Lucas Schirmer
@lschirmer.bsky.social
Neurologist physician-scientist at Heidelberg University interested in chronic neuroinflammation and how to improve resilience in muscle and brain diseases. Check out @schirmerlab.bsky.social and www.schirmerlab.com for lab.
Pinned
Lucas Schirmer
@lschirmer.bsky.social
· Dec 5
Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions - Nature Neuroscience
Lerma-Martin et al. generated a paired single-nucleus RNA sequencing and spatial transcriptomics dataset from subcortical multiple sclerosis lesions, identifying spatial niches and key cell interactio...
www.nature.com
Wonderful to see our latest work out in Nat Neurosci side by side with the special collection articles on single-cell omics in neuroscience. Kudos again to @celialm.bsky.social and @paubadiam.bsky.social for carrying this piece over the line www.nature.com/articles/s41...
Proud to see our work featured in the broader context of the Human Cell Atlas with us focusing on chronic muscle and brain inflammation | www.swr.de/wissen/human...
Ein Nachschlagewerk für den menschlichen Körper
Ein menschlicher Zellatlas soll durch internationale Zusammenarbeit entstehen - ein Nachschlagewerk für den menschlichen Körper. In der Pandemie war das bereits nützlich.
www.swr.de
May 23, 2025 at 7:49 AM
Proud to see our work featured in the broader context of the Human Cell Atlas with us focusing on chronic muscle and brain inflammation | www.swr.de/wissen/human...
Reposted by Lucas Schirmer
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
April 22, 2025 at 9:37 AM
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
Reposted by Lucas Schirmer
Deep cervical lymph nodes of patients with multiple sclerosis have an altered B cell compartment that transcriptionally resembles an EBV infection
@sciimmunology.bsky.social
www.science.org/doi/10.1126/...
@sciimmunology.bsky.social
www.science.org/doi/10.1126/...
February 21, 2025 at 7:10 PM
Deep cervical lymph nodes of patients with multiple sclerosis have an altered B cell compartment that transcriptionally resembles an EBV infection
@sciimmunology.bsky.social
www.science.org/doi/10.1126/...
@sciimmunology.bsky.social
www.science.org/doi/10.1126/...
Excellent - congrats
Disease diagnostics using machine learning of B cell and T cell receptor sequences
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
www.science.org
February 21, 2025 at 2:39 PM
Excellent - congrats
Reposted by Lucas Schirmer
🚗 NEW #NatureMedicine paper reports results from a first-in-human trial of CAR-macrophages! Safe & feasible to manufacture, efficacy limited. More work needed in this space! @natureportfolio.nature.com #immunotherapy #CARTcells #macrophages
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CAR-macrophage therapy for HER2-overexpressing advanced solid tumors: a phase 1 trial - Nature Medicine
In a first-in-human phase 1 trial, HER2-specific CAR macrophages were feasible to manufacture and well tolerated, with no dose-limiting toxicities in patients with HER2-overexpressing solid tumors.
www.nature.com
February 10, 2025 at 3:23 PM
🚗 NEW #NatureMedicine paper reports results from a first-in-human trial of CAR-macrophages! Safe & feasible to manufacture, efficacy limited. More work needed in this space! @natureportfolio.nature.com #immunotherapy #CARTcells #macrophages
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lucas Schirmer
Rare disease research relies on collecting genomic and clinical data across multiple countries.
Learn more about the Solve-RD project and how it aims to collect and harmonise #raredisease data across multiple European partners.
🧬🖥️
www.ebi.ac.uk/about/news/a...
Learn more about the Solve-RD project and how it aims to collect and harmonise #raredisease data across multiple European partners.
🧬🖥️
www.ebi.ac.uk/about/news/a...
Solve-RD: supporting rare disease data collection and harmonisation
The Solve-RD project standardises genomic and clinical data across Europe to support rare disease research.
www.ebi.ac.uk
January 28, 2025 at 10:19 AM
Rare disease research relies on collecting genomic and clinical data across multiple countries.
Learn more about the Solve-RD project and how it aims to collect and harmonise #raredisease data across multiple European partners.
🧬🖥️
www.ebi.ac.uk/about/news/a...
Learn more about the Solve-RD project and how it aims to collect and harmonise #raredisease data across multiple European partners.
🧬🖥️
www.ebi.ac.uk/about/news/a...
