Julia Zeitlinger

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 ...

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...

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

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...

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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

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...