New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

Genetic background shapes AI-predicted variant effects [new] ...uncovering heterogeneous predictions where variants shift between pathogenic and benign outcomes across diverse genomic contexts, crucial for interpretation.

It is with great sadness that I'm sharing the news that Dr. Don Moerman passed away this weekend. He was such a legend in the #Celegans and Canadian science community.

The @steinaerts.bsky.social lab published CREsted, an end-to-end modeling framework to 🧬 Train sequence-based enhancer models on large sc datasets 🔍 Decode enhancer logic with nucleotide-level interpretability ⚙️ Design synthetic enhancers with cell-type specificity https://tinyurl.com/ypurmrw5

“My patient is refusing a drug studied in 170,000 people because of side effects that a 124,000-person analysis just confirmed do not exist — while injecting a compound studied in 14 humans, from unregulated sources, based on the recommendation of someone who profits from selling it.”

Stoked to announce that I’m starting a lab as an Assistant Professor in the School of Biomedical Engineering and Centre for Brain Health at UBC! mcdiarmid-lab.sbme.ubc.ca Recruiting at all levels - please share the word! Cheers and happy long weekend all!

AITHYRA is recruiting an AI/ML STARTING PI Generative Models, Large Language Models, Agentic AI, Active & Reinforcement Learning, AI-driven Scientific Discovery & Lab Automation, ML-driven molecular simulations... Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #AI/ML #AITHYRA

AITHYRA is recruiting a LIFE SCIENCE PI We are interested in research questions related to one of our four core disease areas: cancer research, immunological disorders, infectious diseases, neurodevelopment disorders. Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #LS #AITHYRA

"Beyond the baseline: mapping the context-specific regulatory landscape of disease" by Yoav Gilad and Alexis Battle authors.elsevier.com/sd/article/S...

oh my god I cannot stop laughing x.com/om_patel5/st...

New preprint from our lab where we learn some interesting things about the context specificity of TFs in their regulation of gene expression by dissecting MPRA-trained sequence-expression models. Surprising guest appearance from RNA Pol III(!) Thread from 1st author @sambean12.bsky.social 👇

Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation https://www.biorxiv.org/content/10.64898/2026.03.17.712157v1

The Programmable Genomics Lab at @umasschan.bsky.social just officially launched our site! We have a "simple" goal: to develop synthetic regulatory elements that target every cell type in every tissue, and control payload dosage/duration Check it out! programmable-genomics.github.io

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

How do chromatin mark control TF activity and gene regulation? I will unfortunately not be at the @cshlmeetings.bsky.social Systems Biology this year, but very excited that @mpalamin.bsky.social will present her work @embl.org. Spoiler it involves a novel multiplexed single molecule genomics assays!

Abstract deadline approaching soon (March 6)! We welcome both short talks and posters. Travel fellowships up to $500 available for students & postdocs.

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

Congrats to the USA on this milestone www.theglobeandmail.com/gift/2109fef...

Exited to share Current Opinion review on how chromatin hubs involving multiple enhancers and promoters are formed, and their potential roles in gene regulation: www.sciencedirect.com/science/arti...

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e... This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

Registration now open for SynBio 8.0, June 15-17 at the University of Waterloo. www.synbiocanada.org/synbio8 Join us at Canada’s premier synthetic biology conference, bringing the community together to showcase advances from across the country and across the full breadth of the field! #synbio8 🍁🧬

Check out our new protocol paper on molecular recording of transcriptional events in genomic DNA! Super fun pulling this together with @jennynathans.bsky.social @chenomics.bsky.social and @jshendure.bsky.social

🧵 1/ 🎉New paper alert! Pretrained protein language models (#pLMs) are all the hype, but are they really helping us predict protein- protein interactions? 🤔Dive into our thread to see why you should read the full study @natmachintell.nature.com. ⬇️ 🔗 rdcu.be/e3PGD

The @steinaerts.bsky.social lab is looking for a postdoctoral researcher to develop next-generation sequence-to-function models for glioblastoma, one of the most aggressive brain cancers. More info & how to apply 👉 https://vib.ai/en/opportunities#/job-description/130090

Polygenic scores are useful for early detection, but also early prevention! New paper shows people with high genetic risk of T2D have 3x more risk of developing it by age 35. Early detection could trigger lifestyle changes, metformin prescription... doi.org/10.1038/s414...

