Stein Aerts
@steinaerts.bsky.social
Computational biologist interested in deciphering the genomic regulatory code at vib.ai
Reposted by Stein Aerts
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Programming human cell type-specific gene expression via an atlas of AI-designed enhancers
Differentially active enhancers are key drivers of cell type specific gene expression. Active enhancers are found in open chromatin, which can be mapped at genome scale across tissue and cell types. T...
www.biorxiv.org
October 6, 2025 at 4:57 PM
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Reposted by Stein Aerts
One week left to apply! 🚨
We are hiring for two exciting roles at the intersection of AI and life sciences:
👉 Head of the Machine Learning Expertise Unit
👉 LLM Engineer
Don’t miss your chance to apply by October 31!
https://vib.ai/en/opportunities#/job-list
We are hiring for two exciting roles at the intersection of AI and life sciences:
👉 Head of the Machine Learning Expertise Unit
👉 LLM Engineer
Don’t miss your chance to apply by October 31!
https://vib.ai/en/opportunities#/job-list
October 24, 2025 at 5:44 PM
One week left to apply! 🚨
We are hiring for two exciting roles at the intersection of AI and life sciences:
👉 Head of the Machine Learning Expertise Unit
👉 LLM Engineer
Don’t miss your chance to apply by October 31!
https://vib.ai/en/opportunities#/job-list
We are hiring for two exciting roles at the intersection of AI and life sciences:
👉 Head of the Machine Learning Expertise Unit
👉 LLM Engineer
Don’t miss your chance to apply by October 31!
https://vib.ai/en/opportunities#/job-list
Reposted by Stein Aerts
Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
October 17, 2025 at 8:31 AM
Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
Reposted by Stein Aerts
We are thrilled to share our new preprint entitled “The origin and molecular evolution of the mammalian liver cell architecture” www.biorxiv.org/content/10.1...
October 15, 2025 at 12:51 PM
We are thrilled to share our new preprint entitled “The origin and molecular evolution of the mammalian liver cell architecture” www.biorxiv.org/content/10.1...
Reposted by Stein Aerts
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stein Aerts
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍
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...
www.nature.com/articles/s41...
September 24, 2025 at 4:53 PM
The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍
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
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...
Reposted by Stein Aerts
We're growing the VIB.AI Machine Learning Unit, and we're hiring!
📌 Head of the Machine Learning Unit
📌 LLM Engineer
Both roles are based in Leuven, Belgium, at the heart of a thriving research ecosystem.
https://vib.ai/en/opportunities#/job-list
Apply by October 31st.
📌 Head of the Machine Learning Unit
📌 LLM Engineer
Both roles are based in Leuven, Belgium, at the heart of a thriving research ecosystem.
https://vib.ai/en/opportunities#/job-list
Apply by October 31st.
September 23, 2025 at 8:53 AM
We're growing the VIB.AI Machine Learning Unit, and we're hiring!
📌 Head of the Machine Learning Unit
📌 LLM Engineer
Both roles are based in Leuven, Belgium, at the heart of a thriving research ecosystem.
https://vib.ai/en/opportunities#/job-list
Apply by October 31st.
📌 Head of the Machine Learning Unit
📌 LLM Engineer
Both roles are based in Leuven, Belgium, at the heart of a thriving research ecosystem.
https://vib.ai/en/opportunities#/job-list
Apply by October 31st.
Reposted by Stein Aerts
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Stein Aerts
New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT
Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
Faculty Recruitment
chemh.stanford.edu
September 17, 2025 at 6:29 PM
New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT
Reposted by Stein Aerts
Registration deadline for @embo.org workshop EvoChromo extended until September 30.
meetings.embo.org/event/24-evo...
meetings.embo.org/event/24-evo...
September 14, 2025 at 5:00 PM
Registration deadline for @embo.org workshop EvoChromo extended until September 30.
meetings.embo.org/event/24-evo...
meetings.embo.org/event/24-evo...
@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting!
