Julia Zeitlinger
@juliazeitlinger.bsky.social
Genomics, AI, sequence-to-function models, mechanisms of the cis-regulatory code. Investigator at the Stowers Institute.
Nice to see this out. This was a completely new research direction for me 7 years ago. I am so grateful for all the people who made this possible!
How do you teach #AI to read #DNA? 🧬
Investigator @juliazeitlinger.bsky.social is featured by @asbmb.bsky.social for her pioneering work using AI to decode the genome’s hidden grammar.
📖 Read more: bit.ly/4os5H8E
Investigator @juliazeitlinger.bsky.social is featured by @asbmb.bsky.social for her pioneering work using AI to decode the genome’s hidden grammar.
📖 Read more: bit.ly/4os5H8E
AI unlocks the hidden grammar of gene regulation
Using fruit flies and artificial intelligence, Julia Zeitlinger’s lab is decoding genome patterns — revealing how transcription factors and nucleosomes control gene expression, pushing biology toward ...
bit.ly
October 18, 2025 at 10:15 PM
Nice to see this out. This was a completely new research direction for me 7 years ago. I am so grateful for all the people who made this possible!
Reposted by Julia Zeitlinger
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity
Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...
www.biorxiv.org
October 16, 2025 at 12:34 PM
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Reposted by Julia Zeitlinger
Emergence of activation or repression in transcriptional control under a fixed molecular context www.pnas.org/doi/10.1073/...
Emergence of activation or repression in transcriptional control under a fixed molecular context | PNAS
Transcription factors (TFs) can be both activators and repressors of gene transcription.
This can manifest as “duality,” where the transcriptional ...
www.pnas.org
September 24, 2025 at 9:19 AM
Emergence of activation or repression in transcriptional control under a fixed molecular context www.pnas.org/doi/10.1073/...
Reposted by Julia Zeitlinger
Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...
September 9, 2025 at 5:44 PM
Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...
Reposted by Julia Zeitlinger
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
September 19, 2025 at 3:03 AM
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
Reposted by Julia Zeitlinger
It is my pleasure to share with you the latest from @jsvejstrup.bsky.social lab, where we look at how the reduction of RNAPII levels has a severe, yet organized transcriptional response in the cell.
September 19, 2025 at 9:15 AM
It is my pleasure to share with you the latest from @jsvejstrup.bsky.social lab, where we look at how the reduction of RNAPII levels has a severe, yet organized transcriptional response in the cell.
Reposted by Julia Zeitlinger
Very nice talk on this at CSH Mechanisms of Eukaryotic Transcription. Elegant approach!
Have you ever wondered how the exact location of a gene affects it's activity?
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
September 19, 2025 at 8:32 PM
Very nice talk on this at CSH Mechanisms of Eukaryotic Transcription. Elegant approach!
Happy to see my lab here, too! Please follow if you are passionate about regulatory genomics and deep learning.
Excited to join Bluesky! Looking forward to seeing the cool research everyone posts!
September 20, 2025 at 1:43 AM
Happy to see my lab here, too! Please follow if you are passionate about regulatory genomics and deep learning.
Reposted by Julia Zeitlinger
Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.
August 19, 2025 at 3:51 PM
Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.
Reposted by Julia Zeitlinger
🍷 + 🧬 = a perfect Friday night. Investigator @juliazeitlinger.bsky.social joined the "Science Over Spirits" series at Baldwin City Distillery to share "How to use Al to read the language of DNA".
August 18, 2025 at 10:13 PM
🍷 + 🧬 = a perfect Friday night. Investigator @juliazeitlinger.bsky.social joined the "Science Over Spirits" series at Baldwin City Distillery to share "How to use Al to read the language of DNA".
Reposted by Julia Zeitlinger
Only ~2% of our DNA codes for proteins. What about the rest?
#AI tools are helping scientists, including Investigator @juliazeitlinger.bsky.social , decipher how non-coding #DNA shapes health and disease. 🧬
📖 Read more @nature.com: go.nature.com/4mLGGEl
#AI tools are helping scientists, including Investigator @juliazeitlinger.bsky.social , decipher how non-coding #DNA shapes health and disease. 🧬
📖 Read more @nature.com: go.nature.com/4mLGGEl
August 19, 2025 at 9:14 PM
Only ~2% of our DNA codes for proteins. What about the rest?
#AI tools are helping scientists, including Investigator @juliazeitlinger.bsky.social , decipher how non-coding #DNA shapes health and disease. 🧬
📖 Read more @nature.com: go.nature.com/4mLGGEl
#AI tools are helping scientists, including Investigator @juliazeitlinger.bsky.social , decipher how non-coding #DNA shapes health and disease. 🧬
📖 Read more @nature.com: go.nature.com/4mLGGEl
Looking forward to my first talk in a distillery!
Check out this pop up event hosted by @stowersinstitute.bsky.social and Baldwin City Distillery!
August 15, 2025 at 1:35 PM
Looking forward to my first talk in a distillery!
