I am very pleased with our latest paper showing that cells can remember past injury for a long time! Here a simple interpretable AI was used as a discovery tool to pinpoint the DNA code and biological mechanism. Big foundation models failed. www.science.org/doi/10.1126/...

This is a paper I am super proud of, long in the making, packed with important concepts. It was old data and n=1 (most stronge claims backed with patients), metastatic clones are endowed with plasticity to adapt to multiple organ environments.

Transcriptomic Plasticity is a Hallmark of Metastatic Pancreatic Cancer, by Christine Iacobuzio-Donahue, @danapeer.bsky.social et al. pubmed.ncbi.nlm.nih.gov/41379552/ introduces a new single-cell method named PICASSO: Phylogenetic Inference of CNA in Single-cell RNA [...] github.com/dpeerlab/pic...

Celebrating Christina Curtis and her well-deserved Paul Marks Prize! Some tumors are born bad. Christina uses math to find them early, predict their paths, and outsmart them. A win for cancer biology and for MSK to cheer.

My lab shows up every day to take on the rare cancers. Now we’re getting on the bikes together for Cycle for Survival. Every gift is matched (yes, doubled!), and 100% goes to rare cancer research at MSK—where rare cancers are our daily reality and the science moves the needle. bit.ly/3Y1m4xx

Meet the keynote speakers for the 2025 scverse conference! John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI 🧵 #scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

A great read for anyone interested in perturbations and cell-fate decisions. Top notch work.

New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data. 📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social

Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h www.cell.com/cell-systems...

This is brilliant!

Again I would like to thank the Pezcoller Foundation for inviting me to the 36th Pezcoller Symposium in beautiful Trento. They were warm, pampering and wonderful hosts and science was top notch and delightful. I had fabulous time!

A huge congratulations to my better half, Itsik Pe'er, @iscb.bsky.social

This is a great tool!

And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be: www.youtube.com/watch?v=8t8R...

The line up for this conference is amazing and I am really looking forward to all the talks and discussions tomorrow!

Deadline in 9 days - apply now!

For ESIs dealing with grants being rescinded: if an investigator’s 1st substantial independent research award is terminated within the first 3 years of the project period (not due to scientific misconduct ) they can request the reinstatement of ESI status grants.nih.gov/news-events/...

I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...

I am so honored to be an awardee from a foundation that recognizes and funds innovation. I wish more foundations shared the Mark foundations vision. Also, the Pezcoller meeting was so fantastic this year, we were hardly the only highlights.

Please check out our new approach to modeling somatic mutation signatures. DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪 www.biorxiv.org/content/10.1...

The Single-cell Analytics Innovation Lab @mskcancercenter.bsky.social is expanding and looking for ML-oriented computational biologists. Join our team based in NYC to work on cutting-edge single-cell & spatial transcriptomics methods in collaboration with leading research labs. bit.ly/4lTEr2t

David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏 youtu.be/8YhJM6zxYDw?...

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

🚨 Impressive PhD work by Manu! Our new method scDORI decodes plasticity regulators at single-cell multi-omic resolution — scaling to millions of cells and uncovering the regulatory logic driving glioblastoma heterogeneity. 🔍 Dive into the thread below and the preprint for all the insights!

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

I am pleased to share our recent publication, fruit of a wonderful collaboration with truly amazing colleagues @adrienneboire.bsky.social and @meningojan.bsky.social, whose work was a tour de force demonstrating that immunology in the brain is a different beast -> www.nature.com/articles/s41...

Basic science matters!

This collaboration was a true pleasure, with great scientists and wonderful people, leading to amazing science

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Great advice

Congratulations David

MSK's Dr. Alexandra Joyner is hanging up her lab coat following an illustrious 40-plus-year career. When asked what advice she has for new scientists, she shares: "You have to decide: Why are you going into this career? And then you have to stay true to that." Learn more about her legacy & impact ⬇️

From great collaborations come great things. Excited to share Segger, the solution to segmentation of spatial transcriptomics (ST) data, with the @steglelab.bsky.social and @moritzgerstung.bsky.social labs, spearheaded by the great Andrew Moorman and Elyas Heidari www.biorxiv.org/content/10.1...

So proud of this work, this was a great collaboration and I highly recommend this read and tool. My own tweetorial shortly but @steglelab.bsky.social tutorial is great.

Completely agree and have thought this for a decade

We are looking for a talented postdoctoral bioinformatician @thedawsonlab.bsky.social to work with us on single cell multiomics incorporating lineage tracing and spatial technologies- we specifically want someone curious, fearless with a licence to innovate!! Come join us!!

Welcome to Blusky!

Congratulations to all new fellows, especially my better half Itsik Pe'er

So far this conference is quite amazing, great friends and colleagues, kick-ass science and fun vibe. Meetings are stimulating and uplifting

Congratulations to the new fellows.

This was a wonderful and fun collaboration with the brilliant @agnelsfeir.bsky.social with SAIL's Max Land as a computational lead. Mitochondria are fascinating and here we present a cool way of perturbing and studying them.

The best lab in the world and our team

My lab team (Peak Pe'erformers) are about to ride in Cycle for Survival to raise money for rare cancer research at Memorial Sloan Kettering. I am proud of my lab and and I’m hoping for your support! 100% of donations go directly to rare cancer research at MSK: mskcc.convio.net/site/TR/Cycl...

1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...

You have made MSK a better place and will be sorely missed

(1/2) Results from a phase 1 clinical trial of the #mRNA-based therapeutic cancer vaccine autogene cevumeran for treating #pancreaticcancer is published in @nature.com. bit.ly/4b9ofEZ

Bring your samples into focus! A new version of the #Cellpose cell boundary mapping tool, developed at @hhmijanelia.bsky.social by @computingnature.bsky.social and @marius10p.bsky.social, now works on less-than-perfect microscopy images that are noisy, blurry, or undersampled.

More on these FDA firings www.usatoday.com/story/news/p...

Welcome to the neighborhood, excited to have you across the street soon