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Reposted by Leif S. Ludwig

Ana Janeva @anajaneva.bsky.social · Jan 26

I am thrilled to share that our latest pre-print from the @evahoermanseder.bsky.social lab 🐸🧬, is now online! Check it out here:
www.biorxiv.org/content/10.1...

Highlights and key findings from our study in the thread below 👇

Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes

Fates of differentiated cells in our body can be induced to change by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling can be produced. However, the eff...

www.biorxiv.org

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Leif S. Ludwig @leifludwig.bsky.social · 14d

🙏 Thanks to @caleblareau.bsky.social l, @hattaca.bsky.social, @helenaradbruch.bsky.social ky.social, Benedikt Obermayer, Marie Cotta, Frank Hepper, David Capper, Wolfram Kunz, Markus Schülke & all team members for their contributions!

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Leif S. Ludwig @leifludwig.bsky.social · 14d

Together, scmtMPM & scwMSS provide a quantitative framework for somatic mtDNA mosaicism, advancing mitochondrial genetics & disease research.

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Leif S. Ludwig @leifludwig.bsky.social · 14d

Using POLG-mutant cells, healthy donors & patients, we show:
🔹 Complex single-cell mutational landscapes
🔹 Negative selection against truncating & pathogenic variants 
🔹 Constrained mutations in Complex I

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Leif S. Ludwig @leifludwig.bsky.social · 14d

🔥 Our second preprint, led by Josch, introduces a new framework to measure mtDNA mutational burden & constraint at single-cell resolution. We present:
🔹 scmtMPM (mutations per Mb)
🔹 scwMSS (heteroplasmy-weighted local constraint) 👉 www.researchsquare.com/article/rs-6...

Single-cell multi-omics resolved analysis of mitochondrial genome-wide mutational burden, constraint, and mosaicism

Mitochondria contain their own circular, multi-copy genome, encoding essential components of the mitochondrial respiratory chain vital for cellular metabolism. Mitochondrial DNA (mtDNA) mutations occu...

www.researchsquare.com

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Leif S. Ludwig @leifludwig.bsky.social · 14d

In short: Cryo-mtscATAC-seq enables cell state–informed clonality from frozen specimens, opening new avenues to leverage biobanked tissue in health & disease.

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Leif S. Ludwig @leifludwig.bsky.social · 14d

Cryo-mtscATAC-seq + our mitoBender computational tool: 🔹 Works on archival frozen tissue
🔹 Extends mtDNA genotyping to brain, glioblastoma, neuroblastoma & vascular tissue
🔹 Reveals clonal gliogenesis, microglial expansions, chemo-induced heterogeneity & smooth muscle oligoclonality

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Leif S. Ludwig @leifludwig.bsky.social · 14d

🚨 New preprints from our lab! First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”). 👉 www.biorxiv.org/content/10.1...

Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues

High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fr...

www.biorxiv.org

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Reposted by Leif S. Ludwig

Emma R Andersson @anderssonlab.bsky.social · Apr 4

Hot off the press! 🧬🔬

We developed in utero nano-injection to label & trace the mouse neural plate and otic placode using next generation single cell lineage tracing. We couple progenitors to mature cell types in the CNS & resolve the lineages of cells in the hearing organ:

doi.org/10.1126/scie...

Ectoderm barcoding reveals neural and cochlear compartmentalization

Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day ...

doi.org

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Reposted by Leif S. Ludwig

John Ray @jraylab.bsky.social · 20d

Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...

Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics

Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...

www.nature.com

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Reposted by Leif S. Ludwig

Steven Salzberg @stevensalzberg.bsky.social · Sep 3

We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

www.science.org

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Reposted by Leif S. Ludwig

immunoboys @immunoboys.bsky.social · Sep 2

A synonymous mitochondrial variant is negatively selected against in short-lived CD8 effectors – How?
The variant changes tRNA pairing from Watson-Crick-Franklin to wobble, thereby reducing translational efficiency in high energy demand. 🧪 ⑂
Lareau et al – 2025
www.pnas.org/doi/10.1073/...

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Reposted by Leif S. Ludwig

Viktoria Flore @viktoriaflore.bsky.social · Aug 7

Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)

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Reposted by Leif S. Ludwig

Max Delbrück Center @mdc-berlin.bsky.social · Aug 4

Lead your independent research project as a #postdoc in our 3-year #fellowship.

The program includes full-time employment with competitive salary, budget, structured co-supervision, mentoring and advanced training

Apply from August 4 to August 28
👉 www.mdc-berlin.de/postdocs#t-g...

Please share!

three scientists discuss. Text: "MDC Global Fellow postdoctoral program"

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Reposted by Leif S. Ludwig

Itai Yanai @itaiyanai.bsky.social · Jul 29

🚀 Today we're launching the 'Night Science Institute', a non-for-profit organization to lead a cultural shift in science! You may say we're dreamers 😉, but we think we're not the only ones. Perhaps today you will join us to make the Day Science and Night Science parts of the process live as one!

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Reposted by Leif S. Ludwig

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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Reposted by Leif S. Ludwig

Lars Velten @larsplus.bsky.social · May 21

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature

The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...

doi.org

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Reposted by Leif S. Ludwig

Lars Velten @larsplus.bsky.social · May 8

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵

Design principles of cell-state-specific enhancers in hematopoiesis

Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...

www.cell.com

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Reposted by Leif S. Ludwig

Stefanie Grosswendt @stefaniegrosswendt.bsky.social · May 13

Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants

(Some of the) speakers and co-organizers of the ISCO conference 2025

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Reposted by Leif S. Ludwig

Julia Belk @juliabelk.bsky.social · Apr 18

Happy to share our paper describing SPACE-seq - a new approach to spatial multiomics and lineage tracing - out today in @pnas.org! 🧵(1/5)

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Reposted by Leif S. Ludwig

Alexis Caulier @hemagene.bsky.social · Apr 3

Out today in @science.org!
What if you could chart cells' regulatory programs at unprecedented resolution?
In my work with Jorge Martin-Rufino from the @bloodgenes.bsky.social lab, we dissect the genome’s control circuits and find where key genetic variation hides
bit.ly/3YhBMoO

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

bit.ly

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Reposted by Leif S. Ludwig

Carl de Boer @carldeboer.bsky.social · Mar 20

Last call for a postdoc position in single cell analysis/perturb-seq with @nikashakiba.bsky.social at UBC in beautiful Vancouver Canada!
ubc.wd10.myworkdayjobs.com/en-US/ubcfac...

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Reposted by Leif S. Ludwig

Caleb Lareau @caleblareau.bsky.social · Mar 14

Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1

a baby is eating a piece of food while sitting on the ground .

ALT: a baby is eating a piece of food while sitting on the ground .

media.tenor.com

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Reposted by Leif S. Ludwig

Itai Yanai @itaiyanai.bsky.social · Mar 13

Join us at "Innovations in Single Cell Omics" in Berlin 5.12-13 (+ night science workshop!)
www.isco-conference.eu
Organizers:
@stefaniegrosswendt.bsky.social, @simonhaas.bsky.social
@leifludwig.bsky.social, Ashley Sanders, @larsplus.bsky.social, @elimereu.bsky.social, @alejofraticelli.bsky.social

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Reposted by Leif S. Ludwig

Itai Yanai @itaiyanai.bsky.social · Feb 27

"Innovations in Single Cell Omics" Berlin 5.12-13.
Organizers:
@stefaniegrosswendt.bsky.social
@simonhaas.bsky.social
@leifludwig.bsky.social
Ashley Sanders
@larsplus.bsky.social
@elimereu.bsky.social
@alejofraticelli.bsky.social

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