Reposted by Julia Zeitlinger
Registration & abstract submission now open for #SRCKC25 AI-Driven Approaches to Emergent Protein Behaviors Oct. 22–24. Join a community of researchers exploring how artificial intelligence is advancing our understanding of complex protein behaviors. #ResearchSky
Register: bit.ly/3GgsQtC
Register: bit.ly/3GgsQtC
July 18, 2025 at 1:43 PM
Registration & abstract submission now open for #SRCKC25 AI-Driven Approaches to Emergent Protein Behaviors Oct. 22–24. Join a community of researchers exploring how artificial intelligence is advancing our understanding of complex protein behaviors. #ResearchSky
Register: bit.ly/3GgsQtC
Register: bit.ly/3GgsQtC
Reposted by Julia Zeitlinger
*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Evaluating the representational power of pre-trained DNA language models for regulatory genomics - Genome Biology
Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of ...
genomebiology.biomedcentral.com
July 16, 2025 at 12:16 PM
*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA
Reposted by Julia Zeitlinger
How bats developed their wings? 🦇
Turns out they reutilize existing gene programs 🔧
Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs
www.nature.com/articles/s41...
Turns out they reutilize existing gene programs 🔧
Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs
www.nature.com/articles/s41...
Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development - Nature Ecology & Evolution
Single-cell comparison of developing bat and mouse limbs reveals conservation of cell populations and gene expression patterns, and suggests repurposing of genes involved in proximal limb development ...
www.nature.com
July 17, 2025 at 1:47 PM
How bats developed their wings? 🦇
Turns out they reutilize existing gene programs 🔧
Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs
www.nature.com/articles/s41...
Turns out they reutilize existing gene programs 🔧
Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs
www.nature.com/articles/s41...
Reposted by Julia Zeitlinger
#cryoEM confluence in Munich #womeninSTEM
July 17, 2025 at 9:44 PM
#cryoEM confluence in Munich #womeninSTEM
There is still time until July 18 to submit an abstract to CSH Asia conference “Nuclear Architecture and Function”. Check out the fantastic lineup of speakers!
www.csh-asia.org?content/2743
www.csh-asia.org?content/2743
WELCOME-Meetings-Cold Spring Harbor Asia
www.csh-asia.org
June 30, 2025 at 7:42 PM
There is still time until July 18 to submit an abstract to CSH Asia conference “Nuclear Architecture and Function”. Check out the fantastic lineup of speakers!
www.csh-asia.org?content/2743
www.csh-asia.org?content/2743
Reposted by Julia Zeitlinger
That’s a GARrrrr wrap! The BeeGees had a great time at the @asbmb.bsky.social Symposium on Gene Expression Evolution @stowersinstitute.bsky.social! Many enlightening talks, great networking, and new collaborations. Thanks to co-organizers @juliazeitlinger.bsky.social, David Arnosti, and Justin Fay!
June 30, 2025 at 4:56 PM
That’s a GARrrrr wrap! The BeeGees had a great time at the @asbmb.bsky.social Symposium on Gene Expression Evolution @stowersinstitute.bsky.social! Many enlightening talks, great networking, and new collaborations. Thanks to co-organizers @juliazeitlinger.bsky.social, David Arnosti, and Justin Fay!
Reposted by Julia Zeitlinger
The @asbmb.bsky.social #Evolution & Core Processes in Gene Expression meeting is underway at the Institute! This week, attendees will dive into gene expression—combining evolutionary biology, synthetic #biology, deep learning, & more.
📍Scenes from check-in as the #science starts to unfold.
📍Scenes from check-in as the #science starts to unfold.
June 26, 2025 at 5:59 PM
The @asbmb.bsky.social #Evolution & Core Processes in Gene Expression meeting is underway at the Institute! This week, attendees will dive into gene expression—combining evolutionary biology, synthetic #biology, deep learning, & more.
📍Scenes from check-in as the #science starts to unfold.
📍Scenes from check-in as the #science starts to unfold.
Reposted by Julia Zeitlinger
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 2:29 PM
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
Reposted by Julia Zeitlinger
This was a great collaboration with Michael Kosicki @axelvisel.bsky.social and Len
Thanks to Boyang (ex-PD) and Vivian (staff scientist) from my lab who helped train & interpret ChromBPNet models.
Thanks to Boyang (ex-PD) and Vivian (staff scientist) from my lab who helped train & interpret ChromBPNet models.
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 7:27 PM
This was a great collaboration with Michael Kosicki @axelvisel.bsky.social and Len
Thanks to Boyang (ex-PD) and Vivian (staff scientist) from my lab who helped train & interpret ChromBPNet models.
Thanks to Boyang (ex-PD) and Vivian (staff scientist) from my lab who helped train & interpret ChromBPNet models.
Reposted by Julia Zeitlinger
Last week I released bpnet-lite v0.5.0.
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
June 18, 2025 at 9:48 AM
Last week I released bpnet-lite v0.5.0.
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
Reposted by Julia Zeitlinger
Reposted by Julia Zeitlinger
This beautiful #MicroscopyMonday shows a mouse embryo that contains fluorescently labeled proteins that are important in early development. Ellie Hart (@juliazeitlinger.bsky.social Lab) #SciSky #ResearchSky 🔬
June 16, 2025 at 3:04 PM
This beautiful #MicroscopyMonday shows a mouse embryo that contains fluorescently labeled proteins that are important in early development. Ellie Hart (@juliazeitlinger.bsky.social Lab) #SciSky #ResearchSky 🔬