We are hiring a staff member to support various projects in our lab. Please reach out with questions! wd5.myworkdaysite.com/recruiting/u...

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

Our paper on the evolution of XIST regulatory network in primates is now published in Science Advances! Check out the paper www.science.org/doi/10.1126/... or a digest of our findings emmanuelczt.github.io/posts/2026/0... A short 🧵 of our main findings 👇

We're testing AlphaGenome. It's a very valuable step forward towards the goal of identifying functional non-coding variants (FNCVs) causing human diseases. Congrats to @avsecz.bsky.social and the team for this landmark publication. www.nature.com/articles/s41...

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...

Deadline TODAY January 23 - please join the Systems Biology: Global Regulation of Gene Expression meeting in beautiful @cshlnews.bsky.social (March 11-14). Register and submit your abstract here: meetings.cshl.edu/meetings.asp.... Please Repost!

Metabolites can be quantified using a combination of aptamers and DNA barcodes go.nature.com/42BbXTQ rdcu.be/eZ8BP

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Dear American Friends, I’m here with an uncomfortable message: watching in horror is not good enough. Sitting idly by makes you complicit. Things will keep getting worse until Americans act.

1/ We found that deep sequence models memorize atomic facts "geometrically" -- not as an associative lookup table as often imagined. This opens up practical questions on reasoning/memory/discovery, and also poses a theoretical "memorization puzzle."

Vaccines, the most impressive public health intervention in medical history, and where we could be headed if there was not efforts to negate truth, facts, and evidence A great, open-access, review and perspective by @scientificdiscovery.dev

Looking to start your lab in generative biology / AI? Come join us at the @sangerinstitute.bsky.social Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways! pls RT tinyurl.com/GenGenFaculty

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits https://www.biorxiv.org/content/10.64898/2025.12.23.696273v1

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

www.cell.com/cell/fulltex... On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.

👋@sbmeubc.bsky.social and @bccancerfdn.bsky.social are seeking a successful candidate for the Dr. Connie Eaves Chair in Cancer Stem Cell Research (Professor or Associate Professor with tenure). Please apply if you have innovative engineering solutions and technologies! www.nature.com/naturecareer...

Our latest preprint revisits the classic model of mutation-selection balance. Do human recessive genes fit Haldane's 100-year old model? This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io www.biorxiv.org/content/10.6...

Great opportunity! Deadline DEC 17 The CIFAR MacMillan Multiscale Human School explores interdisciplinary models to build a virtual twin that accurately capture development. cifar.ca/next-generat... @smbmathbiology.bsky.social @stemcellnetwork.ca @the-node.bsky.social @biologists.bsky.social

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

🧬🎉Join us on Dec 17th for our last session of 2025! 🎉🧬Two fantastic talks on transcriptional regulation: 🔬JB Lalanne on developmental enhancers (and starting a lab in 2025?) 🔬 @rberrens.bsky.social on transposable elements in development 📋Register here: us06web.zoom.us/webinar/regi...

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

We are hiring a PhD intern for Summer 2026 in ML for regulatory genomics at ReLU/BRAID/Genentech! Work on DNA sequence models for the noncoding genome (e.g. DNA design, models of MPRA and genetic variants)! 🥳

I wrote a guide on constructive peer review. This is a polished version of an internal guide I had for my group. Of course, constructive feedback is welcome, peers! deboer.bme.ubc.ca/2025/12/09/g...

I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories! link.springer.com/collections/...