Niklas Schmacke

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

Want your biology AI model to learn spatial relationships? Add images as a modality!

scPortrait enables fast, standardized generation and use of single-cell image datasets, powering AI/ML-based discovery.

GitHub ⭐️: github.com/MannLabs/scP...
Preprint 📚: www.biorxiv.org/content/10.1...

Programme Leader Track - MRC Laboratory of Medical Sciences We are recruiting Programme Leader Track positions focusing on 1) Metabolic Physiology using murine and/or human in vivo models and 2) Immunometabolism.

We're recruiting junior team leaders @mrc-lms.bsky.social This time we're looking for those working in human metabolic disease.

It's a great place to start your lab. Fantastic colleagues, exciting science, world class facilities. Join us!

lms.mrc.ac.uk/work/vacanci...

Tomtom-lite: Accelerating Tomtom enables large-scale and real-time motif similarity scoring Summary Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete characters. With the growing prevalence of machine lear...

I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.

www.biorxiv.org/content/10.1...

NUCLEATE Cluster of Excellence: beacon of nucleic acid research The new NUCLEATE Cluster of Excellence is all about nucleic acids. The research alliance seeks to better understand their various functions and open up new areas of application.

Wow, so cool!🌟
Excellence in Nucleic Acid Sciences and Technologies: NUCLEATE Cluster selected for national recognition
Led by spokesperson Veit Hornung, the NUCLEATE Cluster secures funding in Germany’s Excellence Strategy
🥂🥳🤩
www.lmu.de/en/newsroom/...
@v-hornung.bsky.social

Join us for our next Kipoi Seminar with Laura Martens, Gagneur lab, TUM @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
🐕scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
📅Wed May 7, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky

Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease...

New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology.
www.biorxiv.org/content/10.1...

Hi, everyone! My name is Alex. I'm a microbiologist/cell biologist/biochemist, and I'm sharing some of my career biography today for #YoungScientistNetworking.
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Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems

CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems

Congrats Tana Wein! Thank you Kranzusch lab!
www.nature.com/articles/s41...

Had the pleasure of hearing this story at the recent inflammasomes meeting #3 in Munich. Really exciting data!