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
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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 www.biorxiv.org/content/10.64898/2026.03...
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
It is difficult to imagine them actually suing over it. If they did, I think they would be massively shooting themselves in the foot as everyone would now be too scared to publish there.
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.
Apparently the search capabilities here are trash. Sorry!
Sorry for missing the tag... searched but did not find legendary @charliebell.bsky.social !
Participants of the meeting posing on a staircase looking fantastic.
Thanks to co-authors Charles C. Bell, Brendan R. Camellato,
M. Joaquina Delás, Daniel M. Ibrahim, and @michaeltmont.bsky.social
And also to all the participants of the 2024🤨 Company of Biologists meeting that inspired this.
A quote: “We would like to know, for example, what the initiation and termination signals for RNA polymerase are, what kind of sequences are recognized by repressors, by host modification and host restrictive enzymes and by enzymes involved in genetic recombination and so on. For these studies eventually what is required is the ability to synthesize long chains of DNA with specific non-repeating sequences.” H. Gobind Khorana, 1968 (Khorana, 1968) Sadly, the quote was cut from the final version of our paper.
One thing I learned while contributing to this was how much foresight pioneers of DNA synthesis technology had in understanding the importance of their work to studying genome regulation. Found this 1968 gem from Khorana (who , incidentally, was at UBC for a time):
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/...
Communicating your results is a key part of the work. If you never publish or bury it, that should be considered, no?
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
