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danapeer.bsky.social

@danapeer.bsky.social
4K followers 156 following 125 posts
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danapeer.bsky.social @danapeer.bsky.social · 27/03/2026
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
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danapeer.bsky.social @danapeer.bsky.social · 27/03/2026
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/...
science.org
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....
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danapeer.bsky.social @danapeer.bsky.social · 27/01/2026
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.
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Nicolas Robine 🇪🇺🇫🇷🇺🇸 @nicorobine.bsky.social · 12/12/2025
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...
pubmed.ncbi.nlm.nih.gov
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 …
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danapeer.bsky.social @danapeer.bsky.social · 05/12/2025
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.
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danapeer.bsky.social @danapeer.bsky.social · 02/12/2025
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
bit.ly
Cycle for Survival
Join the ride today!!!
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scverse @scverse.bsky.social · 30/10/2025
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
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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025
@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
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danapeer.bsky.social @danapeer.bsky.social · 12/08/2025
We had many hundreds of applications for that position... Sorry
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danapeer.bsky.social @danapeer.bsky.social · 07/08/2025
thank you!
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danapeer.bsky.social @danapeer.bsky.social · 06/08/2025
A great read for anyone interested in perturbations and cell-fate decisions. Top notch work.
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Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · 05/08/2025
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
bit.ly
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...
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Yogesh Goyal @goyallab.bsky.social · 07/07/2025
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...
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danapeer.bsky.social @danapeer.bsky.social · 28/07/2025
This is brilliant!
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danapeer.bsky.social @danapeer.bsky.social · 28/07/2025
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!
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danapeer.bsky.social @danapeer.bsky.social · 22/07/2025
A huge congratulations to my better half, Itsik Pe'er, @iscb.bsky.social
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danapeer.bsky.social @danapeer.bsky.social · 20/07/2025
This is a great tool!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 24/06/2025
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...
youtube.com
Bioimaging | UZH Research Spotlight
YouTube video by Universität Zürich
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danapeer.bsky.social @danapeer.bsky.social · 11/07/2025
The line up for this conference is amazing and I am really looking forward to all the talks and discussions tomorrow!
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Stegle Lab @steglelab.bsky.social · 04/07/2025
Deadline in 9 days - apply now!
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 02/07/2025
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/...
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.
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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.
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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 ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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 ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
9) Thus the progenitor states orchestrates tissue remodeling of self reinforcing tumor like niches through robust feedback loops among cell compartments ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
8) Bi-directional cell-cell communication changes along this axis, enable new modes of communication between all cell compartments in the niche ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
7) This tissue remodeling trajectory culminates in progenitor cells residing with niches abundant in activated fibroblasts and immunosuppressive myeloid cells reminiscent of advanced PDAC ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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 ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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 ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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 ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
3) These progenitor cells accumulate in disorganized lesions upon inflammation and are reminiscent of highly plastic cells found in normal regeneration. Thus we find an additional role for P53 as putting the breaks on plasticity and keeping it in check ->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
2) We find that P53 is uniquely activated in the highly plastic progenitor state. This highly plastic state activates KRAS + other oncogenic signals, P53 + other tumor suppressors. This state expands under inflammation, from 1% to 30%. -->
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danapeer.bsky.social @danapeer.bsky.social · 03/07/2025
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...
biorxiv.org
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. ...
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danapeer.bsky.social @danapeer.bsky.social · 27/06/2025
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.
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Quaid Morris @quaidmorris.bsky.social · 03/06/2025
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...
biorxiv.org
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 ...
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danapeer.bsky.social @danapeer.bsky.social · 26/05/2025
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
bit.ly
Computational Biologist (Single-cell Genomics / ML) – Single-cell Analytics Innovation LabChaligne Lab Website
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 24/05/2025
David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏 youtu.be/8YhJM6zxYDw?...
youtu.be
Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company
YouTube video by Amanpour and Company
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Manu Saraswat @manusaraswat.bsky.social · 16/05/2025
🧠 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🧵👇
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Stegle Lab @steglelab.bsky.social · 16/05/2025
🚨 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!
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Omer Ali Bayraktar @bayraktarlab.bsky.social · 16/05/2025
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 🧵
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danapeer.bsky.social @danapeer.bsky.social · 15/05/2025
5) To further clarify the full cell circuit see the image below: T cells produce IFNγ, supporting maturation of conventional DC2 cells into migratory CCR7+ DCs. These DCs produce IL-12 and IL-15 to support the survival and proliferation of NK cells, which control the expansion of metastatic cells.
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
4) Rigorous and basic science that elucidates how tumor immunology works in the leptomeningeal space can lead to better therapies for this lethal and debilitating metastatic site. Basic science matters!
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
3) Good computation played a role in deciphering this unique anti-tumor cell circuit. It required sophisticated factor based methods to find gene programs developed by @russellkunes.bsky.social and our psuedo-time algorithms which @meningojan.bsky.social expertly applied ->
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
2) Biology works differently in the leptomeningeal space, which is why normal therapies fail there. Anti-tumor immunity is different: independently of antigen presentation: Interferon gamma drives maturation of dendritic cells into supporters of NK cell-mediated tumor killing ->
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
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...
nature.com
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...
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
Basic science matters!
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danapeer.bsky.social @danapeer.bsky.social · 14/05/2025
This collaboration was a true pleasure, with great scientists and wonderful people, leading to amazing science
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Selin Jessa @selinjessa.com · 03/05/2025
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 🧬🖥️
biorxiv.org
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...
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danapeer.bsky.social @danapeer.bsky.social · 06/04/2025
Great advice
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danapeer.bsky.social @danapeer.bsky.social · 06/04/2025
Congratulations David
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