Niklas Schmacke
@niklas_a_s
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Shared PostDoc in Veit Hornung’s lab and Fabian Theis’ lab in Munich. Let‘s go.
Joined September 2011
One week ago, I finally defended my PhD ✨ I am deeply grateful to my supervisor @v_hornung, as well as to all collaborators and present and past lab members who made these past years fly by. Looking forward to everything that comes next.
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I would say my biggest takesway from spending the last 8 months singlemindedly studying bioML is that understanding the biology actually is important
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🚀 Excited to share our preprint scConcept: a contrastive pretraining framework for technology-agnostic single-cell representations. We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics. 📘
biorxiv.org
Recent large-scale single-cell foundation models have shown promise for exploring cellular states, yet they often underperform compared to simpler, domain-specific methods, raising concerns about...
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Munich is now the #2 AI ecosystem in Europe (after Paris) and #11 globally, per Dealroom’s Global Tech Ecosystem Index 2025! 🇩🇪🤖🇫🇷 Proud of the growing strength of the Bavarian AI ecosystem 👉 https://t.co/Z4KgwtP9Gh 🔗 https://t.co/LmO0xPSJyJ
#AI #Munich #baiosphere
dealroom.co
This report is the conclusion of a data-driven analysis of 201 tech ecosystems. This set of actionable benchmarks is meant as a tool to help ecosystems understand and measure their maturity and...
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🧬 Excited to share Nicheformer out now in Nature Methods! A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization. Led by Ale Tejada & Anna Schaar 👏 👉 https://t.co/ba9DX7h2xg
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🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): https://t.co/NSfnCblwHh We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it.🔁
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scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @thisisjohahi @lauradmartens @gagneurlab @TU_Muenchen
https://t.co/NEEyeEgtAZ
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Using machine learning from biological structures to increase the resolution of microscopy images during acquisition. Very cool! Acting as an engine optimizing iterative data acquisition in real time instead of just being an endpoint is a compelling use case for ML in biology.
Fourier-based transformers for adaptive optics—no guide stars, no wavefront sensor High-resolution tissue imaging often breaks down inside real specimens: cells bend light, blurring fine structure and wasting photons. Classical adaptive optics fixes this using guide stars—tiny
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🚀 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. 🔗 https://t.co/VXHrCBgdDh
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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 ⭐️: https://t.co/EEiqWnkLgZ Preprint 📚:
biorxiv.org
Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are...
Our preprint on scPortrait is out! We built a framework + format to turn microscopy into standardized single-cell image datasets. scPortrait scales >100M cells, integrates with scverse, & enables cross-modality modeling from morphology to transcriptomics https://t.co/50rSlikuQj
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🎉🎬 @zeynepakata erhält den „ZukunftsWissen“-Preis von Leopoldina & Commerzbank-Stiftung. Die Informatikerin @TU_Muenchen @HelmholtzMunich spricht über ihre Forschung zur erklärbaren #KI. Zum vollständigen Video auf YouTube: https://t.co/wKK2oYneJY
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Marleen Bérouti (@BeroutiMarleen) from the lab of Veit Hornung @LMU_Muenchen (Ludwig-Maximilians-Universität München). 👏🏾 2/
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In the latest issue! Pseudouridine RNA avoids immune detection through impaired endolysosomal processing and TLR engagement
cell.com
Toll-like receptors (TLRs) 7 and 8 detect RNA degradation products to sense infection. However, modified nucleosides common in self-RNA—most notably pseudouridine—evade recognition. This study finds...
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🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉 We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025! Details in thread! 🧵 1/3
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#InterferonPower! Thrilled for our latest work @CellCellPress! With @dfrboehmer, we dug into tons of papers & created what we hope will be a go-to resource for immunologists & non-immunologist about type I, II, III (& IV😉) #interferons! Free link 👉 https://t.co/gYwGir0npB
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We discovered that the skull bone marrow has direct connections to brain surface & mirrors brain inflammation, making it a new site for diagnosing & monitoring brain pathologies. Kolabas…Ertürk, Cell: https://t.co/o8jTfgI1Ms
https://t.co/2sPQra6sHZ
https://t.co/NWNp39efaX
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Excited to share the first paper of my PhD, published in @jbiolchem. Huge thanks to all authors, especially to co-first author @sbauernfried, collaborators from @Horswill_Lab and @labs_mann, and my supervisor @v_hornung! https://t.co/Yl6FYGEnkb
jbc.org
Interleukin-1β (IL-1β) is a pivotal mediator of innate immunity, essential for orchestrating the acute inflammatory response. While the canonical activation of IL-1β involves cleavage of its inactive...
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Really excited to share this Perspective from John Danial covering how technology is moving the field of fluorescence microscopy toward structural biology.
nature.com
Nature Methods - This Perspective introduces a framework for defining, measuring and reporting resolution in super-resolution microscopy and details the current state of the art in using...
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