomic single-cell analysis identifies von Willebrand factor and TIM3-expressing BCR-ABL1+ CML stem cells

This study identifies VWF and TIM3-expressing BCR-ABL1+ CML stem cells using multiomic single-cell analysis, suggesting they are targets for sustained LSC elimination.

RapTCR: Rapid exploration and visualization of T-cell receptor repertoires

RapTCR provides a tool for rapid visualization and analysis of T-cell receptor repertoires, capturing both global and local sequence similarities.

Differentiation and Expansion of Tumor-Infiltrating T Cell Clonotypes Occurs in the Spleen Following Immune Checkpoint Blockade

This study identifies spleen-resident intermediate-exhausted T cells as key to ICB efficacy, showing their expansion and differentiation into tumor-infiltrating clonotypes.

ShIVA, a user-friendly and interactive interface giving biologists control over their single-cell RNA-seq data.

ShIVA provides a user-friendly interface for biologists to analyze single-cell RNA-seq and CITE-seq data using Seurat v4, enabling reproducible analysis and visualization.

Glioblastoma-infiltrating CD8+ T cells are predominantly a clonally expanded GZMK+ effector population

The paper analyzes TILs in GBM using CITE-seq and scRNA-seq to show that CD8+ T cells are predominantly clonally expanded GZMK+ effector cells, lacking canonical exhaustion.

Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

The paper provides a Bioconductor package with curated landmark datasets for single-cell multimodal data, enabling easy access and analysis of seven different technologies.

ediTONSIL: Activation-Neutral Gene Editing of CD4 T cells in Human ex Vivo Tonsil Cultures

The paper introduces ediTONSIL, a method to edit resting CD4 T cells from human tonsil tissue without activation, achieving >90% knockout efficacy and preserving cell function.

STREAK: A Supervised Cell Surface Receptor Abundance Estimation Strategy for Single Cell RNA-Sequencing Data using Feature Selection and Thresholded Gene Set Scoring

STREAK improves receptor abundance estimation in scRNA-seq by using supervised learning and gene set scoring, outperforming existing methods on human tissue datasets.

Single cell multi-omics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response

This paper uses single-cell multi-omics to analyze CML patient data, showing that cellular heterogeneity correlates with therapy response and identifies markers for LSCs and HSCs.

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

CellBender removes systematic background noise from droplet-based single-cell data using a deep generative model, improving alignment with established gene expression patterns.

Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures

This study introduces moETM, a deep learning method for analyzing single-cell multi-omic data, and shows it identifies immune signatures and COVID-19 severity biomarkers.

Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

The paper analyzes human TCR repertoires across thymic development stages and individuals, finding that inter-individual variability persists through maturation and that local sequence similarity correlates with cell type information.

TriTan: An efficient triple non-negative matrix factorisation method for integrative analysis of single-cell multiomics data

TriTan is a triple non-negative matrix factorisation method for single-cell multiomics data integration, offering efficient computation and improved interpretability.

Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software

The paper provides a framework and interactive software tools for manually annotating cell types in single-cell multi-omics datasets, demonstrating how different modalities can be combined to improve annotation accuracy.

Single-cell T cell receptor sequencing of paired tissue and blood samples reveals clonal expansion of CD8+ effector T cells in patients with calcific aortic valve disease

The paper uses single-cell T cell receptor sequencing to analyze paired tissue and blood samples from CAVD patients, identifying clonal expansion of CD8+ effector T cells and potential epitope targets in the valve.

A Combined Immunophenotypic And Transcriptional Single-Cell Map Of First Trimester Human Fetal Liver Hematopoiesis

The paper presents a single-cell map of first trimester human fetal liver hematopoiesis, identifying molecular and immunophenotypic differences from adult cells and linking findings to pediatric leukemia.

Anti-CD117 CAR T cells incorporating a safety switch eradicate human acute myeloid leukemia and hematopoietic stem cells

This study develops anti-CD117 CAR T cells with a safety switch to target and eliminate acute myeloid leukemia and hematopoietic stem cells in preclinical models.

AIRRSHIP: simulating human B cell receptor repertoire sequences

AIRRSHIP generates synthetic human B cell receptor sequences to evaluate repertoire analysis tools and understand sources of inaccuracy.

Ensemble deep learning of embeddings for clustering multimodal single-cell omics data

SnapCCESS improves clustering of multimodal single-cell omics data by integrating multiple data modalities using an ensemble deep learning framework.

COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells

The paper develops a database linking cell surface proteins and transcription factors in immune cells using CITE-seq data from COVID-19 patients and healthy controls.

Leveraging T-cell receptor - epitope recognition models to disentangle unique and cross-reactive T-cell response to SARS-CoV-2 during COVID-19 progression/resolution

The paper uses TCR-epitope recognition models to analyze CD8+ T-cell responses in COVID-19 patients, finding that non-critical patients develop unique SARS-CoV-2-specific T-cell responses not seen in critical patients.

Stem cell memory EBV-specific T cells control post-transplant lymphoproliferative disease and persist in vivo

This study develops a protocol to expand EBV-specific stem cell memory T cells, showing improved tumor control and persistence in a PTLD model compared to existing ACT methods.