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...

CloneSelect published in Nature Biotechnology @natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...

🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.

A tour de force study from Taipale&Yin labs. It expands the vocabulary of the Regulatory Code by adding 1131 TF:TF composite motifs that are different from the individual TF motifs. The new composite motifs are enriched in cell-type specific elements and active in vivo www.nature.com/articles/s41...

⏰Abstract deadline for the Cascadia Advanced Genomic Technologies Meeting is April 30!⚠️ We're hoping this will be the first of many, catalyzing collaboration and leveraging our regional strength in advanced genomics technologies! See you there! de-boer-lab.github.io/CAGT_meeting/

Join us for the 2025 SynBio7.0 conference in Toronto, June 1-3! SynBio is Canada's largest academic synthetic biology conference. More details on our website! synbio7.vercel.app

Our latest work now online in Cell: Rewriting regulatory DNA to dissect and reprogram gene expression Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression Thread 👇

Reminder: abstract deadline for the Cascadia Advanced Genomic Technologies Meeting is April 30! We're hoping this will be the first of many, catalyzing collaboration and leveraging our regional strength in advanced genomics technologies! Please spread the word! de-boer-lab.github.io/CAGT_meeting/

Latest preprint from the lab describing a super fast way to clone arrays of CRISPR guide RNAs. If you want to target multiple sites simultaneously, and want fast iteration on building and testing arrays of guides, look no further! Bonus: it's named after a Pokemon🔥🦄

UBC is hosting US Applicant Week from April 14-18, which allows US students to apply during an extended application period for graduate studies. Sixty graduate programs will be reopening applications for US applicants for September 2025 and January 2026 start dates - www.grad.ubc.ca/us-applicant...

Openness guides discovery @naturebiotech.bsky.social "To paraphrase Dwight D. Eisenhower’s aphorism: in research, planning is indispensable, but detailed plans are useless". Spot on by @itaiyanai.bsky.social and MJ Lercher www.nature.com/articles/s41...

Very proud of two new preprints from the lab: 1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...

Base-editing screens of primary T cells reveal genetic variants beneficial to immunotherapies go.nature.com/3yxjW7q rdcu.be/ef95o

Join us June 19-20, 2025 in Vancouver BC for the Cascadia Advanced Genomic Technologies meeting! Featuring Keynote speaker Calin Plesa @calin.bsky.social Abstract deadline April 30🔔, but registration is capped so don't wait! 😱 de-boer-lab.github.io/CAGT_meeting/

Are U.S. tariffs a threat to Canadian health sciences innovators – or a golden opportunity? www.theglobeandmail.com/business/eco...

Last call for a postdoc position in single cell analysis/perturb-seq with @nikashakiba.bsky.social at UBC in beautiful Vancouver Canada! ubc.wd10.myworkdayjobs.com/en-US/ubcfac...

Come work with us in Vancouver! UBC’s Department of Medical Genetics, in collaboration with The Life Sciences Institute, seeks an Assistant Professor working in chromatin regulation or genetic regulatory mechanisms. ubc.wd10.myworkdayjobs.com/en-US/ubcfac...

Stoked to share my research journey next week! I'll walk through my PhD work in the lab of @crougeulle.bsky.social on XIST regulation evolution, and a short preview of my current work with @carldeboer.bsky.social at @sbmeubc.bsky.social at the interface of gene regulation, synthetic biology and ML 🧬

New (and hotly anticipated - at least by me) preprint from my group describing a better way to partition training data for genomic-trained models to solve the long-neglected problem of homology-based data leakage. Thread from first author @muntakimrafi.bsky.social 👇

Amid concerning times, sharing a bit of positivity: our 1st preprint of 2025 (funded VIA NIH COMMON FUND), heroically led by Marty Yang (@martyyang.bsky.social) w/ huge assist from @genophoria.bsky.social lab. Lots to cover so let’s get this tweetorial started (1/n)! www.biorxiv.org/content/10.1...

Very excited about this new work from our lab! Explainer thread coming soon @minetoota.bsky.social

New preprint from our group on the genetic architecture of complex disease. Thread from 1st author @chapelmadison.bsky.social 👇. Here, I give a some context of why I am particularly excited about this.

Variant effects depend on polygenic background: experimental, clinical, and evolutionary implications https://www.biorxiv.org/content/10.1101/2025.01.07.631805v1

Deep learning with data beyond the genome: Our paper on active machine learning to model regulatory DNA is out today in Cell Systems. With functional assays and DNA synthesis you can generate any training examples, not just genomic sequences. 🧵 kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...

Great opportunity to gain experience with perturb-seq experiments and analysis in iPSC lung models. Joint PD with Nika Shakiba (UBC) ubc.wd10.myworkdayjobs.com/en-US/ubcfac...