A. Yermanos

A novel bioinformatics pipeline for the identification of immune inhibitory receptors as potential therapeutic targets

The paper introduces a bioinformatics pipeline to identify known and putative immune inhibitory receptors as therapeutic targets using machine learning and transcriptomics data.

Asymmetric cell division safeguards memory CD8 T cell development

This study shows that asymmetric cell division supports memory CD8 T cell development under strong TCR stimulation but not weak stimulation.

ePlatypus: an ecosystem for computational analysis of immunogenomics data

ePlatypus provides a computational ecosystem for immunogenomics data analysis, integrating diverse modalities and tools to study adaptive immunity and computational immunology.

Persistent virus-specific and clonally expanded antibody secreting cells respond to induced self antigen in the CNS

The paper identifies virus-specific, clonally expanded antibody-secreting cells in the CNS that persist and respond to induced self-antigen, with parallels in multiple sclerosis patients.

Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity

The paper profiles clonal selection of B and T cells in murine models of infection and autoimmunity using single-cell sequencing, linking repertoire features to cell phenotypes.

Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen-specificity

The paper generates a single-cell B cell atlas to link antibody repertoires, transcriptomes, and antigen specificity in murine immunization models.

Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes

Echidna simulates single-cell immune receptor repertoires and transcriptomes, enabling benchmarking of clonotyping and phylogenetic analysis tools.

Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells

This study investigates whether clonal expansion of plasma cells is deterministic or stochastic by analyzing antigen-specificity, affinity, and epitope convergence in antibody repertoires.

Clonally expanded virus-specific CD8 T cells acquire diverse transcriptional phenotypes during acute, chronic, and latent infections

This study examines clonal expansion and transcriptional diversity in virus-specific CD8 T cells across different infection stages using single-cell sequencing and a new bioinformatic tool.

A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients

This study uses single-cell sequencing to analyze immune repertoires and transcriptomes in convalescent COVID-19 patients, revealing age-related differences in T and B cell responses.

Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2

Single-cell sequencing and screening identify expanded plasma cell clones in COVID-19 patients producing SARS-CoV-2-specific neutralizing antibodies.

Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes

Platypus integrates single-cell immune repertoires with transcriptomes to analyze lymphocyte features and transcriptional profiles in convalescent COVID-19 patients.

Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice

This study uses single-cell sequencing to show that aged mouse brains have clonally expanded and transcriptionally distinct lymphocytes, potentially contributing to neuroinflammation.

Profiling virus-specific Tcf1+ T cell repertoires during acute and chronic viral infection

The paper analyzes Tcf1+ and Tcf1- T cell repertoires during acute and chronic LCMV infection, finding they are not clonally distinct and show minor differences in repertoire parameters.

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

This study compares IgM antibody repertoires in blood and bone marrow plasma cells of mice after viral infection, finding that they are mouse-specific but not infection-specific.