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/sc…

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 ous 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

Excited to be at #COLM2026 in SF, Oct 6–9! 🎉

We'll present "SkillFoundry: Building Self-Evolving Agent Skill Libraries from Heterogeneous Scientific Resources"

📍 Poster #17, Imperial Ballroom
🕟 Tue, Oct 6, 4:30–6:30 PM PDT

We would love to meet up and chat!

🚀Please help share widely! We're excited to launch the new #AI4BIO #Fellows Program @SCSatCMU to recruit exceptional early-career scientists pursuing bold, independent research at the intersection of AI and biology.

Fellows will be supported by The Center for AI-Driven I4BIO) @SCSatCMU and co-mentored by two CMU School of Computer Science faculty members, with opportunities spanning AI models, computational biology, and autonomous science, including engagement with the CMU AI Science Foundry (ai-science-foundry.cmu.edu).

We are looking for truly exceptional candidates who want to help define new directions for AI-driven biomedical discovery.

📅 Apply by November 15, 2026.

🧬 Program information: cmu.edu/ai4bio/apply/i…
🤖 Application via Interfolio: apply.interfolio.com/190197

RT @BillGates: Ken’s incredible generosity will make a huge, lasting impact.

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.

Breaking News: The hedge fund executive Kenneth Griffin pledged $3 billion to Carnegie Mellon, the largest ever single donation in American higher education. The record-breaking gift will largely go toward the development of a campus in Miami. nyti.ms/4hkSZrw

As part of Citadel founder and CEO Ken Griffin’s transformative investment, we’re now known as the Kenneth C. Griffin School of Computer Science! With this new support, we’re ready to ask bigger questions!
cmu.edu/news/stories/a…

Today, Carnegie Mellon University and Ken Griffin, founder and CEO of Citadel and founder of Griffin Catalyst, announced a historic $3 billion gift to elevate Carnegie Mellon in Pittsburgh and launch Carnegie Mellon University Miami. #CMUMiami

Learn more: cmu.edu/news/stories/a…

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 ms 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/10.648…
🚀 Led by the amazing Junjie Tang @JJTang_1995 in the lab.

SCOOP: Top researchers at Columbia, Stanford, and others thought they were elected to elite scientific societies alongside Nobel laureates. The catch? The organizations are a sham.

I spent the last month investigating a massive academic scam, for @Nature

nature.com/articles/d4158…

I highly recommned the essay on antedisciplinary science by Sean Eddy written 21 years ago.

journals.plos.org/ploscompbiol/a…

It seems to me that we are currently experiencing the birth of a new discipline: mathematics engineering.

Please help spread the word! We are recruiting multiple Postdoctoral Fellows as part of the recently launched Bakar Computational Biomedicine Initiative (BCBI) at UC Berkeley and UCSF.

BCBI website: bcbi.berkeley.edu
Apply by Nov 1, 2026: berkeley.infoready4.com/#freeformCompe…
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Life. Today.

@CMU_ECE is hiring. We are looking for both tenure-track and teaching-track positions this cycle, and doing a broad search in all areas of ECE

Here is the official link to apply: apply.interfolio.com/193699

TMLR has faced a deluge of submissions, necessitating stricter desk rejection policies due to limited reviewer capacity

Co-EiC Nihar Shah reached out to authors of 10 papers slated for desk reject. Could they answer questions about their *own* submission?
medium.com/@TmlrOrg/askin…

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/d4158…

CMU is hiring an Assistant Professor in NeuroAI!

Come join our awesome NeuroAI community 🧠🤖: apply.interfolio.com/189268

We are thrilled to share that our GPN-Star manuscript is now published and freely available:
doi.org/10.1038/s41586…
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