Lucas Schirmer

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.

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...

🚨 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...

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/...

Excellent - congrats

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.

🚗 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...

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.

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...

Great piece of work, congrats

Lysosomes finely control macrophage inflammatory function via regulating the release of lysosomal Fe2+ through TRPML1 channel
www.nature.com/articles/s41...
@naturecomms.bsky.social

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...

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!

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...

Molecular dynamics of neural stem cells (NSCs) and their surrounding niche in the #aging mouse #hippocampus using multimodal transcriptomics 🧪🧠

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

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...

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...

Method of moments framework for differential expression analysis of single-cell RNA sequencing data www.cell.com/cell/fullte...

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 ...

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...

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 ...

A single-cell mass cytometry-based atlas of the developing mouse brain 🧪🧠

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...

Transsynaptic labeling and transcriptional control of zebrafish neural circuits using trans-Tango 🧪🧠

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

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....

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/...

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/

Big congrats to the team - beautiful single cell atlas of MS brain pathology

Big congrats

Fantastic work - congrats

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...

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

@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, ...

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...

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!

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...

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...

Excellent, big congrats!

Big congrats!

Beautiful collection - was fun contributing, thanks

Health and Life Science Alliance Explore!Tech Program open till January 24, 2025

Our Alliance provides seed-funds for testing innovative ideas develop high-end technologies.
Call for all Alliance members to apply jointly with Core Facility / Technology Platform members.
Apply by January 24, 2025.
More details on our webpage:
www.health-life-sciences.de/opportunitie...