CITE-seq

Mapping the Antibody Repertoires in Ferrets with Repeated Influenza A/H3 Infections: Is Original Antigenic Sin Really "Sinful"?

This study uses a new computational tool to analyze antibody repertoires in ferrets after repeated influenza infections, finding that broadly neutralizing antibodies can emerge despite original antigenic sin.

CRISPR-enhanced human adipocyte 'browning' as cell therapy for metabolic disease

This paper uses CRISPR to enhance browning of human adipocytes, improving metabolic health in mice without immunogenic Cas9 exposure.

Brain Antibody Sequence Evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning

BASE is a software tool for analyzing single-cell immunoglobulin cloning data, providing automated analysis with high accuracy and additional plasmid sequence confirmation.

Vaccination reshapes the virus-specific T cell repertoire in unexposed adults

This study examines how pre-existing T cell characteristics influence the immune response to a yellow fever vaccine, finding that memory T cells and rare populations shape post-vaccination responses.

Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC

The paper introduces PHAGE-ATAC, a method for simultaneous single-cell measurement of surface proteins, chromatin accessibility, and mtDNA-based clonal tracing, and demonstrates its application in human immune cells.

Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice

The paper uses single-cell RNA sequencing and C1 CAGE to identify distinct phases of pluripotency during the naive-to-primed transition in mice.

Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

This study shows that CISH knockout in TIL enhances neoantigen reactivity and synergizes with PD1 blockade to improve tumor regression.

SCIM: Universal Single-Cell Matching with Unpaired Feature Sets

SCIM matches single-cell measurements across technologies by learning a technology-invariant latent space and applying bipartite matching, achieving high accuracy in real-world datasets.

GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data

GLaMST reconstructs lineage trees from BCR sequencing data by interpolating unobserved sequences using a minimum spanning tree, outperforming existing methods in simulations with high mutation rates.

Dissecting the landscape of activated CMV-stimulated CD4+ T cells in human by linking single-cell RNA-seq with T-cell receptor sequencing

This study uses single-cell RNA-seq and TCR sequencing to analyze CMV-reactivated CD4+ T cell subsets, revealing their heterogeneity, functional roles, and interactions.

Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses.

The paper analyzes single-cell BCR and transcriptome data from influenza-infected mice to reveal organ-specific B cell dynamics and clonal responses.

T-bet fate mapping identifies a novel ILC1-ILC2 subset in vivo

The paper identifies a novel ILC1-ILC2 subset using T-bet fate mapping and shows its dependence on T-bet and cytokine expression capabilities.

Restricted differentiative capacity of Wt1-expressing peritoneal mesothelium in postnatal and adult mice.

This study shows that Wt1-expressing peritoneal mesothelial cells in postnatal and adult mice have limited differentiative capacity, only maintaining themselves and not contributing to other visceral tissues or blood vessels.

Extensive age-dependent loss of antibody diversity in naturally short-lived turquoise killifish

This study examines age-related loss of antibody diversity in turquoise killifish, showing rapid decline in whole-body and intestinal repertoires with age.

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in non-small cell lung cancer patients

The paper identifies two CD8+ TIL subpopulations in NSCLC, one circulating and one resident, which transition into terminally differentiated cells through a unique state.

Natural food intake patterns do not synchronize peripheral clocks

The paper shows that natural feeding patterns do not synchronize peripheral clocks, as clock phases are better predicted by rest-activity cycles than food schedules.

Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

SegRNA identifies unannotated transcripts by analyzing multi-experiment transcriptomic data without relying on pre-existing annotations.

Human thymopoiesis produces polyspecific CD8+ alfa/beta T cells responding to multiple viral antigens

The paper shows human thymopoiesis produces CD8+ T cells with polyspecific TCRs that recognize multiple viral antigens, supporting broad antiviral immunity.

Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data from CITE-seq

Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories

This study integrates multi-omic data from COVID-19 patients to identify immune response patterns linked to disease severity.

CITEseq analysis of non-small-cell lung cancer lesions reveals an axis of immune cell activation associated with tumor antigen load and TP53 mutations

The paper analyzes CITEseq data from NSCLC lesions to identify an immune cell activation module linked to tumor antigen load and TP53 mutations.

AncesTree: an interactive immunoglobulin lineage tree visualizer

AncesTree provides an interactive GUI for visualizing immunoglobulin lineage trees and mutations derived from Phylip analysis of antibody repertoires.

Loss of Circadian Protection in Adults Exposed to Hyperoxia as Neonates

This study shows neonatal hyperoxia disrupts circadian protection from Influenza A in adulthood through lung intrinsic clock mechanisms, not viral burden.

Programming Multifaceted Pulmonary T-Cell Immunity by Combination Adjuvants

This study defines how combination adjuvants induce multifaceted pulmonary T-cell immunity and enhance protection against influenza viruses.

Artificial-Cell-Type Aware Cell Type Classification in CITE-seq

CITE-sort improves cell type classification in CITE-seq by addressing artificial cell types caused by multiplets, achieving better clustering performance than existing methods.

Profiling the Intratumoral Immune Landscapes of Primary and Syngeneic Kras-driven Sarcoma Mouse Models

The paper compares immune profiles of primary and syngeneic Kras-driven sarcoma mouse models, finding significant differences in immune infiltration and T cell composition between them.

Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope

Private Antibody Repertoires Are Public

The paper demonstrates overwhelming functional overlap between antibody repertoires from 20 individuals, showing shared antigen-binding capacities that decline with age.

Evidence of Increased Hemangioblastic and Early Hematopoietic Potential in Chronic Myeloid Leukemia (CML)-derived Induced Pluripotent Stem Cells (iPSC)

This study shows that CML-derived iPSC have expanded hemangioblast and hematopoietic progenitor potential compared to H1-ESC, with AHR signaling as a potential therapeutic target.

Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors

The paper introduces ELATE, an autoencoder-based method to estimate local T cell repertoire density, enabling classification of samples and prediction of TCR-peptide binding.