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

Sapporo cancer meeting

Amichai

Robert Creeley

Wonderful discussion with @landau.bsky.social visiting us at @institut-leucemie.bsky.social @hopitalsaintlouis.bsky.social in sunny Paris to give an inspiring talk on cutting-edge single-cell technologies. Thank you so much Dan for stopping by and see you soon! @lobrylab.bsky.social

Excited to share our exploration @naturemethods.bsky.social into new horizons opening up in the era of low cost sequencing! 🔥 Deeper sequencing at WGS scale for PPM sensitivity of tumor informed MRD 🔥Duplex sequencing at WGS scale for plasma only exploration of ctDNA Check out thread 👇

To celebrate National Poetry Month at @georgiatech Poetry@Tech put up our Pause for Poetry yard signs all over campus @gt_lmc thanks to @expeditionpress for helping to curate our lines @ivanallencollege.bsky.social

If Trump can disappear green card holders for protesting war, he can disappear you. If he can disappear visa holders for criticizing him, he can disappear you. If he can disappear asylum seekers for tattoos, he can disappear you. We must speak out now — before there is no one left to speak out.

Say what you want about the camera person. This is remarkable to watch

Thrilled to share new work led by @jieyang437.bsky.social in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U

and so it begins...

Friends! The science that we love is under threat. World-wide, there're forces seeking to make it corporate-like, focused on deliverables, or even the enemy of society. Take a stand & celebrate science & music! #theconferencetoendallconferences - Registration starts NOW! woodstock.img.cas.cz

Rest in power to an absolute queen. What a wonderfully talented person. Her solo work is incredible, and her duets with Donny Hathaway are immortal. Thank you for everything, Ms. Flack. variety.com/2025/music/n...

Excited to share a major breakthrough from the lab! D&D-seq is a new technology that bridges a key gap in single-cell multi-omics/genomics : the ability to map DNA:Protein interactions (e.g., TFs or chromatin remodellers). Led by Ivan Raimondi, Wei-Yu Chi and Sang-Ho Yoon

Wishing everyone a Jo & Ab 2025!

His friends will never believe him. They also may never see him again.

Happy winter solstice 🌌