Leander
@le-and-er.bsky.social
Postdoc between Helmholtz Munich and ETH Zurich | Theis Lab & Treutlein Lab | Computational Biology, Machine Learning & Organoids
Reposted by Leander
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.
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 - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples.
Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator
github.com
March 28, 2025 at 4:53 PM
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.
Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.
Reposted by Leander
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
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
April 23, 2025 at 9:26 AM
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
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
Reposted by Leander
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
🚨🧠 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
🧵👇
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
🧵👇
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.
www.science.org
February 21, 2025 at 10:14 AM
🚨🧠 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
🧵👇
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
🧵👇
Reposted by Leander
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 🧪
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.
www.science.org
February 15, 2025 at 8:59 AM
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 🧪
Reposted by Leander
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...
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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 ...
nature.com
February 19, 2025 at 6:49 PM
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...
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Reposted by Leander
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
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...
tinyurl.com
January 23, 2025 at 8:42 AM
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
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.
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...
www.spiegel.de
December 19, 2024 at 4:05 PM
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.
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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Find out how it can serve you ⏬
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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...
www.nature.com
November 21, 2024 at 10:11 AM
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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Find out how it can serve you ⏬
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