The trick was recasting the problem and training an AI model to predict which DNA regions retain memory over time, pinpointing the exact DNA bps that are responsible for this memory

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood....

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 - PubMed Metastasis is the leading cause of cancer deaths. To develop strategies for intercepting metastatic progression, a better understanding of how tumor cells adapt to vastly different organ contexts is needed. To investigate this question, a single-cell transcriptomic atlas of primary tumor and diverse …

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.

Cycle for Survival Join the ride today!!!

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

We had many hundreds of applications for that position... Sorry

thank you!

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

Joint representation and visualization of derailed cell states with Decipher - Genome Biology Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or character...

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!

Bioimaging | UZH Research Spotlight YouTube video by Universität Zürich

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!

My First Substantial Independent Research Award Was Terminated Early. Can My ESI Status Be Reinstated? June 12, 2025 Investigators lose their Early Stage Investigator (ESI) eligibility when they successfully compete for and receive a substantial independent research award. In the event an investigator’s first substantial independent research award is terminated within the first three years of the project period, and this was not due to scientific misconduct or other disqualifying events, the investigator can request the reinstatement of ESI status, using the ESI Extensions request tool in eRA commons. See Requesting an Extension for instructions. For more, see the Early Stage Investigators FAQ page.

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/...

12) In summary P53 is a guardian of plasticity. Its loss loss promotes malignant progression by enabling epithelial plasticity and immune evasion. p53 activation or KRAS inhibition removes progenitor cells and dismantles their tumor-like niche.

11) Loss of p53 allows for the stabilization and progression of the malignant niche, allowing the progenitor cells. to persist and progress to more mesenchymal states and for their accompanying niche to stabilize and expand in size ->

10) The progenitor state and its niche are dependent on KRAS signaling. Inhibition of KRAS via drug blunts the progenitor state and dismantles their surrounding tumor like niche ->

9) Thus the progenitor states orchestrates tissue remodeling of self reinforcing tumor like niches through robust feedback loops among cell compartments ->

8) Bi-directional cell-cell communication changes along this axis, enable new modes of communication between all cell compartments in the niche ->

7) This tissue remodeling trajectory culminates in progenitor cells residing with niches abundant in activated fibroblasts and immunosuppressive myeloid cells reminiscent of advanced PDAC ->

6) We found coordinated changes in gene expression across multiple cell type compartments along this axis, including changes in expression of cell-cell communication genes. Just defining a pseudo-time of niche remodeling from a single spatial snapshot ->

5) To track this remodeling we anchored spatial neighborhoods (niches) around epithelial cells, placed these niches the gastric to progenitor axis based on their mean epithelial state and characterized how all other TME states change along this axis ->

4) The gastric to progenitor axis is the strongest axis of variation among epithelial pre-malignant cells. Thus we collected Xenium data to understand the tissue remodeling that occurs along this axis ->