As an important aside for any differential co-expression analysis: while we often hope that the latent factor driving differential co-expression is biological, it is very difficult to rule out a latent technical factor.
New publication from @epsteinstatgen.bsky.social's crew describing LIT; a kernel method to map genetic variants with interaction effects on multiple phenotypes in biobanks - in Genome Medicine genomemedicine.biomedcentral.com/articles/10....
Differential co-expression arises from shared unmodeled biological variation involving an observed risk factor and an unobserved (or latent) factor. We developed a method to detect such variation in a pathway for general gene expression studies!
from shared unmodeled biological variation involving an observed risk factor and a latent factor. Our approach, KDCA, uses a flexible kernel-based framework to detect complex differential co-expression patterns while handling continuous or categorical risk factors and batch effects!
New work with @chr1sw.bsky.social on increasing GWAS power by leveraging summary statistics of related traits! Package available at github.com/ajbass/sffdr.
Software: github.com/ajbass/sffdr
We have software you can use on GitHub: github.com/ajbass/kdca. Work with @epsteinstatgen.bsky.social and @davecutler.bsky.social.
A preprint of my first post-doc paper w/ Shijia Bian, Aliza Wingo, Thomas Wingo, David Cutler and @epsteinstatgen.bsky.social is out!
www.biorxiv.org/content/10.1...
Excited to see our (w/ @chr1sw.bsky.social) work published in @natcomputsci.nature.com! We developed a new framework, surrogate functional false discovery rate (sffdr), that integrates summary statistics of related traits to improve power in GWASs.
Paper: www.nature.com/articles/s43...
Happy to see this out w/ @epsteinstatgen.bsky.social and @davecutler.bsky.social (paper: doi.org/10.1093/bioi...)! We tackled the problem of identifying dysregulated pathways (i.e. differentially co-expressed) in gene expression studies. We show that differential co-expression arises ...