Matthew Stephens

Disease-associated loci share properties with response eQTLs under common environmental exposures.

Many disease-associated genetic variants likely exert context-dependent regulatory effects that are underrepresented in healthy, steady-state adult tissues. To investigate gene regulation across diverse environmental and cellular contexts, we exposed heterogeneous differentiating cultures from 51 human induced pluripot...

A Gene-Program Architecture of Mouse T cells

We present a gene-program framework for resolving mouse T cell heterogeneity across the immgenT atlas. On ∼800,000 T cells spanning lineages, organs, and immune challenges, we defined 200 reproducible gene programs, discovered by empirical Bayes matrix factorization approach and validated through a new deep learning ap...

Genetic factor analysis for characterizing phenome-wide patterns of genetic pleiotropy.