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Reposted by Dominic Grün

Christophe Zimmer @chzimmer.bsky.social · 3d

** Now seeking postdocs **

Join our interdisciplinary and transnational team in Würzburg (Germany) or Paris (France) to drive projects in translational biology and antibiotic drug discovery.
Backgrounds in computational biology, AI, physics, or microbiology are all welcome. Please spread the word.

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Dominic Grün @dominicgrun.bsky.social · 7d

Registration for our "Advances in Single-Cell Technologies" meeting is still open and we invite abstract submissions until October 30th. Join us in beautiful Freiburg together with an excellent line-up of single-cell technology experts!
www.uniklinik-freiburg.de/single-cell-...

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Dominic Grün @dominicgrun.bsky.social · Jul 21

Join our "Advances in Single-Cell Technologies" meeting in December in Freiburg, co-organised with Marco Prinz and @katrinkierdorf.bsky.social. Excellent line-up of speakers covering spatial technologies, lineage tracing, computational methods, and more.
www.uniklinik-freiburg.de/single-cell-...

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Dominic Grün @dominicgrun.bsky.social · Jul 16

New preprint from the lab! Using multiplexed spatial analysis and single-cell multiomics, we resolved the portal liver immune niche and identified crosstalk between cholangiocytes, dendritic cells and gdT cells that controls fibrosis in a mouse cholangitis model.
www.biorxiv.org/content/10.1...

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Stegle Lab @steglelab.bsky.social · Jul 4

Join us for a series of presentations from leading data science experts, including @francescafinotello.bsky.social, @dominicgrun.bsky.social, Johanna Klughammer, Malte Lücken, @fabiantheis.bsky.social and @jwrth.genomic.social.ap.brid.gy.

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Dominic Grün @dominicgrun.bsky.social · Jul 2

Few dates left to apply for this tenure-track professorship on Single-Cell Systems Biology in my department at @uni-wuerzburg.de. Competitive package and highly attractive research environment at the Institute of Systems Immunology.

Dominic Grün @dominicgrun.bsky.social · Jun 2

We have an attractive opening for a tenure-track professorship in Single-Cell Systems Biology. Excellent package and infrastructure at @uni-wuerzburg.de Institute of Systems Immunology. Great place to live and work in the heart of the franconian wine region!

jobs.sciencecareers.org/job/673667/j...

junior professorship position (f/m/d) in Single-Cell Systems Biology - Würzburg (Stadt), Bayern (DE) job with Julius-Maximilians-University Würzburg - Faculty of Medicine | 673667

The Julius-Maximilians-University Würzburg, Faculty of Medicine is offering one junior professorship position (f/m/d) in Single-Cell Systems Biology.

jobs.sciencecareers.org

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Dominic Grün @dominicgrun.bsky.social · Jun 11

Consider attending the MOPITAS autumn school on Spatial Transcriptomics in Munich with expert lectures and hands-on sessions for all steps of spatial transcriptomics data analysis.
event.sdu.dk/mopitas-scho...

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Dominic Grün @dominicgrun.bsky.social · Jun 2

We have an attractive opening for a tenure-track professorship in Single-Cell Systems Biology. Excellent package and infrastructure at @uni-wuerzburg.de Institute of Systems Immunology. Great place to live and work in the heart of the franconian wine region!

jobs.sciencecareers.org/job/673667/j...

junior professorship position (f/m/d) in Single-Cell Systems Biology - Würzburg (Stadt), Bayern (DE) job with Julius-Maximilians-University Würzburg - Faculty of Medicine | 673667

The Julius-Maximilians-University Würzburg, Faculty of Medicine is offering one junior professorship position (f/m/d) in Single-Cell Systems Biology.

jobs.sciencecareers.org

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Shalin H. Naik @shalinhnaik.bsky.social · May 16

A triumph of perseverance from twitterless Tom Weber, Christine Biben and the team, our in vivo barcoding "LoxCode mouse" used to resolve epiblast fate to fetal organs is finally published in @cellpress.bsky.social and available through @jacksonlab.bsky.social www.sciencedirect.com/science/arti...

LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs

Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding…

www.sciencedirect.com

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Dominic Grün @dominicgrun.bsky.social · May 17

Congrats, Shalin and team! Really looking forward to read this!

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Dominic Grün @dominicgrun.bsky.social · May 14

Registration for the upcoming symposium "Imaging the Immune System VI" in Würzburg is still open. Fantastic speaker line-up at a beautiful historic venue in the centre of Würzburg.

imaging-immune-system.wuesi.com

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The New Yorker @newyorker.com · Apr 28

Barry Blitt’s cover for this week’s issue, “The First Hundred Days.” #NewYorkerCovers nyer.cm/ysrCZ47

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Dominic Grün @dominicgrun.bsky.social · Apr 4

Congrats Nina and team!! Great to see this beautiful study published!

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Nina Cabezas-Wallscheid @ninacabezas.bsky.social · Apr 2

Extremely happy to share our study on the regulation of HSCs in the context of myocardial infarction published in Nature Cell Biology! Driven by two amazing scientists in my lab - Jasmin and Maricarmen and co-led with the awesome cardiologist Timo! Huge thanks also to all our collaborators 👏🏻👏🏻

Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · Apr 2

New research by the @ninacabezas.bsky.social lab & collaborators from @uniklinik-fr.bsky.social.

