Niklas Schmacke
@nik-as.bsky.social
Shared PostDoc in Veit Hornung’s lab and Fabian Theis’ lab in Munich. Let‘s go.
Reposted by 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...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 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...
🔗 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...
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...
September 28, 2025 at 10:10 AM
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...
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...
Reposted by Niklas Schmacke
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...
It's a great place to start your lab. Fantastic colleagues, exciting science, world class facilities. Join us!
lms.mrc.ac.uk/work/vacanci...
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.
lms.mrc.ac.uk
July 7, 2025 at 8:14 AM
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...
It's a great place to start your lab. Fantastic colleagues, exciting science, world class facilities. Join us!
lms.mrc.ac.uk/work/vacanci...
Reposted by Niklas Schmacke
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
June 3, 2025 at 6:02 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Niklas Schmacke
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
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
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.
www.lmu.de
May 22, 2025 at 6:03 PM
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
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
Reposted by Niklas Schmacke
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
🐕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
May 2, 2025 at 11:01 AM
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
🐕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
Reposted by Niklas Schmacke
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 5, 2025 at 3:40 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Niklas Schmacke
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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April 24, 2025 at 4:41 PM
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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Reposted by Niklas Schmacke
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...
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...
January 30, 2025 at 3:40 AM
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...
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!
Sterile- or pathogen-induced endolysosomal damage activate the NLRP6 inflammasome in human intestinal epithelial cells https://www.biorxiv.org/content/10.1101/2025.01.23.634286v1
January 25, 2025 at 8:42 AM
Had the pleasure of hearing this story at the recent inflammasomes meeting #3 in Munich. Really exciting data!