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Reposted by Koen Rademaker

Bas van Steensel lab (NKI) @basvansteensellab.bsky.social · Sep 2

Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!

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Koen Rademaker @krademaker.bsky.social · Jun 30

Bayraktar, Bassett and Lotfollahi labs are studying how neurodegenerative diseases (ALS, PD, AZ) spatially organise 🧠🧬

Join us to generate & analyse wealths of Xenium data:
- Tech specialist: sanger.wd103.myworkdayjobs.com/en-US/Wellco...
- AI postdoc: sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Technical Specialist: Neurodegenerative Disease Spatial Transcriptomics and Data Generation

Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...

sanger.wd103.myworkdayjobs.com

Reposted by Koen Rademaker

Manu Saraswat @manusaraswat.bsky.social · May 16

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

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Reposted by Koen Rademaker

Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

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Reposted by Koen Rademaker

Erick Armingol @erickarmingol.bsky.social · May 15

I’m happy to share that our scCellFie manuscript is finally on bioRxiv — a project that was an amazing opportunity to return to my roots in metabolism!
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025...

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Reposted by Koen Rademaker

Lucía Barbadilla Martínez @luciabarmar.bsky.social · May 14

Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗

Nature Reviews Genetics @natrevgenet.nature.com · May 14

Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social

Predicting gene expression from DNA sequence using deep learning models - Nature Reviews Genetics

Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new in...

go.nature.com

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Reposted by Koen Rademaker

Jimmy Lee @drjimmylee.bsky.social · Mar 12

Thrilled to share our new @naturecomms.bsky.social study with @sam-n-barnett.bsky.social on early vs late #COVID19 lung damage 🫁.
Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org

Wellcome Sanger Institute @sangerinstitute.bsky.social · Mar 10

How lung damage worsens during COVID-19 has been mapped at a cellular level. 🦠

By understanding how our lungs respond to the virus over time, this new knowledge may help identify future therapies for COVID-19.

www.sanger.ac.uk/news_item/ce...

Cellular changes as lung damage worsens in COVID-19 revealed

Researchers uncover cellular changes as damage to alveoli in the lungs progresses during COVID-19.

www.sanger.ac.uk

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Koen Rademaker @krademaker.bsky.social · Mar 3

Another great computational method out of the Bayraktar lab!

Alexander Aivazidis has been a great colleague in our lab and it's amazing to see the capstone of his PhD is now published.

Wellcome Sanger Institute @sangerinstitute.bsky.social · Mar 3

Read ‘Cell2fate infers RNA velocity modules to improve cell fate prediction’ from @sangerinstitute.bsky.social @embl.org and @dkfz.bsky.social in @naturemethods.bsky.social
here: bit.ly/3Diarf5

Cell2fate infers RNA velocity modules to improve cell fate prediction - Nature Methods

Cell2fate improves RNA velocity analysis of single-cell and spatial transcriptomics data by module decomposition of realistic biophysical models of transcription dynamics.

bit.ly

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Koen Rademaker @krademaker.bsky.social · Mar 1

And the talented PhD student Feri from @mhaniffa.bsky.social’s
lab is running for Refuge:
supporting women and their children to overcome the impact of domestic abuse.

www.justgiving.com/page/feri-to...

Feri's fundraiser for Refuge

Help Feri Torabi raise money to support Refuge

www.justgiving.com

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Koen Rademaker @krademaker.bsky.social · Mar 1

Our lab’s computational wizard @drjimmylee.bsky.social is supporting Alzheimer’s Research UK: www.justgiving.com/page/jimmy4a...

Jimmy's fundraiser for Alzheimer's Research UK

Help Jimmy Lee raise money to support Alzheimer's Research UK

www.justgiving.com

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Koen Rademaker @krademaker.bsky.social · Mar 1

Next weekend I will run the Cambridge half marathon with @sangerinstitute.bsky.social colleagues 🏃‍♂️

Two amazing people are running for charities, please support them!

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Reposted by Koen Rademaker

Anshul Kundaje @anshulkundaje.bsky.social · Dec 4

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

Tomàs Montserrat Ayuso @tmontsay.bsky.social · Dec 3

scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
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