Great piece of work, congrats
Our paper presenting spatial-Mux-seq is now out 🥳 pushing the frontiers of spatial Multiomics! It has been a great pleasure to work alongside with Yanxiang. DBiT is a really flexible platform and this paper clearly demonstrates that. Congrats to all involved!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues - Nature Methods
Spatial-Mux-seq offers a multimodal spatial platform capable of profiling multiple molecular modalities, including the transcriptome, chromatin accessibility, histone modifications and targeted protei...
www.nature.com
January 27, 2025 at 9:32 PM
Great piece of work, congrats
Reposted by Lucas Schirmer
Lysosomes finely control macrophage inflammatory function via regulating the release of lysosomal Fe2+ through TRPML1 channel
www.nature.com/articles/s41...
@naturecomms.bsky.social
www.nature.com/articles/s41...
@naturecomms.bsky.social
January 24, 2025 at 4:46 PM
Lysosomes finely control macrophage inflammatory function via regulating the release of lysosomal Fe2+ through TRPML1 channel
www.nature.com/articles/s41...
@naturecomms.bsky.social
www.nature.com/articles/s41...
@naturecomms.bsky.social
Reposted by Lucas Schirmer
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
January 22, 2025 at 10:46 PM
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...
Great work, Ethan and team, congrats!
New paper out from the lab! Led by @gdfnunes.bsky.social and Lindsay Osso in collaboration with the lab of Dan Denman. Check it out! 🔬 🐭 🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Incomplete remyelination via therapeutically enhanced oligodendrogenesis is sufficient to recover visual cortical function - Nature Communications
Remyelination can restore neural function. Here, the authors characterize the drivers and limits of endogenous remyelination and explore a therapy that rescued remyelination deficits and accelerated n...
www.nature.com
January 19, 2025 at 9:20 AM
Great work, Ethan and team, congrats!
Reposted by Lucas Schirmer
Molecular dynamics of neural stem cells (NSCs) and their surrounding niche in the #aging mouse #hippocampus using multimodal transcriptomics 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multimodal transcriptomics reveal neurogenic aging trajectories and age-related regional inflammation in the dentate gyrus - Nature Neuroscience
Multimodal transcriptomics unveil the molecular dynamics of neural stem cells and their surrounding niche in the aging mouse hippocampus and provide a resource to understand age-related molecular chan...
www.nature.com
January 10, 2025 at 4:59 PM
Molecular dynamics of neural stem cells (NSCs) and their surrounding niche in the #aging mouse #hippocampus using multimodal transcriptomics 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lucas Schirmer
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
A foundation model of transcription across human cell types - Nature
A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...
www.nature.com
January 8, 2025 at 4:27 PM
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
Reposted by Lucas Schirmer
Method of moments framework for differential expression analysis of single-cell RNA sequencing data www.cell.com/cell/fullte...
January 7, 2025 at 2:45 PM
Method of moments framework for differential expression analysis of single-cell RNA sequencing data www.cell.com/cell/fullte...
Reposted by Lucas Schirmer
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Lucas Schirmer
A single-cell mass cytometry-based atlas of the developing mouse brain 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A single-cell mass cytometry-based atlas of the developing mouse brain - Nature Neuroscience
In recent years, valuable mRNA-based developmental atlases of the mouse brain have been made available. Here, the authors use single-cell mass cytometry to build a protein-based single-cell profiling ...
www.nature.com
January 2, 2025 at 3:28 PM
A single-cell mass cytometry-based atlas of the developing mouse brain 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lucas Schirmer
Transsynaptic labeling and transcriptional control of zebrafish neural circuits using trans-Tango 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transsynaptic labeling and transcriptional control of zebrafish neural circuits - Nature Neuroscience
The trans-Tango genetic strategy, which mediates signaling across synapses, was adapted to identify neural connections in a vertebrate nervous system, with synaptic partners confirmed in the retina an...
www.nature.com
January 3, 2025 at 2:45 PM
Transsynaptic labeling and transcriptional control of zebrafish neural circuits using trans-Tango 🧪🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy holidays with a new review about what glial cells are doing in MS patholoy featuring latest developments and tools, thanks @kooistrasm.bsky.social for teaming up and putting this together - have fun reading: onlinelibrary.wiley.com/doi/10.1002/...
Multiple Sclerosis: Glial Cell Diversity in Time and Space
Glial cells and their subtypes are key drivers of lesion progression in multiple sclerosis with roles in both tissue damage and repair depending on the surrounding tissue environment and the function....
onlinelibrary.wiley.com
December 26, 2024 at 11:54 AM
Happy holidays with a new review about what glial cells are doing in MS patholoy featuring latest developments and tools, thanks @kooistrasm.bsky.social for teaming up and putting this together - have fun reading: onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Lucas Schirmer
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
December 25, 2024 at 11:48 PM
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
Big congrats to the team - beautiful single cell atlas of MS brain pathology
news.ki.se/ms-brain-atl...