A vitamin A metabolite may offer a targeted therapeutic strategy for heart attack patients by regulating HSCs to minimize excessive inflammation and preserve long-term heart function.

Healing a broken heart

A vitamin A metabolite, 4-oxo-retinoic acid, can regulate the activity of hematopoietic stem cells and thereby reduce inflammation after a heart attack, ultimately improving heart function in the long...

www.ie-freiburg.mpg.de

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Stegle Lab @steglelab.bsky.social · Mar 18

1/ New preprint! 🍳

@elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins!

doi.org/10.1101/2025...

Message passing intuition behind the segger’s link-prediction model and the network architecture

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Reposted by Dominic Grün

Sten Linnarsson @sten.linnarsson.org · Mar 17

We're looking to hire a research assistant for flow cytometry of brain tumor immune cells! Apply here -> ki.varbi.com/en/what:job/...

Research Assistant in the field of glioblastoma immunology

Do you want to contribute to top quality medical research? The Sten Linnarsson lab is a part of Unit of Molecular Neurobiology at the Department of Medical Biochemistry and Biophysics (MBB) . Linnarss

ki.varbi.com

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Saez-Rodriguez Group @saezlab.bsky.social · Mar 17

6 days left to apply to the Post-doc opening in our lab
@ebi.embl.org to develop&apply #bioinformatics & #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data: embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Postdoctoral fellow - Saez-Rodriguez Group

Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...

embl.wd103.myworkdayjobs.com

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Rachael Sirianni, PhD @docsirianni.bsky.social · Mar 12

This is my institution. These are the people I work with making these decisions. The situation is heartbreaking. Public medical schools have no other choice; there is no other source of funding, and everyone in academia is at extreme risk right now.

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David Fischer @davidsebfischer.bsky.social · Mar 13

Currently, there's a lot of interest in quantitative models that would help us understand and predict features of the complex cellular systems that underlie human health and disease - think about virtual cells, for example. On can trace some of these ideas back to the early days of systems biology.

Nature Reviews Genetics @natrevgenet.nature.com · Mar 11

Adapting systems biology to address the complexity of human disease in the single-cell era go.nature.com/3XBo6Vh #Review by @davidsebfischer.bsky.social, Martin A. Villanueva, Peter S. Winter & Alex K. Shalek @broadinstitute.org @mitofficial.bsky.social @ragoninstitute.bsky.social

Adapting systems biology to address the complexity of human disease in the single-cell era - Nature Reviews Genetics

Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review systems-focused approaches to identify and co...

go.nature.com

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Katie Sandlin @kmsandlin.bsky.social · Feb 14

Today, along with 2,000 other NIH employees, I had to clear out my office 😭

It was truly the honor of my life to work with such incredibly passionate people focused on improving human health. I’ve never experienced a more positive culture where *everyone* cared about their job and serving others.

Office desk without any personal items or decor

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Nature Reviews Genetics @natrevgenet.nature.com · Feb 21

New online! Decoding cell–cell communication using spatial transcriptomics

Decoding cell–cell communication using spatial transcriptomics

Nature Reviews Genetics, Published online: 21 February 2025; doi:10.1038/s41576-025-00824-3In this Tools of the Trade article, Ankit Agrawal introduces the computational framework NiCo (Niche Covariation), which integrates spatial transcriptomics with…

www.nature.com

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Dominic Grün @dominicgrun.bsky.social · Feb 21

Check out this nice "Tools of the Trade" piece in Nature Reviews Genetics written by Ankit Agrawal on our NiCo algorithm for the analysis of single-cell spatial transcriptomics data from platforms like Xenium, MERSCOPE, seqFISH etc.
Feel free to reach out for advice.
www.nature.com/articles/s41...

Decoding cell–cell communication using spatial transcriptomics - Nature Reviews Genetics

In this Tools of the Trade article, Ankit Agrawal introduces the computational framework NiCo (Niche Covariation), which integrates spatial transcriptomics with single-cell RNA-sequencing data to stud...

www.nature.com

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Reposted by Dominic Grün

Sri Kosuri @srikosuri.bsky.social · Feb 8

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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Fabian Theis @fabiantheis.bsky.social · Jan 22

Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at www.nature.com/articles/s41...

Mapping cells through time and space with moscot - Nature

Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

www.nature.com

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Dominic Grün @dominicgrun.bsky.social · Jan 15

That looks super interesting…

Prisca Liberali @priscaliberali.bsky.social · Jan 15

A perfect start in the new year! 🌱 Regenerating tissues are just an amazing spatio temporal controlled process! Our new manuscript explores how cell heterogeneity and bistability orchestrate intestinal regeneration. 🧵 biorxiv.org/cgi/content/...

Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration

Tissue regeneration relies on the ability of cells to undergo de novo patterning. While tissue patterning has been viewed as the transition from initially identical un-patterned cells to an arrangemen...

biorxiv.org

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