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! ⬇️

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...

Check out this great resource of single cell multiome data, cell annotations, regulatory DNA models of cell type resolved chromatin accessibility & comprehensive annotation of motifs & sequence syntax for multiple tissues in early human development 1/

👏 Join us in congratulating Stowers Investigator Jerry Workman, Ph.D., on his election to the National Academy of Sciences—one of the highest honors in #science. Elected for his pioneering #research in gene regulation. #NASMember Read more: bit.ly/4cZ6fhJ

Congratulations to the new NAS member @jkpritch.bsky.social. Was very very happy to hear the news! Exceptionally well deserved!

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics. Preprint: www.biorxiv.org/content/10.1... GitHub: github.com/jmschrei/led...

So excited to see Yawei's manuscript on long-range MPRAs out! Some really great insights into distal enhancer regulation 🙂

My father-in-law, Jack Strominger, and I wrote a letter to the @wsj.com editor about the current threats to science due to Trump's funding freeze. Please repost! www.wsj.com/opinion/scie...

Institutional independence and academic freedom are not national issues — they are global ones. I wrote this open letter to President Garber at @harvard.edu to express my support and solidarity. Let’s speak out together when science and its core values are under threat.

Some encouraging news for cross-gene generalization of allele effects in S2F models. www.biorxiv.org/content/10.1...

A question for the experts: Can you recognize nucleosomes and linker DNA in this data? Find an updated version of our manuscript in www.biorxiv.org/content/10.1...

New #research from the @juliazeitlinger.bsky.social Lab uses #AI to decipher how cells respond to developmental cues, potentially paving the way for personalized #medicine + original artwork from the lab was selected for the cover of Cell Genomics (@cellpress.bsky.social). Read more: bit.ly/426OoSg

Our new preprint is out! Want to better visualize what your sequence-to-function profile learned? Here is PISA. It also comes in a new BPNet package, which can be used to train many genomics data sets, including MNase-seq data.

Pleased to share our latest work. Extremely fun project with @jamesbriscoe.bsky.social l and @jcornwallscoones.bsky.social y.social Curious about how cis-regulatory elements encode information? Passionate about patterning (re)engineering? Please read! (🧵 by Jake below) bsky.app/profile/jcor...

We have released the weights of our model, Decima, that predicts pseudobulk scRNA counts from DNA sequence. Use it for variant effect prediction, interpretation, design and more! Preprint: www.biorxiv.org/content/10.1... Code: github.com/Genentech/de... Original tweetorial: x.com/lal_avantika...

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

Exciting news! Our paper on the cis-regulatory sequence rules of Hippo signaling is finally out. Check it out. www.cell.com/cell-genomic...

An excellent overview of mutual information: medium.com/swlh/a-deep-...