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/...

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....

science.org

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.

Nicolas Robine 🇪🇺🇫🇷🇺🇸@nicorobine.bsky.social · 8mo ago

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...

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...

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 …

pubmed.ncbi.nlm.nih.gov

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

Cycle for Survival

Join the ride today!!!

bit.ly

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.

Thomas Norman@normanlab.bsky.social · 12mo ago

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

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

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...

bit.ly

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!

Memorial Sloan Kettering Cancer Center@mskcancercenter.bsky.social · last yr.

New in @natbiotech.nature.com: a team led by scientists at MSK and ‪University of Toronto have developed a new platform to facilitate the study of RNA-biding proteins (RBPs) across hundreds of species of plants, insects, and animals.

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!

Stegle Lab@steglelab.bsky.social · last yr.

@elihei.bsky.social is gonna present our new tool segger, developed in collaboration with Moritz Gerstung and @danapeer.bsky.social, for fast and accurate segmentation of spatial transcriptomics using attention-based graph neural networks. #MLCSB 📅 July 22 | 🕑 15:50 | 📍 Room 01A

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...

Bioimaging | UZH Research Spotlight

YouTube video by Universität Zürich

youtube.com

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

American Association for Cancer Research (AACR)@theaacr.bsky.social · last yr.

Computational Approaches to Mapping Cells, Tissues, and Tumor Progression: Where Does AI Help? #AACRFellows Dana Pe’er addressed this question in a keynote lecture to open the AACR Special Conference on Artificial Intelligence and Machine Learning. #AACRai25

Deadline in 9 days - apply now!

Oliver Stegle@oliverstegle.bsky.social · last yr.

Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...

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...

Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis

The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. ...

biorxiv.org

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.

The Mark Foundation for Cancer Research@themarkfdn.bsky.social · last yr.

Of course, hearing from our awardees is always a highlight! Today’s presenters included Endeavor Award team member @danapeer.bsky.social, who discussed tissue architecture, and Emerging Leader Award winner @vanallenlab.bsky.social, who shared his work using AI to enhance precision cancer medicine.

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...

Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes

Mutational signatures of single-base substitutions (SBSs) characterize somatic mutation processes which contribute to cancer development and progression. However, current mutational signatures do not ...

biorxiv.org

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?...

Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company

YouTube video by Amanpour and Company

youtu.be

🧠 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!

Manu Saraswat@manusaraswat.bsky.social · last yr.

🧠 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🧵👇

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...

Interferon-γ orchestrates leptomeningeal anti-tumour response - Nature

Independent of antigen presentation, migratory CCR7+ dendritic cells orchestrate the influx, proliferation and cytotoxic action of natural killer cells to control cancer cell growth in the leptomening...

nature.com

Basic science matters!

Adrienne Boire@adrienneboire.bsky.social · last yr.

I am so very proud of our collective work, and of our message: understanding fundamental biology is essential to the understanding of human disease. Basic science matters!

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

Adrienne Boire@adrienneboire.bsky.social · last yr.

I am delighted to share that our work focused on anti-tumor immunity in the leptomeningeal space was published today: www.nature.com/articles/s41... @meningojan.bsky.social

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 🧬🖥️

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

biorxiv.org