Julia Zeitlinger
@juliazeitlinger.bsky.social
Genomics, AI, sequence-to-function models, mechanisms of the cis-regulatory code. Investigator at the Stowers Institute.
Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!
The new updates for Charles McAnany’s preprint “Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models” (www.biorxiv.org/content/10.1...) are up!
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
www.biorxiv.org
February 6, 2026 at 4:25 PM
Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!
The abstract submission deadline is March 6.
Want to share your #science on stage? #SRCKC26 will feature talks selected from submitted abstracts, alongside invited speakers & tandem talks.Your research could help shape the conversation. Meeting organized by Neşet Özel, @saukaspengler.bsky.social, & @juliazeitlinger.bsky.social.
bit.ly/4rMvVoI
bit.ly/4rMvVoI
Stowers Research Conferences: Development, Regulatory Genomics & AI
Organized by Julia Zeitlinger, Ph.D., Neşet Özel, Ph.D., and Tatjana Sauka-Spengler, Ph.D.
bit.ly
February 6, 2026 at 4:15 PM
The abstract submission deadline is March 6.
Reposted by Julia Zeitlinger
AlphaGenome is out in @nature.com today along with model weights! 🧬
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
January 28, 2026 at 9:02 PM
AlphaGenome is out in @nature.com today along with model weights! 🧬
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
Reposted by Julia Zeitlinger
Today @nature.com, it's #AlphaGenome, to decipher and determine functionality of the regulatory (very challenging) variants in our genome.
Another big step of AI for advancing life science
nature.com/articles/s41...
Another big step of AI for advancing life science
nature.com/articles/s41...
January 28, 2026 at 4:19 PM
Today @nature.com, it's #AlphaGenome, to decipher and determine functionality of the regulatory (very challenging) variants in our genome.
Another big step of AI for advancing life science
nature.com/articles/s41...
Another big step of AI for advancing life science
nature.com/articles/s41...
Reposted by Julia Zeitlinger
Finally had a chance to read this beautiful paper from Susan Mackem's lab. It's interesting that even well-established paradigms, like Sonic Hedgehog's role as a traditional morphogen in limb development, can be proven wrong over time.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Sonic hedgehog is not a limb morphogen but acts as a trigger to specify all digits in mice
Limb patterning by Sonic hedgehog (Shh), via either graded spatial or temporal signal integration, is a paradigm for “morphogen” function, yet how Shh…
www.sciencedirect.com
January 26, 2026 at 10:39 PM
Finally had a chance to read this beautiful paper from Susan Mackem's lab. It's interesting that even well-established paradigms, like Sonic Hedgehog's role as a traditional morphogen in limb development, can be proven wrong over time.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Julia Zeitlinger
Thanks to
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
RECOMB-RSG 2026 | Regulatory Genomics Satellite
recomb-rsg.github.io
January 27, 2026 at 4:21 AM
Thanks to
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
Our work on TFIID is finally out as preprint!
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
TLDR; TFIID behaves differently depending on promoter type. More below:
High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo
TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with and functions at different promoter types in vivo ...
www.biorxiv.org
January 9, 2026 at 11:52 PM
Our work on TFIID is finally out as preprint!
Reposted by Julia Zeitlinger
Don't miss Bing Ren (@columbiauniversity.bsky.social) as the keynote speaker for #SRCKC26! Ren's work in #epigenomics and gene regulation continues to transform our understanding of #genome function. Organized by: @saukaspengler.bsky.social, @juliazeitlinger.bsky.social, Neşet Özel
🔗 bit.ly/4rMvVoI
🔗 bit.ly/4rMvVoI
January 8, 2026 at 4:35 PM
Don't miss Bing Ren (@columbiauniversity.bsky.social) as the keynote speaker for #SRCKC26! Ren's work in #epigenomics and gene regulation continues to transform our understanding of #genome function. Organized by: @saukaspengler.bsky.social, @juliazeitlinger.bsky.social, Neşet Özel
🔗 bit.ly/4rMvVoI
🔗 bit.ly/4rMvVoI
Reposted by Julia Zeitlinger
Interested in spending the summer doing #science? Don't miss your chance to apply for the #StowersGrad Summer Scholars program! Applications close 1/16. ⬇️
⏳Don’t miss the chance to spend your summer doing #science alongside Stowers researchers! Summer Scholars Program applications close next Friday, 1/16.
🔗 Apply here: www.stowers.org/gradschool/s...
🔗 Apply here: www.stowers.org/gradschool/s...
January 6, 2026 at 6:37 PM
Interested in spending the summer doing #science? Don't miss your chance to apply for the #StowersGrad Summer Scholars program! Applications close 1/16. ⬇️
Reposted by Julia Zeitlinger
🧬 @science.org A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform | Science www.science.org/doi/10.1126/... @ckadoch.bsky.social @danafarber.bsky.social @harvardmed.bsky.social @broadinstitute.org @hhmi-science.bsky.social 🔬 #chromatin #transcription #cancer 🧫
A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform
Mammalian SWI/SNF chromatin remodeling complexes modulate DNA accessibility and gene expression; however, their genomic targeting mechanisms remain incompletely understood. Here, we identify SWIFT (SW...
www.science.org
January 1, 2026 at 7:53 PM
🧬 @science.org A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform | Science www.science.org/doi/10.1126/... @ckadoch.bsky.social @danafarber.bsky.social @harvardmed.bsky.social @broadinstitute.org @hhmi-science.bsky.social 🔬 #chromatin #transcription #cancer 🧫
Please consider attending and RT. Great lineup of speakers!
Registration is OPEN for #SRCKC26: Development, Regulatory Genomics & AI! Organized by Neşet Özel, @juliazeitlinger.bsky.social, & @saukaspengler.bsky.social.
Join us April 22–24 in #KansasCity to explore cis-regulatory logic, genomics & #AI.
📅 Register now: bit.ly/4rMvVoI
Join us April 22–24 in #KansasCity to explore cis-regulatory logic, genomics & #AI.
📅 Register now: bit.ly/4rMvVoI
December 18, 2025 at 9:20 PM
Please consider attending and RT. Great lineup of speakers!
Reposted by Julia Zeitlinger
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 4:45 PM
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 11:38 PM
Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!
Reposted by Julia Zeitlinger
It's always special when you find your own paper in the table of contents of the journal 😍
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
November 18, 2025 at 4:11 PM
It's always special when you find your own paper in the table of contents of the journal 😍
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
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