New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu! www.science.org/doi/10.1126/...

NYC SN❄️❄️❄️❄️❄️❄️❄️❄️❄️W

"We're changing our approach to science philanthropy" -> they're funding AI, just like everyone else

Proud to announce our 2026–2027 Research Grantees! Their innovative research is advancing ovarian cancer early detection and prevention—bringing us closer to a future where every woman has a fighting chance. tinaswish.org/grants-26-27/

The unfounded move by HHSGov against mRNA vaccines will hurt our future potent immune therapy vs cancer. Another point of progress for triple-negative breast cancer with individualized neoantigen mRNA vaccines today Adds to pancreatic, renal cell, melanoma reports nature.com/articles/s41...

As Valentine’s Day #ValentinesDay arrives, here’s one of Ireland’s greatest love poems: Dark-Haired Miriam Ran Away by Patrick Kavanagh (1946), inspired by Hilda Moriarty, a 22-year-old med student he became infatuated with. Later set to music as Raglan Road and famously sung by Luke Kelly.

@landau.bsky.social @rdrapkin8-penn.bsky.social Paul Mischel, and Adam Widman are searching for pre-cancerous signals of ovarian cancer in the blood, laying the foundation for non-invasive screening test. 🩸@tinaswish.bsky.social @weillcornell.bsky.social @mskcancercenter.bsky.social

Absolutely remarkable: striking effects of infusion time-of-day on immunochemotherapy efficacy in nonsmall cell lung cancer in a randomized phase 3 trial www.nature.com/articles/s41...

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...

Doing the housework and thinking of this poem from Tess Gallagher.

Now online in Cancer Discovery @aacrjournals.bsky.social: Genotype-to-Phenotype Mapping of Somatic Clonal Mosaicism via Single-Cell Co-Capture of DNA Mutations & mRNA Transcripts by @dennisjyuan.bsky.social, @landau.bsky.social, et al. doi.org/10.1158/2159... @nygenome.org @weillcornell.bsky.social

Happy new year/paper! A new tech (scG2P) maps genotype (DNA) to phenotype (RNA) in single cells, bringing together the worldviews of genetic & transcriptional heterogeneity. With scG2P we define how mosaicism drivers increase clonal fitness in the aging esophagus aacrjournals.org/cancerdiscov...

Now online in Cancer Discovery @aacrjournals.bsky.social: LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture - by Michael Lee, Yuannyu Zhang, Jian Xu, and colleagues doi.org/10.1158/2159... @stjuderesearch.bsky.social

Excited to see this out www.nature.com/articles/s41...! Nonparametric kernel-based tests for spatially variable isoform usage in spatial transcriptomics. So many interesting examples in the CNS and cancer, we're only scratching the surface!

i hate elon musk for a lot of reasons but one of them is that now sometimes i first see interesting papers on linkedin LINKEDIN

Delighted to have our work on 🧬 resilience to 🩸cancer led by @g-agarwal.bsky.social & amazing collaborators, including @kharaslab.bsky.social, published in @science.org: www.science.org/doi/10.1126/... 🧵

His soul swooned slowly as he heard the snow falling faintly through the universe and faintly falling ~ James Joyce Fred Stein

“…when grief weighs you down like your own flesh…” #smallpoemsunday @tomsnarsky.bsky.social #poetry

“I had hemophilia for nearly five decades. I went to Philadelphia and had a 45-minute infusion, and my hemophilia was gone.” Genes-> Medicine nature.com/articles/s41...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Super cool paper from Sheel Chandra + Ziyue Gao. kmer context matters a lot for mutability of both methylated and unmethylated CpGs. But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs! www.biorxiv.org/content/10.1...

Honored to be recognized by @usnews.com as a 2025 #BestLeader alongside so many incredible colleagues and individuals I admire! www.usnews.com/news/best-le...

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

You are infinitely closer to struggling than you ever will be to billionaires

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

Trying to work from home with my kids around

🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.

Big, beautiful trees!! SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life. www.biorxiv.org/content/10.1...

I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...

Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems? Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

If you want to deep dive in to immunology you could do worse than Gabriel's evolutionary landscaping www.biorxiv.org/content/10.1...

It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!

Well don't I feel stupid

Seven years. Over 400 pages. About 750 references. Over 40 figures. Finally I get to hold the finished book. It’s a big day. #EpigeneticsBook @cshlpress.bsky.social

Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀 Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com 📄 www.nature.com/articles/s41... 🧵1/n

Major advance for refractory lupus by engineering the T cells in the patient's body (in vivo) and achieving success in 5 patients @nejm.org (uses mRNA/nanoparticle package) www.nejm.org/doi/full/10....

Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...

I feel deeply honored to receive the 2025 Dr. Josef Steiner Cancer Research Award for our work on decoding and rewiring the immune-evasive TME. It truly is a recognition of the entire team past and present as well as our collaborators and mentors.🙌 Thank you for your trust!

2. www.nature.com/articles/s41...

Paper from me, Michelle Curtis, @soumya-boston.bsky.social and co out now in @natmethods.nature.com! We now call it starCAT instead of *CAT but the strategy is the same: Build a catalog of ~50 interpretable T cell gene expression programs + use them to interpret new data nature.com/articles/s41...

Microbiomes are interactive, multispecies communities, but bulk analysis obscures functional diversification from environmental and genetic heterogeneity. In our new review we describe how single-bacterium transcriptomics dissects microbiomes at cellular resolution. www.science.org/doi/10.1126/...

Postscript by Seamus Heaney who died twelve years ago today

Looks interesting! www.nature.com/articles/s41...

🧨Exciting new pre-print 🧨 Introducing ppmSeq - cost effective, scalable dual-strand 🧬🧬 sequencing. Scalability & ultra-low error in one! A game changer for somatic genome discovery science and cfDNA clinical apps. Check out thread for deets!

Donald Judd