Koen Rademaker
@krademaker.bsky.social
Running code and kilometers in Cambridge.
Spatial omics, neurodevelopment and more in Bayraktar lab,
@sangerinstitute.bsky.social
Spatial omics, neurodevelopment and more in Bayraktar lab,
@sangerinstitute.bsky.social
Reposted by Koen Rademaker
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1
February 8, 2026 at 4:54 PM
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
The webinar series on spatial transcriptomics analysis is now open for registration!
Join me on 18 March to learn how we at @bayraktarlab.bsky.social integrate single-cell and spatial transcriptomics to map the rules of neurological conditions.
Join me on 18 March to learn how we at @bayraktarlab.bsky.social integrate single-cell and spatial transcriptomics to map the rules of neurological conditions.
We're pleased to announce that our next webinar series is now live.
Decoding spatial transcriptomics through sequences, pixels, and bioinformatics will run from 18 February – 8 April 2026: www.ebi.ac.uk/training/eve...
Coordinated by: @ajaymishra24.bsky.social, Kristy Ou, and Flaminia Zane.
🧬🖥️📊
Decoding spatial transcriptomics through sequences, pixels, and bioinformatics will run from 18 February – 8 April 2026: www.ebi.ac.uk/training/eve...
Coordinated by: @ajaymishra24.bsky.social, Kristy Ou, and Flaminia Zane.
🧬🖥️📊
January 29, 2026 at 8:03 PM
The webinar series on spatial transcriptomics analysis is now open for registration!
Join me on 18 March to learn how we at @bayraktarlab.bsky.social integrate single-cell and spatial transcriptomics to map the rules of neurological conditions.
Join me on 18 March to learn how we at @bayraktarlab.bsky.social integrate single-cell and spatial transcriptomics to map the rules of neurological conditions.
Beyond excited to share my first work with Omer's group at Sanger!
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
Which human brain circuits are implicated in neurodevelopmental conditions? We bridged human genetics, spatial transcriptomics and neurodevelopment to discover the convergence of autism-associated genes in the developing human thalamus! www.biorxiv.org/content/10.1...
November 11, 2025 at 9:00 PM
Beyond excited to share my first work with Omer's group at Sanger!
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
Reposted by Koen Rademaker
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!
September 2, 2025 at 5:26 PM
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!
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...
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
June 30, 2025 at 10:54 AM
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...
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...
Reposted by Koen Rademaker
🧠 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🧵👇
May 16, 2025 at 10:05 AM
🧠 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🧵👇
Reposted by Koen Rademaker
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 🧵
May 16, 2025 at 11:44 AM
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 🧵
Reposted by Koen Rademaker
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...
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025...
May 15, 2025 at 8:21 AM
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...
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025...
Reposted by Koen Rademaker
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
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
May 14, 2025 at 3:43 PM
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
Reposted by Koen Rademaker
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
Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org
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...
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
March 12, 2025 at 6:35 AM
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
Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org
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.
Alexander Aivazidis has been a great colleague in our lab and it's amazing to see the capstone of his PhD is now published.
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
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
March 3, 2025 at 1:16 PM
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.
Alexander Aivazidis has been a great colleague in our lab and it's amazing to see the capstone of his PhD is now published.
Next weekend I will run the Cambridge half marathon with @sangerinstitute.bsky.social colleagues 🏃♂️
Two amazing people are running for charities, please support them!
Two amazing people are running for charities, please support them!
March 1, 2025 at 2:00 PM
Next weekend I will run the Cambridge half marathon with @sangerinstitute.bsky.social colleagues 🏃♂️
Two amazing people are running for charities, please support them!
Two amazing people are running for charities, please support them!
Reposted by Koen Rademaker
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/
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!
2/8
2/8
December 4, 2024 at 7:06 AM
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/