Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪 A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today! #InHoxWeTrust

Postdoc opportunity with @tomasbruna.bsky.social here at @jgi.doe.gov @berkeleylab.lbl.gov: Develop, benchmark, and apply Plant Genomic Language Models (gLMs) 🌿🧬💻 jobs.lbl.gov/jobs/computa... #AI #PlantGenomics #gLMs #Postdoc

New preprint from the lab just dropped! Our continued partnership with Irfan Kathiriya from @ucsanfrancisco.bsky.social on gene regulatory networks in atrial disease modeling using iPS cells www.biorxiv.org/content/10.1...

Thrilled to share the story stemming from my PhD! We used mESC neural differentiation, genome editing and bulk & single-cell approaches to uncover how ZIC2 controls early neural fate by playing a dual and sequential regulatory role as a promiscous pioneer and a selective lineage-specific activator.

We are excited to share our new preprint demonstrating that nucleic acid interactions with SUZ12 constrain PRC2 activity, establishing a kinetic buffer essential for targeted gene silencing and revealing vulnerabilities in diffuse midline gliomas. www.biorxiv.org/content/10.1...

How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions. www.cell.com/molecular-ce...

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Staff scientist position (computational): I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record. #sciencejobs

Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social

Thanks to the large consortia like ENCODE, FANTOM5, GTEx, 4DNucleome for generating key training data. And finally, thanks to numerous researchers developing inspiring DNA sequence-to-function models, informative evaluations, and interpretation tools.

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 a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4 arxiv.org/abs/2411.11158

An assessment of DNA language models concludes: ◼️ They do not offer compelling gains over baseline models Their performance is inconsistent and requires much more compute. arxiv.org/abs/2412.05430

Damon Runyon Postdoc Fellowship Eligibility: Research relevant to the study of cancer Deadline: August 15, 2025 🧪🧠🧬 www.damonrunyon.org/for-scientis...

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

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

Choose Science. Choose Europe. A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open. With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond. Apply by 10 September → europa.eu/!fBTMgF

Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...

I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...

Today was a big day for the lab. We had two back to back thesis defenses and the defenders defended with great science and character. Congrats to DR. Kelly Cochran & DR. @soumyakundu.bsky.social on this momentous achievement. Brilliant scientists with brilliant futures ahead. 🎉🎉🎉

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.

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

Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models. 🔗 doi.org/10.1093/bioa... #Genomics #Bioinformatics #RegulatoryGenomics

If you're feeling angry or lost, do what @donmoyn.bsky.social urges & submit a public comment opposing the proposed OPM rule to politicize public services (Schedule F). Get specific! Get snarky! Channel your energy here - it's concrete, quick, & meaningful: donmoynihan.substack.com/p/here-is-a-...

We have updated our database of funding opportunities for Early-Career Researchers (private foundations, federal, international) We have 456 entries, for which we provide $ amount, deadline, eligibility criteria, etc. Download this massive database here for free: research.jhu.edu/rdt/funding-...

As Chair of the Department of Global and Public Health @healthsciences.mcgill.ca, I am pleased to share two open junior faculty positions! mcgill.wd3.myworkdayjobs.com/en-US/mcgill... mcgill.wd3.myworkdayjobs.com/en-US/mcgill...

(1/n) New preprint from @claricehongky.bsky.social Fan Fang Varshini Ramanathan in collab w Jie Liu. Q: How do we get ultra-high-res 3D genome maps? A: New deep learning model, Cleopatra. Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.

Come join us at @westernuresearch.bsky.social as a Canada Excellence Research Chair! DM me with questions/interest about theme 2! Be a part of a strong and well-equipped (e.g., imaging, behaviour) neuroscience community! uwo.ca/research/cer... @westernuwin.bsky.social @westernubrainscan.bsky.social

All resources released with the preprint 2/2 bsky.app/profile/seli...

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/

Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....

We're one month away from the short talk abstract and scholarship deadlines. Short Talk Abstract Deadline: May 20th, 2025 Scholarship Deadline: May 20th, 2025 Early Registration Deadline: July 17th, 2025 Poster Abstract Deadline: August 21st, 2025

Working with a great team to organize @keystonesymposia.bsky.social AI in MolecularBiology, this September! We aimed for a wide range of biological topics, and emphasized speakers who blend sophisticated machine learning with compelling biological questions and analysis.

How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social

New preprint from the @arnausebe.bsky.social lab! 💐 Here @crisnava.bsky.social, @seanamontgomery.bsky.social & collaborators develop a novel ChIPseq protocol, and demonstrate its huge potential to study the evolution of chromatin function and regulation across the eukaryotic tree of life.

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

⚡Next Wednesday! In our next #FragileNucleosome seminar session, we are delighted to host, @baluapuri.bsky.social and @juliecocquet.bsky.social! If you've registered to one of our previous 2025 sessions, you can use the same link to join our next session. If not: us06web.zoom.us/webinar/regi...

It’s out! The first paper from my postdoc – and first from the @bhadurilab.bsky.social – is now live @natneuro.nature.com . 🧠✨ Using a new meta-atlas generation strategy, we identified functional gene networks that more fully explain how cell types are formed in the human cortex. (1/13)

Delighted to share our new preprint, the outcome of many years of collaborative work with Giuseppe Testa’s group, both at the bench & in front of the computer, probing human brain evolution using organoids. We tried something cool, and learned a lot 🧪🧫🧠🧬 [follow 🧵] www.biorxiv.org/content/10.1...

Scalable high-performance single cell data analysis with BPCells https://www.biorxiv.org/content/10.1101/2025.03.27.645853v1

I am hiring for a research technician role in my new lab at UC Irvine studying how transcription factors control cell identity. If you know any graduating undergrads or postbacs looking for a position, please spread the word! Apply by May 9 for full consideration. recruit.ap.uci.edu/JPF09594

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...

Want to make a real impact with your science—right in your own community? Join the McClintock Letters initiative to sharpen your science communication skills, connect with fellow scientists, and craft a powerful op-ed that advocates for science where it matters most: locally. #McClintockLetters

In this study, Hermant et al. describe the evolution of the retrotransposon MERVL and its cis-regulatory transcription factor binding motifs, highlighting the phyloregulatory adaptation at play during early embryogenesis. Learn more here: ➡️ tinyurl.com/gd352270