Leif S. Ludwig
@leifludwig.bsky.social
Emmy Noether Research Group leader at Berlin Institute of Health at Charité and Berlin Institute for Medical Systems Biology (MDC)
Reposted by Leif S. Ludwig
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...
www.cell.com/cell/fulltex...
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...
www.cell.com
November 14, 2025 at 4:47 PM
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...
www.cell.com/cell/fulltex...
Reposted by Leif S. Ludwig
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...
www.nature.com/articles/s41...
Functional dominance in the central dogma of tumor mitochondrial genetics - Nature Genetics
We have discovered recurrent, somatic mutations in mitochondrial ribosomal RNA genes across all tumor types assessed. In contrast with the established idea that the majority of mitochondrial DNA molec...
www.nature.com
November 3, 2025 at 2:56 PM
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...
www.nature.com/articles/s41...
Reposted by Leif S. Ludwig
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
rdcu.be/eN1jm
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...
rdcu.be
November 3, 2025 at 11:15 AM
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
rdcu.be/eN1jm
Reposted by Leif S. Ludwig
🚀 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/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
October 9, 2025 at 11:00 AM
🚀 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/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Reposted by Leif S. Ludwig
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 👇
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
January 26, 2025 at 12:10 PM
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 👇
www.biorxiv.org/content/10.1...
Highlights and key findings from our study in the thread below 👇
🚨 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
September 24, 2025 at 12:39 PM
🚨 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...
Reposted by Leif S. Ludwig
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...
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
April 4, 2025 at 6:24 AM
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...
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...
Reposted by Leif S. Ludwig
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
September 18, 2025 at 8:50 PM
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...
Reposted by Leif S. Ludwig
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
September 3, 2025 at 8:45 PM
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...
Reposted by Leif S. Ludwig
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/...
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/...
September 2, 2025 at 1:59 PM
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/...
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/...
Reposted by Leif S. Ludwig
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)
August 7, 2025 at 8:48 PM
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)
Reposted by Leif S. Ludwig
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!
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!
August 4, 2025 at 7:00 AM
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!
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!
Reposted by Leif S. Ludwig
🚀 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!
July 29, 2025 at 2:59 PM
🚀 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!
Reposted by Leif S. Ludwig
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...
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
June 2, 2025 at 9:29 AM
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...
jobs.sciencecareers.org/job/673667/j...
Reposted by Leif S. Ludwig
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...
🧵
🧬 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
May 21, 2025 at 3:44 PM
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...
🧵
🧬 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...
🧵
Reposted by Leif S. Ludwig
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...
🧵
🧬🩸 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
May 8, 2025 at 4:07 PM
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...
🧵
🧬🩸 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...
🧵
Reposted by Leif S. Ludwig
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
May 13, 2025 at 9:16 PM
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
Reposted by Leif S. Ludwig
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
April 18, 2025 at 6:36 PM
Happy to share our paper describing SPACE-seq - a new approach to spatial multiomics and lineage tracing - out today in @pnas.org! 🧵(1/5)
Reposted by Leif S. Ludwig
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
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
April 3, 2025 at 9:20 PM
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
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
Reposted by Leif S. Ludwig
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...
ubc.wd10.myworkdayjobs.com/en-US/ubcfac...
March 20, 2025 at 9:40 PM
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...
ubc.wd10.myworkdayjobs.com/en-US/ubcfac...
Reposted by Leif S. Ludwig
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
March 14, 2025 at 1:29 PM
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
Reposted by Leif S. Ludwig
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
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
March 13, 2025 at 2:08 PM
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
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
Reposted by Leif S. Ludwig
"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
Organizers:
@stefaniegrosswendt.bsky.social
@simonhaas.bsky.social
@leifludwig.bsky.social
Ashley Sanders
@larsplus.bsky.social
@elimereu.bsky.social
@alejofraticelli.bsky.social
February 27, 2025 at 9:40 PM
"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
Organizers:
@stefaniegrosswendt.bsky.social
@simonhaas.bsky.social
@leifludwig.bsky.social
Ashley Sanders
@larsplus.bsky.social
@elimereu.bsky.social
@alejofraticelli.bsky.social
Reposted by Leif S. Ludwig
New pre-print from Thomas Höfer, Daniel Hübschmann, @haas_lab and myself, with first authors @Esther_RCorrea @FloGrunschlager and Tamar Nizharadze doi.org/10.1101/2025... @DKFZ @NCT_HD @ChariteBerlin @hi_stem_lab BIH & MDC
A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells
Residing at the top of the hematopoietic hierarchy, long-term hematopoietic stem cells (HSCs) are capable of self-renewal and sustained blood cell regeneration. Over the past decades, single-cell and ...
doi.org
February 5, 2025 at 10:55 AM
New pre-print from Thomas Höfer, Daniel Hübschmann, @haas_lab and myself, with first authors @Esther_RCorrea @FloGrunschlager and Tamar Nizharadze doi.org/10.1101/2025... @DKFZ @NCT_HD @ChariteBerlin @hi_stem_lab BIH & MDC
Reposted by Leif S. Ludwig
📢 Job Alert! The NOVA Institute for Medical Systems Biology (NIMSB) is hiring 3 Technology Platform Leaders in:
🧬 Genomics (single-cell & spatial)
🧪 Metabolomics/Proteomics
📊 Data Science
Join a cutting-edge research environment! Apply by 16 March 2025 👉 nimsb.unl.pt/join-us/
(1/3)
🧬 Genomics (single-cell & spatial)
🧪 Metabolomics/Proteomics
📊 Data Science
Join a cutting-edge research environment! Apply by 16 March 2025 👉 nimsb.unl.pt/join-us/
(1/3)
Join us - NIMSB
nimsb.unl.pt
February 4, 2025 at 3:23 PM
📢 Job Alert! The NOVA Institute for Medical Systems Biology (NIMSB) is hiring 3 Technology Platform Leaders in:
🧬 Genomics (single-cell & spatial)
🧪 Metabolomics/Proteomics
📊 Data Science
Join a cutting-edge research environment! Apply by 16 March 2025 👉 nimsb.unl.pt/join-us/
(1/3)
🧬 Genomics (single-cell & spatial)
🧪 Metabolomics/Proteomics
📊 Data Science
Join a cutting-edge research environment! Apply by 16 March 2025 👉 nimsb.unl.pt/join-us/
(1/3)