Leif S. Ludwig

🚨 NEW
@FraticelliLab
PREPRINT JUST WENT LIVE

biorxiv.org/content/10.6...

Here, we describe PLSTCs, Soluplus-based expansion cultures of primary mouse *Acute Myeloid Leukemia* Stem Cells. And then we use LARRY barcoding to identify drivers of leukemogenicity and drug resistance!

🔔HIRI has opened a new call to recruit Group Leaders. If you are interested in opening an RNA Biology and Infection lab, join us! Deadline: February 15. More info here 👇

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

Only 10 Days Left for MYELOID2026 early Bird registration! Prices go up on 1/16!

Please share!

Register Here: HOME - FIFTEENTH INTERNATIONAL WORKSHOP ON MOLECULAR ASPECTS OF MYELOID STEM CELL DEVELOPMENT AND LEUKEMIA share.google/6UyBgsz0TqDW...

Current Job Offers - BIH at Charité Current Job Offers - Berliner Institut für Gesundheitsforschung - Charité und Max-Delbrück-Centrum

🚀 BIH is recruiting for its PhD Program! Work on cutting-edge translational projects spanning immunotherapy, genomics, AI, hematopoiesis, precision medicine & more.
Apply by Jan 19, 2026.
🔗 Join us in turning research into health! www.bihealth.org/en/career/wo...

We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona!

🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)

Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social

Submit your abstract and present your research!

www.isco-conference.eu

Our paper on the second Berlin patient came out in Nature today and I’m really happy we can share this story on World AIDS Day. I want to thank everyone on the team and all co-authors for their work over the years.

www.nature.com/articles/s41...

Also, here’s an accessible video intro:

Single-cell susceptibility to viral infection is driven by variable cell states Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)!

www.cell.com/cell/fulltex...

For those who’d like a high level summary of our paper today, please check out the accompanying research briefing:

www.nature.com/articles/s41...

Functionally dominant hotspot mutations of mitochondrial ribosomal RNA genes in cancer Nature Genetics - Analysis of 14,106 tumor genomes highlights recurrent mutations in mitochondrial ribosomal RNA encoded within the mitochondrial genome. Mutations occur at hotspot positions and...

Excited to share our latest work in collaboration with the @edreznik.bsky.social lab @mskcancercenter.bsky.social, where we describe functionally dominant mitochondrial DNA mutations in patient tumors. So, what is functional dominance in mitochondrial genetics, I hear you ask?

rdcu.be/eN1jm

🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.

Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.

👉 Apply now: www.mdc-berlin.de/career/jobs/...

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...

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 👇

🙏 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!

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

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

🔥 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...

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

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

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...

🚨 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...

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 ...

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...

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 ...

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...

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.

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...

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/...

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)

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!

🚀 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!

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.

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...

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...

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...
🧵