Hannah V. Meyer

gcat, its_a_scam: modular tools for single cell data processing and per-cellquality control

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.

Gene regulatory logic underlying the differentiation of mixed lineages in human thymic epithelial cells

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.

Dynamical consequences of context-dependent mutation: visualizing antibody sequence evolution during somatic hypermutation

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: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics

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

Sparse, random sampling is sufficient for central tolerance

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.

Cystatin C is glucocorticoid-responsive, directs recruitment of Trem2+ macrophages and predicts failure of cancer immunotherapy

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

Snakeobjects: an object-oriented workflow management system

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

Genomic analysis reveals a functional role for myocardial trabeculae in adults

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: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

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