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Reposted

Anshul Kundaje @anshulkundaje.bsky.social · Aug 19

@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 · Aug 12

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

danapeer.bsky.social @danapeer.bsky.social · Aug 7

thank you!

danapeer.bsky.social @danapeer.bsky.social · Aug 6

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

Thomas Norman @normanlab.bsky.social · Aug 6

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.

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Reposted

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Aug 5

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

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Reposted

Yogesh Goyal @goyallab.bsky.social · Jul 7

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 · Jul 28

This is brilliant!

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · Jul 28

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.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology

RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

www.nature.com

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danapeer.bsky.social @danapeer.bsky.social · Jul 28

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 · Jul 21

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

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danapeer.bsky.social @danapeer.bsky.social · Jul 20

This is a great tool!

Stegle Lab @steglelab.bsky.social · Jul 19

@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

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Reposted

Virginie Uhlmann @virginieuhlmann.bsky.social · Jun 24

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

www.youtube.com

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danapeer.bsky.social @danapeer.bsky.social · Jul 11

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 · Jul 11

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

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Reposted

Stegle Lab @steglelab.bsky.social · Jul 4

Deadline in 9 days - apply now!

Oliver Stegle @oliverstegle.bsky.social · Jun 26

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...

Postdoctoral Researcher in Computational Genetics

The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...

embl.wd103.myworkdayjobs.com

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Reposted

Mark Peifer (He, him) @peiferlabunc.bsky.social · Jul 2

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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 · Jul 3

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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