Sebastiaan (Seb) Vanuytven
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svanuytven.bsky.social
Sebastiaan (Seb) Vanuytven
@svanuytven.bsky.social
Computational postdoc @cedric-blanpain.bsky.social Lab | Tackling cancer one cell at the time | Science, Coffee, Chess, Running & Bouldering | Views are my own
https://behindthebioinformatics.substack.com/
Pinned
For my first Bluesky post, I want to re-highlight my co-first author manuscript published in #Nature last year, where we describe how pharmacological targeting of netrin-1 inhibits epithelial-to-mesenchymal transition ( #EMT) (1/23).
www.nature.com/articles/s41...
Pharmacological targeting of netrin-1 inhibits EMT in cancer - Nature
Netrin-1 is upregulated in cancer models that undergo spontaneous epithelial-to-mesenchymal transition, and its targeting blocks the progression of tumour cells to a late mesenchymal state, suggesting...
www.nature.com
Reposted by Sebastiaan (Seb) Vanuytven
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
Weekly reads 3/11/2025
Prewritten fates: how space, stress, and systemic signals shape cancer

open.substack.com/pub/behindth...

#Immunology #Epigenetics #TrajectoryInference #Cancer #SystemsBiology #Spatial #Singlecell
Weekly reads 3/11/2025
Prewritten fates: how space, stress, and systemic signals shape cancer
open.substack.com
November 11, 2025 at 1:54 PM
Reposted by Sebastiaan (Seb) Vanuytven
Getting Rosalind Franklin’s story right is crucial, because she has become a role model for women going into science

www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 10, 2025 at 9:44 AM
Weekly reads 27/10/25
How cells and whales keep control
open.substack.com
November 2, 2025 at 6:17 PM
Weekly reads 20/10/25:
"From aging clones to generative genomics: evolution meets AI in modern biology"

open.substack.com/pub/behindth...

#AIinBiology #SingleCell #SpatialOmics #MultiOmics #DrugDiscovery #Genomics #DeepLearning
Weekly reads 20/10/25
From aging clones to generative genomics: evolution meets AI in modern Biology
open.substack.com
October 26, 2025 at 1:16 PM
Couldn’t be prouder of my friend Nacho for publishing his first preprint! 🎉

Multi-omics integration and batch correction using a modality-agnostic deep learning framework www.biorxiv.org/content/10.1...

#SingleCell #SpatialOmics #DeepLearning
Multi-omics integration and batch correction using a modality-agnostic deep learning framework
State-of-the-art biotechnologies allow the detection of different molecular species on the same biological sample, generating complex highly-dimensional multi-modal datasets. Gaining a holistic unders...
www.biorxiv.org
October 23, 2025 at 7:47 AM
Reposted by Sebastiaan (Seb) Vanuytven
Big, beautiful trees!!

SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.

www.biorxiv.org/content/10.1...
October 14, 2025 at 2:37 PM
Weekly reads 29/9/25

🧠 DNA that learns like a neural net
🧬 SMAD4 flips roles by organ in PDAC
🧫 scPortrait + BAG-seq + RAEFISH push imaging & multi-omics forward
🤖 scKAN & Tangram2 make #single-cell #AI interpretable & #spatial

open.substack.com/pub/behindth...
Weekly reads 29/9/25
When molecules learn and models see
open.substack.com
October 5, 2025 at 3:24 PM
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
www.cell.com/cell/fulltex...
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
RAEFISH delivers whole-transcriptome (>20,000 genes) imaging at single-molecule resolution in cells and tissues and enables direct gRNA detection for high-content, image-based CRISPR screens.
www.cell.com
October 2, 2025 at 7:23 AM
Reposted by Sebastiaan (Seb) Vanuytven
How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology
McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.
www.nature.com
September 29, 2025 at 4:45 PM
Reposted by Sebastiaan (Seb) Vanuytven
So happy to see that Nature Cancer had chosen our picture as the cover of their September issue together with the publication of our paper on stem cell plasticity during prostate tumor initiation. Congratulations to @ChenJiang919 and @yura__song
🍂Our September issue is OUT NOW!

