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Leander

@le-and-er.bsky.social
273 followers 137 following 15 posts

Postdoc between Helmholtz Munich and ETH Zurich | Theis Lab & Treutlein Lab | Computational Biology, Machine Learning & Organoids

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Reposted by Leander
mariuslange.bsky.social @mariuslange.bsky.social · 28/03/2025
Happy to share CellAnnotator, a lightweight Python package to query OpenAI models for initial cell type annotations: github.com/quadbio/cell... Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.
github.com
GitHub - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples.
Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator
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Reposted by Leander
dominik1klein.bsky.social @dominik1klein.bsky.social · 23/04/2025
From cell lines to full embryos, drug treatments to genetic perturbations, neuron engineering to virtual organoid screens — odds are there’s something in it for you! Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
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Reposted by Leander
Luke Zappia @lazappi.bsky.social · 18/03/2025
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16
nature.com
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Leander @le-and-er.bsky.social · 21/02/2025
🚨🧠 New paper alert: Stress alters neuronal balance in the developing brain 🧠🚨 Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids. @mpi-psychiatry.bsky.social @drcricru.bsky.social 🧵👇
science.org
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids during brain development leads to priming of the inhibitory neuron lineages in organoids.
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Reposted by Leander
Cedric Boeckx @cedricboeckx.bsky.social · 15/02/2025
Insightful study by L. Dony @anthikrontira.bsky.social @drcricru.bsky.social @binderlabmpip.bsky.social @silvianeuro.bsky.social @fabiantheis.bsky.social on the effects of chronic exposure to glucocorticoids for neurodevelopment. Organoid model reveals amplification of inhibitory neuron cell fate 🧪
science.org
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids during brain development leads to priming of the inhibitory neuron lineages in organoids.
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Reposted by Leander
Vladimir Shitov @shitovhappens.bsky.social · 19/02/2025
When applying machine learning to human health data, it is not enough to just improve a metric by another percent. We have to go deeper. In our perspective in Nature Cell Biology, we discuss caveats and biases of human single-cell data analysis: nature.com/articles/s41... 🧵 1/10
nature.com
Biases in machine-learning models of human single-cell data - Nature Cell Biology
This Perspective discusses the various biases that can emerge along the pipeline of machine learning-based single-cell analysis and presents methods to train models on human single-cell data in order ...
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Reposted by Leander
dominik1klein.bsky.social @dominik1klein.bsky.social · 23/01/2025
Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep
tinyurl.com
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...
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Leander @le-and-er.bsky.social · 19/12/2024
If diving into scientific papers isn’t on your pre-Christmas to-do list, @spiegel.de has you covered! 📰 They featured our Neural Organoid Atlas in a piece on the Human Cell Atlas and related advancements in machine learning. 🤖🧬 It’s a great overview of this exciting field and the work behind it.
spiegel.de
Meinung: »Human Cell Atlas«: Das wird die wichtigste Wissenschaft des 21. Jahrhunderts - Kolumne
Gerade ist ein ganzes Bündel Publikationen aus einem einzigen Forschungsprojekt erschienen. Sie weisen in die Zukunft einer neuen Wissenschaft: Lernende Maschinen helfen jetzt, die Maschinerie des Leb...
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Leander @le-and-er.bsky.social · 21/11/2024
Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...
 Find out how it can serve you ⏬
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nature.com
An integrated transcriptomic cell atlas of human neural organoids - Nature
A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...
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