Hannah V. Meyer

The paper introduces gcat and its_a_scam, modular tools for single cell genomic data processing and quality control, showing they produce results comparable to proprietary pipelines.

The paper identifies 17 human thymic epithelial cell subsets using single-cell data and shows they share a common ancestor and regulatory logic, with some conservation in mice.

The paper develops a framework to analyze long-term sequence dynamics from context-dependent mutation processes, applied to somatic hypermutation in antibodies, revealing mutational biases and their effects on sequence evolution.

plinkQC is an R package that performs ancestry inference, sample selection, and quality control in population genetics, achieving 98% accuracy with minimal marker overlap.

The paper shows that sparse, random sampling of self peptides in the thymus is sufficient for T cell tolerance to most peripheral self peptides, supported by experimental data and machine learning analysis.

This study compares human innate-like T cells (Tinn) with conventional T cells and mouse models, revealing distinct transcriptional programs and developmental pathways.

The paper introduces a database of TCR-peptide mutational assays and a Bayesian model to predict TCR cross-reactivity, showing improved performance over existing methods.

This paper introduces copepodTCR, a tool for designing and interpreting TCR specificity assays, which efficiently identifies antigen-specific TCRs using combinatorial peptide pooling and Bayesian modeling.

This study identifies Cystatin C as a glucocorticoid-responsive factor that recruits Trem2+ macrophages and predicts immunotherapy failure in cancer.

Snakeobjects extends Snakemake to simplify workflow development, improve readability, and maintain portability and scalability.

The paper identifies genetic associations with myocardial trabecular complexity using UK Biobank data and shows a causal link to ventricular function and electrical activity.

LiMMBo enables efficient joint genetic analysis of high-dimensional phenotypes using linear mixed models and bootstrapping, showing power advantages and scalability.