Featuring, among others:
- A Perspective on #drugconjugates
- #immunotherapy studies
- research on GBM invasion
- method for #singlecell analyses of #CTCs

🔗 www.nature.com/natcancer/vo...
September 28, 2025 at 4:51 PM
Reposted by Sebastiaan (Seb) Vanuytven
We are hiring a Postdoctoral Fellow in Computational Biology at EMBL-EBI (Cambridge, UK). Focus: methods to study cell–cell communication from sc/spatial omics data (building on LIANA+ and NicheNet), in collab with @yvansaeys.bsky.social VIB/Ghent.

Details & apply by 13/10/25: tinyurl.com/4shdw8dk
Current Vacancies
Whether you're a scientist, IT specialist, accountant or administrator, you'll help us tackle the challenges of improving human health & biodiversity in the face of climate change on a global scal...
tinyurl.com
September 26, 2025 at 10:16 AM
Weekly reads 22/09/25

🧠 Bladder cancer co-opts macrophages
👁️ OSK factors rejuvenate vision via GSTA4
🧬 SPP1 sustains aggressive pancreatic tumors
📍 AMICI + EpiAgent + scFME push spatial & single-cell AI forward

#Cancer #Aging #SingleCell #Spatial #AI

open.substack.com/pub/behindth...
Weekly reads 22/09/25
Macrophages, molecules, and models: highlights across cancer and computation
open.substack.com
September 28, 2025 at 11:54 AM
Reposted by Sebastiaan (Seb) Vanuytven
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
September 24, 2025 at 3:12 PM
Reposted by Sebastiaan (Seb) Vanuytven
We have two open positions for a ML and a LLM engineer to launch a machine learning expertise unit in our center @vibai.bsky.social, see vib.ai/en/opportuni...
vib.ai
September 23, 2025 at 11:21 AM
Weekly reads 15/09/22

🧬 DNA methylation as both cancer driver & evolutionary clock
🧫 SPACE brings CRISPR screens into 3D tissues
🤖 AI designs functional phages
🧠 SCLC plugs into brain circuits

open.substack.com/pub/behindth...

#Cancer #SingleCell #SpatialOmics #AI #Epigenetics
Weekly reads 15/09/22
From epigenetic evolution to AI-designed phages
open.substack.com
September 21, 2025 at 7:55 AM
Reposted by Sebastiaan (Seb) Vanuytven
My lab @mpi-muenster.bsky.social is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏 jobs.mpi-muenster.mpg.de/jobposting/0...
Computational image analyst (m/f/d)
The Max Planck Institute for Molecular Biomedicine in Münster, Germany, has an opening for a
jobs.mpi-muenster.mpg.de
September 12, 2025 at 6:17 AM
Reposted by Sebastiaan (Seb) Vanuytven
1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...
September 10, 2025 at 3:48 PM
Reposted by Sebastiaan (Seb) Vanuytven
🚀 We’re hiring! Multiple postdocs & a program manager to push the frontiers of explainable AI in cutting-edge biomedical research—Alzheimer’s, aging, cancer & medical AI. Start immediately. Friends, please RT🙏

Learn more: drive.google.com/file/d/15mMR...

#postdocjobs #AI #BiomedicalScience
September 10, 2025 at 2:16 AM
From nerve damage that blocks #Immunotherapy to mitochondria hand-offs, mechanical squeezing, & smarter spatial integration, this week’s weekly reads show cancer is a master of tricks 🧠🧬

#CancerResearch #SpatialOmics #CompBio

open.substack.com/pub/behindth...
Weekly reads 25/8/25
When cancer talks to nerves, fibroblasts and machines
open.substack.com
August 31, 2025 at 11:53 AM
Weekly reads 18/8/25:

- Tumor architecture + nuclear shape fuel CRC heterogeneity
- Viral infections awaken dormant #cancer
- Engineered bacteria launch an oncolytic virus
- Axonal injury drives #glioblastoma

#SingleCell #SpatialOmics #SystemsBiology

open.substack.com/pub/behindth...
Weekly reads 18/8/25
From structure to signals: new frontiers in cancer, spatial biology, and synthetic therapies
open.substack.com
August 24, 2025 at 8:44 AM
Weekly reads 11/8/25:

- Reprogramming CAFs to boost immunotherapy
- When & how neural nets learn DNA motifs
- Decipher: a generative model for derailed cell states
- Tissue-of-origin constraints on metastasis
- Spatial deconvolution methods adapt to ATAC

open.substack.com/pub/behindth...
Weekly reads 11/8/25
Reprogramming biology: CAFs, motifs, metabolism, and more...
open.substack.com
August 17, 2025 at 9:57 AM