🧵 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/...

We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

(1/13) Excited to share the outcome of the IBIS Challenge! The IBIS challenge united dozens of teams across the world in tackling the problem of modeling transcription factor (TF) binding specificity using a diverse collection of experimental datasets for understudied human TFs.

srsr(at)parl.gc.ca if you want to let the committee know your thoughts... Picard could have written the email I sent to them last weekend.

Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering. Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions. www.massivconference.com Abstract deadline: Nov 14

Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together. Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/ Poster due is Nov 7, but will be extended. With @stemcellnetwork.ca and JST.

How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google. Preprint: www.biorxiv.org/content/10.1... @patiskowronek.bsky.social explains👇

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

Open rank tenure-track position in comp bio at the University of Montreal. Great environment, great position. @futurepislack.bsky.social medecine.umontreal.ca/wp-content/u...

We have space for two postdoctoral fellows in the Taipale Lab at the @sangerinstitute.bsky.social. This is a core-funded open position! Come with your ideas and interests and we can develop a project together. sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...

"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites." www.nature.com/articles/s41...

New preprint from the lab 🎉 on the evolution of gene regulatory network complexity, where we tested whether sexual recombination promotes more complex GRNs using biochemically-inspired evolutionary simulations 🧐. Bluetorial from 1st author @chapelmadison.bsky.social 👇

Defence spending must include health spending too www.theglobeandmail.com/gift/2109fef...

Excited to share our new review on AI-driven protein design - from its origins to today’s breakthroughs, methods, potential, and challenges ahead ! www.cell.com/structure/fu...

New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers. www.biorxiv.org/content/10.1...

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

New paper from our lab on synthetic genome work in yeast is out - Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes. Exciting project led by Jane (Xinyu) Lu in our group, now online. t.co/0LuGwgAWlA

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...