Systems Immunology Lab at @GeneCenter_LMU
Munich, Germany
Joined November 2021
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📢Our new package SlideCNA for spatial copy number alteration detection in spatial transcriptomics data is now out in Genome Biology: doi.org/10.1186/s13059-025-0…
📢BoReMi for manual registration of spatial expression data 🧬 and microscopy images 🔬. When automated tools fail 🥺 BoReMi is your friend💪. Lightweight Jupyter interface, Single cell matching, Non-linear alignment, and more. #spatial_omics #registration #groundtruth
Paper: doi.org/10.1371/journal.pcbi…
Code: github.com/jaspreetishar/BoR…
Test it online ⬆️
📢 Out in Nat Med: Single-cell, nucleus & 4 types of spatial expression data across the clinicopathological diversity of metastatic breast cancer!
We find surprising within-patient stability, spatial EMT phenotypes, local immune exclusion, and more + comparison across methods🔗➡️
📰Paper: nature.com/articles/s41591-0…
🧬Data: singlecell.broadinstitute.or…
🗺️CellxGene: cellxgene.cziscience.com/col…
🗂️HTAN data coordination: humantumoratlas.org/publicat…
🛠️Code: github.com/klarman-cell-obse…
Systems Immunology Lab retweeted
"What do you most hope spatial molecular profiling will help us understand?"
Cell Systems asked @FertigLab @DrMingyaoLi @CosciaLab @KlughammerLab Qing Nie @CJM_lab @ahmetfcoskun and me this question and today you can check out our answers!
cell.com/cell-systems/fullte… @CellSystemsCP
Systems Immunology Lab retweeted
For our first student talk of the day, we welcome @momo_1995mo, QBM student at @KlughammerLab! Mohammad is presenting part of his work and connecting physiological and pathological immune activation scenarios! 🧪
#qbmretreat23
Systems Immunology Lab retweeted
Now on stage is QBM student @JLQuattro, from @KlughammerLab!
Moving the day towards methods, Jan is talking about TACCO, a tool for deciphering high-dimensional biological data. Go, Jan! 🌮
Systems Immunology Lab retweeted
📢 PhD position available in my lab ‼️
🧑🔬 🧑💻 The candidate will investigate the molecular regulation of lymphocyte development using cutting-edge single-cell multimodal approaches
✉️ Reach out via DM or email to discuss in more detail
➡️ Apply via semm.it/education/how-apply
Systems Immunology Lab retweeted
🥳🥳APPLY NOW!!!🥳🥳👇👇QBM is open for applications! 👇👇Please RT & like!🎊🎉
apply here: qbm.genzentrum.lmu.de/applic…
and check out our PhD program:🧪🧫🧬🔬⚗️🩹
qbm.genzentrum.lmu.de/phd-pr…
Systems Immunology Lab retweeted
😲🫢Hard to believe, 39 years ago in May, the research focus "Fundamentals and Applications of Gene Technology" was founded at a ceremony in the Senate Hall of @LMU_Muenchen
🧬The birth of today's Gene Center!
🤔😃Sounds like we can have a big party next year!🥳🥂🎉😀🍻😃🪩💃🕺
📢Come work with us on turning high-dimensional data into biomedical insights. Postdoc or Research Scientist position in single cell & spatial transcriptomics/ compBiomed available. Applications from all quantitative fields 💻 welcome!
@GeneCenter_LMU
⬇️genzentrum.uni-muenchen.de/c…
Systems Immunology Lab retweeted
🌮Tacco is now published in Nature Biotechnology: nature.com/articles/s41587-0… And even more importantly, the package is now also available on conda 🐍: anaconda.org/conda-forge/tac… #SingleCell #spatialomics
🌮From molecular to tissue scale (and beyond): TACCO helps you crack your (spatial) omics data!
Check out our preprint doi.org/10.1101/2022.10.02.5… and Python package github.com/simonwm/tacco
Joint work with @moriel_noa @InbalDavidi @KlughammerLab #AvivRegev @mor_nitzan et al.
🧵1/n
Systems Immunology Lab retweeted
Cheers to @JLQuattro on his first paper, and to everyone that collaborated for TACCO to happen! 🥳
@MunichQbm @GeneCenter_LMU @MagesLab
Check the full paper on nature.com/articles/s41587-0…
Systems Immunology Lab retweeted
TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics go.nature.com/3I99svU
Systems Immunology Lab retweeted
A few weeks ago we just started with a dot product!!😌 inspired by the book of @Sentdex @daniel_kukiela we've created an CNN like LeNet from rare @ThePSF Thanks to the students that have attented the course! Was fun teaching🥰👍👍! @GeneCenter_LMU @HIDAdigital @KlughammerLab
Systems Immunology Lab retweeted
🧬Proud to have contributed to this amazing analysis of genome-scale, base-resolution DNA methylation profiles across 580 ❗️ animal species. Congratulations to the entire team and to @KlughammerLab, @Bocklab and @CeMM_News
Our “epigenetic zoo” is finally published! DNA methylation profiles for 580 animal species and 2443 tissue samples provide an evolutionary perspective on the epigenome.
Full paper: nature.com/articles/s41467-0… (open access) #epigenome #evolution #crossspecies #epigenetics [1/9]
📢Come work with us on turning high-dimensional data into biomedical insights. Postdoc position in single cell & spatial transcriptomics/ computational biomedicine available. Applications from all quantitative fields 💻 welcome! @GeneCenter_LMU ⬇️genzentrum.uni-muenchen.de/c…
Systems Immunology Lab retweeted
What an amazing resource- a #DNA methylome zoo! 🧬 🐄 🐕 🐈⬛ 🐎 🐙 🐠…
@BockLab @KlughammerLab @daria_rom__
Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species | Nature Communications go.nature.com/3CZ4jVP
