PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.

Motivation: Simulation is a critical part of method development and assessment. With the increasing sophistication of multi-trait and multi-locus genetic analysis techniques, it is important that the community has flexible simulation tools to challenge and explore the properties of these methods.

Results: We have developed PhenotypeSimulator, a comprehensive phenotype simulation scheme that can model multiple traits with multiple underlying genetic loci as well as complex covariate and observational noise structure.

Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells.

Promiscuous expression of a plethora of tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs) is essential for central tolerance. This promiscuous gene expression (pGE) is characterized by inclusion of a broad range of TRAs and by its mosaic expression patterns, i.e.