T-cell and B-cell Immunology

The paper shows that differences in co-stimulatory molecule avidity lead to distinct T cell fates through variations in downstream signaling and gene expression.

This study analyzes the TCRB repertoire in human cord blood from 24-38 weeks gestation, finding fetal TCRB repertoires have lower diversity and shorter CDR3s compared to adults, with CDR3 length increasing with gestational age.

The paper introduces immuneREF, a method to quantify immune repertoire similarity across health and disease, finding that healthy and diseased repertoires are more similar than previously thought.

This study identifies an allosteric mechanism where TCR-pMHC binding induces CD3 dynamics through conformational changes, with the TCRβ FG loop acting as a gatekeeper and the connecting peptide as a hinge.

The paper identifies miR-155 as a posttranscriptional regulator of Aire and TRA genes in mTECs, affecting chemotaxis.

The paper quantifies the publicness or privateness of T and B cell clones using information-theoretic metrics applied to synthetic and empirical TCR data.

This study characterizes the reprogramming of mouse fibroblasts into thymic epithelial cells (TECs) by analyzing gene expression changes and identifying factors that enhance the process.

This study uses CITE-seq to analyze thymocyte development and identifies TCR signaling waves and the TCR/calcineurin/NFAT/GATA3 axis as drivers of CD4/CD8 lineage commitment.

The paper identifies gene regulatory networks in human GM-CSF-secreting CD4 T cells using ATAC-seq and RNA-seq data, linking them to autoimmune disease.

This paper systematically evaluates IL-2-Fc fusions to enhance Treg selectivity by exploring valency, orientation, and binding kinetics, identifying multivalency and asymmetry as key factors for improved specificity.

The paper introduces Compass, an algorithm that uses single-cell RNA-Seq and flux balance analysis to characterize metabolic states in Th17 cells, revealing a metabolic switch and novel anti-inflammatory regulators.

The paper introduces an efficient algorithm for clustering T cell receptor sequences, outperforming GLIPH in speed and accuracy on real datasets.

This study shows that low self-reactive thymocytes have shorter TCR signals, delayed positive selection, and retain preselection gene expression signatures, suggesting ion channels modulate TCR sensitivity during development.

The paper defines a shared differentiation trajectory of CD8 T cell dysfunction across cancer and infection using ATAC-seq and RNA-seq data from multiple studies.

The paper introduces a clustering-based method to identify condition-associated TCR CDR3 sequences by comparing immune repertoires across populations.

This study shows that DIDO3 deficiency disrupts B cell differentiation by altering transcription factor expression and somatic recombination.

The paper develops an agent-based model to evaluate CTL killing mechanisms using 2-photon imaging data, finding that increased contact frequency with infected cells raises killing probability, independent of signal integration.

The paper analyzes IGHJ gene usage in BCR repertoires and finds that recombination signal sequences influence their frequencies across physiological and pathological conditions.

This study uses an agent-based model to show that TCR affinity modulation during immunological synapse formation depends on ligand density and F-actin dynamics, with centripetal transport and feedback mechanisms playing key roles.

This study identifies KIAA1841 as a negative regulator of class switch recombination in B cells through a shRNA screen in mouse B cell lines.

This study examines how different computational methods affect the analysis of B cell evolution in murine antibody repertoire sequencing data post-viral infection.

The paper analyzes structural and sequencing data to show minimal constraints on TCRβ chain pairing, allowing maximal diversity in the naive T-cell repertoire.

STIG generates synthetic T cell receptor sequencing data for evaluating repertoire inference tools using customizable virtual repertoires and simulated sequencing.

The paper uses network modeling to identify molecular mechanisms driving T cell exhaustion and validates predictions through experimental testing.

This study shows Notch1 signaling is essential for specifying and expanding the medullary thymic epithelial cell (mTEC) progenitor pool during mouse fetal development.

The paper introduces a method to infer individual immunoglobulin germline genes from B cell receptor sequences, improving accuracy over existing methods.

The paper shows that locus suicide recombination (LSR) occurs in human B-cells during activation, targeting the IgH locus and leading to cell death.

Genomic profiling of CD4 T cell activation reveals a sensitivity switch from TCR in naive to CD28 in memory cells.

The paper extends a Boolean network model of CD4+ T cell differentiation to a continuous model to assess how cytokine concentrations and combinations influence differentiation and plasticity.