Very excited to share our @ScienceMagazine paper on single-cell #3D #genome reorganization in #Alzheimer's disease. We jointly measured gene expression and 3D genome architecture in individual human brain cells using #GAGEseq, then integrated these data w/ chromatin accessibility and spatial transcriptomics. We uncovered increased #compartment #mingling and distance-dependent rewiring of gene regulatory contacts in AD. We also developed #Hicformer, a transformer-based model that integrates DNA sequence with 3D genome features to predict cell type-specific gene expression and prioritize candidate regulatory elements. Huge kudos to co-first authors @zocean636 and @xinyuelu1999; and many thanks to Zhijun Duan @UW, Hansruedi Mathys @PittTweet, & David Bennett @rushalzheimers for the wonderful collaboration, as well as to all our co-authors. @CarnegieMellon @SCSatCMU @CMUCompBio #AlzheimersDisease #3DGenome #SingleCell #AI science.org/doi/10.1126/scie…

I notice many of my academic friends still use photos from 20 years ago on their website and for social media profiles. My recommendation is to update them at least once a decade if you are too busy with your science … CMU recently took some new photos of me, so I finally updated mine (the previous one was from 2017). Will update again in 2035 if not sooner !!

If you are at #COLM2026 this week, talk to @ShenShuaik4260 and @WenduoC - they are doing super cool stuff in my group

A truly historic moment for @CarnegieMellon and our @SCSatCMU. We are now the Kenneth C. Griffin School of Computer Science. Grateful for the opportunity it creates to help shape the future.

We asked a basic unanswered question in tissue biology: Can the many molecular exchanges between neighboring cells be organized into reusable communication programs - much like genes into pathways? We introduce SpiderNet, which learns cell-cell meta-interactions (MIs): directed sender->receiver programs linking sender regulators, ligand-receptor bridges, and receiver responses, while mapping where each program is active in tissue. Across diverse contexts, MIs recur, form multicellular relays, predict neighboring-cell responses to perturbation, and connect local signaling to tissue states and phenotypes. We hope MIs provide an intermediate language for spatial omics, moving from catalogs of local contacts toward interpretable, comparable, and eventually perturbable programs of multicellular regulation. 📚 Preprint: biorxiv.org/content/10.64898… 🚀 Led by the amazing Junjie Tang @JJTang_1995 in the lab.

I spoke with @Nature, alongside several other researchers, about why many AI researchers still choose academia despite the growing pull of industry. Academia's unusual freedom to choose which questions are worth pursuing is powerful. But I do not think academia and industry need to be opposites. As AI reshapes science, we need models that let them co-evolve, combining academia's long-term freedom and openness with industry's resources, scale, and ability to rapidly translate ideas into impact. nature.com/articles/d41586-0…