Clint Miller

Beyond cell atlases: spatial biology reveals mechanisms behind disease - Nature Biotechnology As the next generation of spatial transcriptomics tools hits the market, researchers are uncovering previously unknown interactions that could transform clinical research.

Latest news feature in @natbiotech.nature.com on recent developments in spatial biology to unravel disease mechanisms, with insights from experts in field. @aruthak.bsky.social @nebanovich.bsky.social @ai4pathology.bsky.social @jasmineplummer.bsky.social www.nature.com/articles/s41...

9p21.3 Coronary Artery Disease Risk Locus Drives Vascular Smooth Muscle Cells to an Osteochondrogenic State | Arteriosclerosis, Thrombosis, and Vascular Biology BACKGROUND: Genome-wide association studies have identified common genetic variants at ≈300 human genomic loci linked to coronary artery disease susceptibility. Among these genomic regions, the most i...

Thrilled to share the🥇paper from the lab @ahajournals.bsky.social. Here we continue to unravel the mysteries of the 9p21.3 CAD locus showing it drives VSMC transition into an osteochondrogenic state, promoting calcification. @clintomics.bsky.social @UWMadison CRB.
www.ahajournals.org/doi/10.1161/...

Unraveling the Heart of Type 1 Diabetes — Van der Laan & Science Unraveling the Heart of Type 1 Diabetes: on our U01 grant to study the immune-link between type 1 diabetes, type 2 diabetes and cardiovascular disease.

Did we tell you about this news?

www.vanderlaanscience.nl/news/care-t1d

Glad for the support to be able to collaborate with @clintomics.bsky.social Suna Onengut-Gumuscu and @metecivelek.bsky.social from #UVA.

Excited to finally share our work on attention-based multiple instance learning to quantify and characterize intraplaque haemorrhage in carotid plaque whole slide images from >2500 patients in AtheroExpress. Fun collaboration with @swvanderlaan.bsky.social and Craig Glastonbury labs.

Judge issues preliminary injunction blocking Trump cuts to NIH research overhead payments A federal judge issued a nationwide preliminary injunction blocking the Trump administration from slashing NIH payments for research overhead

Preliminary injunction in nationwide indirect cost rate case.

This means that the judge found that the plaintiffs (AAMC, et al.) are likely to win on the merits when the ruling is finalized.

www.statnews.com/2025/03/05/n...

NIH slashes overhead payments for research, sparking outrage Move to cut indirect cost rate to 15% could cost universities billions of dollars

NIH slashes overhead payments for research, sparking outrage www.science.org/content/arti...

On changes to #NIH indirect rates, there is a law in place that prohibits NIH from making such changes without the approval of Congress. See Division D, Title II Section 224 of The Further Consolidated Appropriations Act, 2024 (Public Law No: 118-47) grants.nih.gov/grants/guide...

Academic Skyers: I am compiling a list of policies and statements from various universities about how they are handling the "pause" in terms of stopping expenditures (or not).

Please respond to this post with your institution and materials.

THANK YOU!

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?

I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

lemur Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or...

R package: bioconductor.org/packages/lemur
Code: github.com/const-ae/lem...
Python implementation: github.com/const-ae/pyl...

New single-cell analysis framework, LEMUR, disentangles covariates and latent cell states from multi-condition data to predict counterfactual gene expression and identify cell neighborhoods with similar DEGs without clustering. doi.org/10.1038/s415... @naturegenet.bsky.social

Delineating the effective use of self-supervised learning in single-cell genomics - Nature Machine Intelligence Self-supervised learning techniques are powerful assets for enabling deep insights into complex, unlabelled single-cell genomic data. Richter et al. here benchmark the applicability of self-supervised...

Delineating the effective use of self-supervised learning in single-cell genomics www.nature.com/articles/s42... @fabiantheis.bsky.social

Very grateful and humbled to receive promotion to tenure at UVA School of Medicine.

Huge thanks to my supportive mentors, colleagues, family, and talented trainees who continue to inspire me along this journey.

Here’s to the work ahead!

Recovery of biological signals lost in single-cell batch integration with CellANOVA - Nature Biotechnology A statistical framework quantifies single-cell batch variation and recovers meaningful biological signals.

New method CellANOVA recovers lost biological signals and evaluates global and gene level distortions introduced from common single-cell batch correction algorithms‬⁩ github.com/Janezjz/cell... www.nature.com/articles/s41...