Matthew Stephens

Glad to see our paper, with @xinhe2 @mstephens999 @wescrouse Sheng and Kevin, is out today at @NatureGenet! nature.com/articles/s4158…. We developed a new statistical method, causal-TWAS or cTWAS, to reliably identify causal genes in genome-wide association studies (GWAS). 1/n

The Department of Human Genetics at University of Chicago is searching for a faculty candidate in Computational genetic and genomics. Please share this job ad with your colleagues: apply.interfolio.com/127605

@wolfgangkhuber Related to this (but different), when you have multiple y variables which should you condition on and which should you treat as outcomes? Different choices corresponds to different models journals.plos.org/plosone/articl…

@aaronquinlan Brings back fond memories of Debbie Nickerson who drove so much development of polyphred before i ever got involved.

@aaronquinlan Im glad at least one person saw it!

As a grad student, my first rotation project was to simulate nematode RIL genomes at a few hundred markers that Stephen Wicks's lab studied. To this day, I find it amazing that simple code can quickly scan entire genomes of pedigrees to find variants that segregate with a trait.

My PhD work "On the Genes, Genealogies, and Geographies of Quebec" is now published in SCIENCE!!🧑‍🔬 🌎We explore the emergence of genetic variation in Quebec's settler population with a detailed model using a genealogy of 5M records. 🔗science.org/doi/10.1126/sc… 🧵for details : 1/7

@molly_przew Thank you so much Molly. I feel so lucky to have had such great mentors, colleagues, and collaborators

recent work from my lab on applying and interpreting topic models for single cell data: biorxiv.org/content/10.110…

PLZ RT: I’m happy to present @nmancuso_ Lab’s new software SuShiE (Sum of Single Shared Effects) that performs variational SNP fine-mapping on multi-ancestry molecular QTL data. Stay tuned for the future manuscript! (1/8) github.com/mancusolab/sus…

@Sun_Y_Lee yes, should work, although i have to admit I have not used the package myself, so questions on that probably best directed to siming or wes...

@mstephens999 Can you additionally include protein expression in this approach? Currently in the package

I missed tweeting this when posted in Dec. Our attempt to ameliorate some problems with confounding in TWAS. Key idea is to compete (imputed) gene expression and SNPs against one another as explanations for an asssocation. biorxiv.org/content/10.110…

Pleased to share our latest preprint. We extended the SuSiE model originally developed by the @mstephens999 Lab to a cross-population fine-mapping method. Led by the talented @KaiYuan1990 with @hailianghuang @RyanLongchamps @AFPopgen + many others. medrxiv.org/content/10.110…

Glad to see this implementation out! We extended the SuSiE model to latent factors with SuSiE-PCA! Using JAX, SuSiE-PCA can run on CPU, GPU, or TPU. Preprint to come shortly, but in meantime, please try it out for your high-dim data settings and share your thoughts!

"Poisson-mash", or how to detect gene expression differences in multi-condition experiments (from the group of @mstephens999, together with Nicolas Chevrier and colleagues). arxiv.org/pdf/2210.00697…

@jgschraiber @lpachter Yes Yusha has worked hard to make the computation tractable here. Gaussian models are definitely easier!

@lpachter @mstephens999 Looks interesting. Back in grad school I was working on something similar using hierarchical Dirichlet processes, but it just didn't work well enough to justify the computational cost (which was very, very, very heavy)

Thanks so much @JovMaksimovic for sharing with us your love for #workflowr and huge thanks to the #workfowr developer @jdblischak for this incredible & easy to use tool that is helping the community towards better analyses & science! Find talk slides github.com/R-LadiesMelbou…

So, this came out ..

We have a new open-rank faculty search in the department of Medicine at the University of Chicago! We are looking for PhD scientists in a wide range of research areas. Please share widely. academicjobs.uchicago.edu/positions/1029…

The University of Chicago, Department of Human Genetics, is searching for a new computational faculty. apply.interfolio.com/112673 We are a small, friendly department doing top-quality science. Come join us! (Please RT)

NIH peer review system is far from perfect, but it's the best I've seen. I just "retired" from the GCAT study section after 4 years' of service, which prompted me to share a few thoughts re computational proposals. These are the points that I also remind myself. Other thoughts?🧵