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
September 11, 2025 at 2:34 PM
@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting!
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
Reposted by Stein Aerts
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
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...
Reposted by Stein Aerts
Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
September 9, 2025 at 10:07 AM
Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
Reposted by Stein Aerts
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
September 4, 2025 at 8:22 AM
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
Reposted by Stein Aerts
New from the lab: Fatty Acid Metabolism Sets the Species-specific Tempo of Cortical Development through Protein Acetylation Dynamics. Led by amazing trio: @ryo2iwata.bsky.social , Isabel Gallego, @emirerkol.bsky.social, together with @steinaerts.bsky.social , @fendtlab.bsky.social
Species-specific Rates of Fatty Acid Metabolism Set the Scale of Temporal Patterning of Corticogenesis through Protein Acetylation Dynamics
Developmental processes display temporal differences across species, leading to divergence in organ size and composition. In the cerebral cortex, neurons of diverse identities are generated sequential...
www.biorxiv.org
September 3, 2025 at 12:19 PM
New from the lab: Fatty Acid Metabolism Sets the Species-specific Tempo of Cortical Development through Protein Acetylation Dynamics. Led by amazing trio: @ryo2iwata.bsky.social , Isabel Gallego, @emirerkol.bsky.social, together with @steinaerts.bsky.social , @fendtlab.bsky.social
Reposted by Stein Aerts
Latest from the lab, the beautiful work of Iryna Mohylyak and colleagues describing a temporal developmental transcriptional program for mitochondrial quality control and synaptic connectivity, with @jdejuan-sanz.bsky.social, Olga Corti and @steinaerts.bsky.social
labs
www.nature.com/articles/s41...
labs
www.nature.com/articles/s41...
Temporal transcriptional regulation of mitochondrial morphology primes activity-dependent circuit connectivity - Nature Communications
This study investigates the developmental transcriptional regulation of mitochondrial quality control. Authors identify the Drosophila factor Mirana, homologous to mammalian TZAP, as a key temporal re...
www.nature.com
September 1, 2025 at 8:50 PM
Latest from the lab, the beautiful work of Iryna Mohylyak and colleagues describing a temporal developmental transcriptional program for mitochondrial quality control and synaptic connectivity, with @jdejuan-sanz.bsky.social, Olga Corti and @steinaerts.bsky.social
labs
www.nature.com/articles/s41...
labs
www.nature.com/articles/s41...
Reposted by Stein Aerts
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
August 27, 2025 at 4:20 PM
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
Reposted by Stein Aerts
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
August 21, 2025 at 4:04 PM
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
Reposted by Stein Aerts
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...
🔗 All positions: ki.se/en/about-ki/...
June 25, 2025 at 10:08 AM
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
Reposted by Stein Aerts
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Stein Aerts
Outstanding Faculty opportunity in the broad area of 'life sciences engineering' @EPFL School of Life Sciences, open to both junior and senior researchers. We may prefer metabolism-centric applications but remain open to outstanding applications across domains:
www.epfl.ch/about/workin...
www.epfl.ch/about/workin...
Faculty Position in Life Science Engineering
The School of Life Sciences at EPFL invites applications for a faculty position in life science engineering. Appointments will be at Tenure Track Assistant Professor or at Associate Professor level. W...
www.epfl.ch
August 6, 2025 at 2:11 PM
Outstanding Faculty opportunity in the broad area of 'life sciences engineering' @EPFL School of Life Sciences, open to both junior and senior researchers. We may prefer metabolism-centric applications but remain open to outstanding applications across domains:
www.epfl.ch/about/workin...
www.epfl.ch/about/workin...
Reposted by Stein Aerts
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...
Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS
Genome-wide association studies (GWAS) have identified thousands of trait-associated loci. Prioritizing causal variants within these loci is critical for characterizing trait biology. Statistical fine...
www.biorxiv.org
July 21, 2025 at 2:51 PM
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...
Reposted by Stein Aerts
SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...
July 11, 2025 at 7:34 AM
SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...