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:

Deadline: 28 Feb!

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.

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...

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!

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. ⬇️

🧬 @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!

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...

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!

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!

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...

Emergence of activation or repression in transcriptional control under a fixed molecular context www.pnas.org/doi/10.1073/...

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!

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

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

🍷 + 🧬 = 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".

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

Looking forward to my first talk in a distillery!

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

*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

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...

#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

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!

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.

#AlphaGenome: #AI for better understanding the #genome deepmind.google/discover/blo...

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

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.

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`

In vivo mapping of mutagenesis sensitivity of human enhancers www.nature.com/articles/s41...

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 🔬

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC! Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track). Registration is now open! (Link below) Please retweet!

Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.

🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics" Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106

It was fun to write this piece with such a great team of colleagues in the field! Also grateful for discussions and feedback from @anshulkundaje.bsky.social @avsecz.bsky.social

There is still time to submit an abstract! The deadline is now extended to May 14.

Like regulatory genomics? Don’t miss this very fun meeting! May 7 is the deadline for early registration and abstract submission www.asbmb.org/meetings-eve...

Register below! ⬇️