Check out the wonderful Bonsai method by @erikvannimwegen.bsky.social and @dhdegroot.bsky.social now published in Nat Biotech! Congrats to all authors!

Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo ago

Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n

Excited to share the results of our wonderful collaboration with @alex-stark.bsky.social on the mechanistic regulation of transcriptional bursting by promoter and enhancer architecture measured by the new BARe-seq method. Read the thread!

Franzi Lorbeer@florbeer.bsky.social · 2mo ago

0/ New preprint from the Stark and Grün labs! @reyna-rosales.bsky.social @dominicgrun.bsky.social @alex-stark.bsky.social We developed BARe-seq to ask what in the DNA controls transcriptional bursting - key findings for anyone working on transcription, gene regulation, or cis-regulatory elements 🧵

BARe-seq enables high-throughput dissection of cis-regulatory control of transcriptional bursting https://www.biorxiv.org/content/10.64898/2026.08.19.745405v1

We’re hiring a Junior Group Leader - AI in immunotherapy - to join our team at the earliest possible date. The position is embedded within my Chair and the Chair of Cellular Immunotherapy (Michael Hudecek), and connected to CAIDAS center for AI. med.uni-wuerzburg.de/fileadmin/03...

Our study on rare immune cell networks governing liver cholangitis is now online! Using multiplexed single-cell and spatial omics, we discovered a triad of cholangiocytes, dendritic cells and gdT cells regulating the inflammatory and fibrotic tissue response. Rare immune cells matter! rdcu.be/fc60M

An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis

Nature Communications - Primary sclerosing cholangitis (PSC) is an autoimmune condition affecting the liver. Here, the authors generate an immunobiliary transcriptomic atlas and show that dendritic...

rdcu.be

Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

Research | Chan et al. generate a high-resolution spatiotemporal atlas of healing hearts and reveal cellular networks of lesion repair, including macrophage-fibroblast interactions that control late-stage fibrosis. doi.org/10.1038/s441... rdcu.be/ePzs6

Spatiotemporal dynamics of the cardioimmune niche during lesion repair - Nature Cardiovascular Research

Chan et al. generate a high-resolution spatiotemporal atlas of healing hearts and reveal cellular networks of lesion repair, including macrophage–fibroblast interactions that control late-stage fibros...

doi.org

We are delighted to announce our #HighlyCited2025 researchers: Ronny Thomale, @angelifriedmann.bsky.social , Georg Gasteiger, @dominicgrun.bsky.social, and Christoph Wanner. Congratulations! ➡️ www.uni-wuerzburg.de/en/news-and-...

Our spatio-temporal map of lesion repair in the heart at single-cell resolution is now published in @natureportfolio.nature.com Cardiovascular Research. www.nature.com/articles/s44... We dissected dynamics of multicellular niches that control cardiac repair. See 🧵 for highlights.

The Roadmap of the Human Liver Cell Atlas is out in @natrevgastrohep.nature.com laying out the scope and goals of our Human Liver Cell Atlas emerging from the @cziscience.bsky.social funded Liver Seed Network. www.nature.com/articles/s41...

** 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.

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-...

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-...

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...

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.

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 · last yr.

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...

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...

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

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…

sciencedirect.com

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

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

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 · 2y ago

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.

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...

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

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

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.

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 · 2y ago

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

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.

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…

nature.com

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...

nature.com