T-cell and B-cell Immunology

Rapid T cell receptor interaction grouping with ting

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

T cell self-reactivity during thymic development dictates the timing of positive selection

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.

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

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.

Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences

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

The chromatin reader Dido3 is a regulator of the gene network that controls B cell differentiation

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

Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments

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 usage of human IGHJ genes follows a particular nonrandom selection: The recombination signal sequence affects the usage of human IGHJ genes

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

Agent-Based Modeling of T Cell Receptor Cooperativity

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.

KIAA1841, a novel SANT and BTB domain-containing protein, inhibits class switch recombination

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

The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection

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

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex

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: Generation and simulated sequencing of synthetic T cell receptor repertoires

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

Integrative network modeling reveals mechanisms underlying T cell exhaustion

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

NOTCH1 signaling establishes the medullary thymic epithelial cell progenitor pool during mouse fetal development

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

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data

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

Locus Suicide Recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues

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 T cell activation reveals dependency of memory T cells on CD28 costimulation

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

A quantitative network modeling approach to evaluate the role of cytokine combinations on CD4+ T cell differentiation, partial polarization, and plasticity

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.

Detecting T cell receptor rearrangements in silico from non-targeted DNA-sequencing (WGS/WES)

The paper develops a method to estimate T cell abundance and identify TCR rearrangements from non-targeted DNA sequencing data without prior amplification.

A systems approach to the characterization and classification of T-cell responses

The paper develops a systems-based approach to classify T-cell responses using transcriptome data from PBMCs stimulated with peptides, identifying new molecular patterns and transcription factors involved in antigen-specific responses.