Emily Wong

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

We are thrilled that our study on the evolution of gene regulation in mammalian cerebellum development – led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social – is now out in @ScienceMagazine! www.science.org/doi/10.1126/...

The Age of Academic Slop is Upon Us what happens when AI automates "normal science"?

The Age of Academic Slop is Upon Us hegemon.substack.com/p/the-age-of...

An expanded registry of candidate cis-regulatory elements - Nature The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types...

Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬

Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!

A "meme-torial" of the science is coming soon 👀

ASPEN: Robust detection of allelic dynamics in single cell RNA-seq Author summary One powerful way to study regulation is to examine hybrids between two inbred species, where each gene has two distinct parental copies, or alleles. Measuring how much each allele is ex...

Latest from our lab: dx.plos.org/10.1371/jour... Congratulations to Veronika for leading this work to model cis-regulatory dynamics in F1s using single-cell allelic data

Motif-based models accurately predict cell type-specific distal regulatory elements - Nature Communications Decoding cell identity from DNA alone is a challenge. Here, the authors demonstrate that counting transcription factor motifs in regulatory DNA can forecast cell-type specificity outperforming deep-le...

New work from our lab: a simple motif-based model can distinguish between distal cell type specific regulatory elements with extremely high accuracy - in all metazoans including plants.
www.nature.com/articles/s41...

Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

How ageing changes our genes — huge epigenetic atlas gives clearest picture yet A map of DNA methylation changes in human organs could help researchers to discover more targets for anti-ageing therapies.

The power of Preprints. Our preprint "DNA Methylation Ageing Atlas Across 17 Human Tissues'
www.researchsquare.com/article/rs-7...

is a subject of a news piece in
@nature.com

How ageing changes our genes — huge epigenetic atlas gives clearest picture yet nature.com/articles/d41...

Half the Funding. Half the Future. - AAMRI The Medical Research Future Fund (MRFF) was designed to deliver $1 billion each year in new, lifesaving funding for medical research. We know through financial modelling that the full amount can be re...

The Medical Research Future Fund (MRFF) funds medical research in Australia. Only half the funds have been released. If you're an Australian and able to vote please use the form below to email your local MP to release the full amount of the MRFF
aamri.org.au/mrff/

📣 Paper alert!

I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...

From MRI to Ozempic: breakthroughs that show why fundamental research must be protected In these financially straitened times, funders must recognize that great discoveries often arise from work that was looking for something completely different.

In praise of fundamental research
Our editorial this week argues that I n these financially straitened times, funders must recognize that great discoveries often arise from work that was looking for something completely different
🧪
@nature.com
www.nature.com/articles/d41...

Cracking the code of the non-coding genome via allele-specific genomics?
Can we link non-coding elements—like lncRNAs and enhancers—to their protein-coding target genes, and in doing so, connect overlapping non-coding disease variants to their protein-coding counterparts?

Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!

Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...

We're now recruiting early career group leaders at the Crick to lead ambitious research programmes and explore bold scientific questions.

Hear our Director, Edith Heard, explain why the Crick is a unique place for curiosity-driven research.

Apply now ➡️ www.crick.ac.uk/careers-stud...

Vertebrate Genome Evolution. Annual Symposium of the @louisjeantetfdn.bsky.social Foundation in Geneva. Free access on site and on line. Great speakers for a super interesting topic. #SvantePaabo #HenrikKaessmann organisers 🙏 See you there! @biology-unige.bsky.social @genevunige.bsky.social

DNA mutagenesis driven by transcription factor competition with mismatch repair Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.

I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...

Cell-extrinsic controls over neocortical neuron fate and diversity Cell-extrinsic cues are key for neocortical cell identity and diversity.

Ever wondered how robust cellular identity is to external perturbations? Here we disrupt cellular environmnent in vivo and in vitro, and find cell population specific sensitivities. Environment sculpts development yes, but not all cells are made of the same wood. www.science.org/doi/10.1126/...

My kids have lafufus

Us too!

I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…

Congrats to Tommy and team, especially to PhD student Veronika Petrova who led the work on our end. Great to see it out! @victorchang.edu.au

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Non-profit journals are on the critical list.

The cause: academics obsession with the Nature brand, coupled with the APC $ model.

Some will argue it doesn’t matter (“all as bad as each other”). But the fact is undeniable and it’s good guys who put money back into science like COB who are losing..

Group Leader - Melbourne (Suburb), Greater Melbourne (Inner) (AU) job with Peter MacCallum Cancer Centre | 12837590 Peter Mac is recruiting a Group Leader to increase the capacity and efficiency of our “discovery to translation” cancer research pipeline.

A group leader position is open at Peter Mac in Melbourne, Australia!
Join us! Applications until May 5.
👇👇

www.nature.com/naturecareer...

Thanks for coming @shazanfar.bsky.social great diversity of science and a beautiful Sydney day!