@annawilliamslab.bsky.social
@willmacnair.bsky.social
@deckardw.bsky.social
@karolinskainst.bsky.social
@edinburghuni.bsky.social
@cp-neuron.bsky.social
and many others....
@annawilliamslab.bsky.social
@willmacnair.bsky.social
@deckardw.bsky.social
@karolinskainst.bsky.social
@edinburghuni.bsky.social
@cp-neuron.bsky.social
and many others....
MS brain atlas could pave the way for personalised treatment
An international research team, including researchers at Karolinska Institutet, has mapped the genes expressed in the brain cells of people with multiple sclerosis (MS). The atlas, which is presented ...
news.ki.se
December 22, 2024 at 9:49 AM
Big congrats to the team - beautiful single cell atlas of MS brain pathology
Reposted by Lucas Schirmer
Fantastic work - congrats
Thrilled to see this paper out!! 🧪
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...
rdcu.be
December 19, 2024 at 8:47 AM
Fantastic work - congrats
Reposted by Lucas Schirmer
Happy to share our review on how different lipids shape microglial biology in #GLIA journal. 💫 onlinelibrary.wiley.com/doi/full/10....
👉🏽with Gaurav Chopra, Caitlin Randolph, and @katherinewalker.bsky.social
👉🏽with Gaurav Chopra, Caitlin Randolph, and @katherinewalker.bsky.social
Lipids: Emerging Players of Microglial Biology
Lipids are crucial in mediating microglial metabolism and function. The microglial lipidome is vast and complex, with over 10,000 lipid species. We discuss key lipid classes and their roles in m...
onlinelibrary.wiley.com
December 17, 2024 at 2:46 PM
Happy to share our review on how different lipids shape microglial biology in #GLIA journal. 💫 onlinelibrary.wiley.com/doi/full/10....
👉🏽with Gaurav Chopra, Caitlin Randolph, and @katherinewalker.bsky.social
👉🏽with Gaurav Chopra, Caitlin Randolph, and @katherinewalker.bsky.social
Reposted by Lucas Schirmer
@marissascavuzzo.bsky.social, @lschirmer.bsky.social, @mtvector.bsky.social, Yin Shen, @sloanlab.bsky.social, Na Sun, @tesarlab.bsky.social, @fabiantheis.bsky.social, @tollkuhn.bsky.social, Maria Antonietta Tosches, Madeleine Urbanek, Christopher Walsh, ...
December 11, 2024 at 5:04 PM
@marissascavuzzo.bsky.social, @lschirmer.bsky.social, @mtvector.bsky.social, Yin Shen, @sloanlab.bsky.social, Na Sun, @tesarlab.bsky.social, @fabiantheis.bsky.social, @tollkuhn.bsky.social, Maria Antonietta Tosches, Madeleine Urbanek, Christopher Walsh, ...
Reposted by Lucas Schirmer
In @science.org this week, Simic, Watchmaker, Zamvil, Okada, and Lim engineer #TCells specific for #CNS #ECM antigens to deliver payloads selectively to the #brain!
Programming tissue-sensing T cells that deliver therapies to the brain
To engineer cells that can specifically target the central nervous system (CNS), we identified extracellular CNS-specific antigens, including components of the CNS extracellular matrix and surface mol...
www.science.org
December 5, 2024 at 10:30 PM
In @science.org this week, Simic, Watchmaker, Zamvil, Okada, and Lim engineer #TCells specific for #CNS #ECM antigens to deliver payloads selectively to the #brain!
Wonderful to see our latest work out in Nat Neurosci side by side with the special collection articles on single-cell omics in neuroscience. Kudos again to @celialm.bsky.social and @paubadiam.bsky.social for carrying this piece over the line www.nature.com/articles/s41...
Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions - Nature Neuroscience
Lerma-Martin et al. generated a paired single-nucleus RNA sequencing and spatial transcriptomics dataset from subcortical multiple sclerosis lesions, identifying spatial niches and key cell interactio...
www.nature.com
December 5, 2024 at 3:31 PM
Wonderful to see our latest work out in Nat Neurosci side by side with the special collection articles on single-cell omics in neuroscience. Kudos again to @celialm.bsky.social and @paubadiam.bsky.social for carrying this piece over the line www.nature.com/articles/s41...