Very interesting new preprint from @jengreitz.bsky.social lab arguing that rather than there being significant enhancer-promoter compatibility, promoters simply differ in their enhancer responsiveness. If promoters are responsive, they respond to all enhancers. www.biorxiv.org/content/10.6...

🚨 Register now for this spring's #SRCKC26! Explore how the cis-regulatory code, genomic technologies, and #AI models are reshaping our understanding of development. 📍 4/22–24 | Kansas City 🔗 bit.ly/4kUvNAn Hosted by @saukaspengler.bsky.social, @juliazeitlinger.bsky.social, and Neşet Özel.

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/... A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy! @milena-bikova.bsky.social @chrsclrksn.bsky.social

Congratulations to Investigator @juliazeitlinger.bsky.social, Ph.D., who has been named a 2026 NextGen Leader by the Kansas City Business Journal! 🎉 The award recognizes emerging leaders across the #KansasCity region who are making an impact in their fields and in the community. 🔗 bit.ly/4rbNAEE

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation: www.sciencedirect.com/science/arti...

Very excited to share my postdoc research in the @jesserdixon.bsky.social lab at @salkinstitute.bsky.social, out online at @natgenet.nature.com today! www.nature.com/articles/s41... We investigated the function of the cohesin accessory protein NIPBL, making two particularly interesting findings:

Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation - Nature Genetics

Acute depletion of NIPBL reveals a class of chromatin loops that are independent of NIPBL for their maintenance but not their establishment and that NIPBL is necessary for the expression of lineage-de...

nature.com

Deadline: 28 Feb!

Wolfgang Huber@wkhuber.bsky.social · 7mo ago

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps. ascona2026.sciencesconf.org

Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!

Zeitlinger Lab@zeitlingerlab.bsky.social · 6mo ago

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:

The abstract submission deadline is March 6.

Stowers Institute@stowersinstitute.bsky.social · 6mo ago

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

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

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...

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...

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…

sciencedirect.com

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

Our work on TFIID is finally out as preprint!

Zeitlinger Lab@zeitlingerlab.bsky.social · 7mo ago

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:

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

Interested in spending the summer doing #science? Don't miss your chance to apply for the #StowersGrad Summer Scholars program! Applications close 1/16. ⬇️

Stowers Grad School@stowersgrad.bsky.social · 7mo ago

⏳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...

🧬 @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...

science.org

Please consider attending and RT. Great lineup of speakers!

Stowers Institute@stowersinstitute.bsky.social · 8mo ago

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

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...

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 ...

biorxiv.org

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!

Zeitlinger Lab@zeitlingerlab.bsky.social · 9mo ago

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!)

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...

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!

Stowers Institute@stowersinstitute.bsky.social · 10mo ago

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

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...

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 ...

biorxiv.org

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 ...

pnas.org

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...

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/

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.

Very nice talk on this at CSH Mechanisms of Eukaryotic Transcription. Elegant approach!

Christine Moene@cmoene.bsky.social · 11mo ago

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

Happy to see my lab here, too! Please follow if you are passionate about regulatory genomics and deep learning.

Zeitlinger Lab@zeitlingerlab.bsky.social · 11mo ago

Excited to join Bluesky! Looking forward to seeing the cool research everyone posts!

Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.

Evgeny Kvon@evgenykvon.bsky.social · last yr.

Attend the CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing, organized by Len Pennacchio, Alex Stark, Zhiping Weng, and Wei Xie (all blueskyless), featuring a great lineup of speakers and a beautiful location in Suzhou. Abstract submission deadline: August 18th.