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

*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

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 ...

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 Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.

#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 - Nature Human enhancers contain a high density of sequence features that are required for their normal in vivo function.

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!

Machine Learning in Computational Biology Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/

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.

Evolution and core processes in gene expression June 26–29, 2025 | Kansas City, Mo.

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! ⬇️

Evolution and core processes in gene expression June 26–29, 2025 | Kansas City, Mo.

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!

Programmatic design and editing of cis-regulatory elements The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...

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 🙂

Opinion | Science Suffers With Trump’s Funding Freeze America’s scientific enterprise demands reliable stewardship, not destabilizing political intervention.

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.

Deep genomic models of allele-specific measurements Allele-specific quantification of sequencing data, such as gene expression, allows for a causal investigation of how DNA sequence variations influence cis gene regulation. Current methods for analyzin...

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