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...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

We tile through ~300 ultra conserved elements 10bp at a time in 6 taxa (some alive, some extinct), to ask, are they the reason the two skulls below- separated by 160 million years of evolution - are so similar? (image from former PhD student Laura Cook)

The evolutionary foundations of transcriptional regulation in animals www.nature.com/articles/s41... (read free: rdcu.be/evDcA) 🧬🖥️🧪

CAGT was fun! Thanks @carldeboer.bsky.social @sudpinglay.bsky.social and the de Boer lab for organizing! Folks from Seattle, Oregon, and other places. Great community. Arman gave a usual super talk, and Sanchit and Dayag won poster prizes☺️

Postdoc🚨! Come join our HFSP team to uncover how chromatin moves in cells and what this means for genome function! Great opportunity to combine single-cell genomics, live imaging and polymer physics in the unique mammalian retina with @andersshansen.bsky.social, Davide Michieletto & Sandra Tenreiro

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

🧠 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🧵👇

Join us on Wednesday next week for two exciting talks on transcription regulation from @kasitc.bsky.social and @davidsuter.bsky.social! You can register at: us06web.zoom.us/webinar/regi...

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. 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.

We quantify the aggregation of >100,000 random protein sequences to train CANYA, a convolution-attention hybrid neural network to predict aggregation from sequence. With @bennibolo.bsky.social www.science.org/doi/10.1126/...

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 🧬🖥️

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...

One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!

Vidéos of the symposium are now available online @collegedefrance.bsky.social Just click and enjoy!🙏🏼🤘

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...

To the top of the "to-read" list. Looks like a heroic amount of work from the Hahn lab (large-scale ChEC-seq compendium!) www.nature.com/articles/s41...

Join the UBC and SFU Postdocs for a social at the Bloedel Conservatory and Queen Elizabeth Park on Thursday 17th April! 4-5 PM - Bloedel Conservatory (Free Entry) 5 PM - BBQ at QE Park Feel free to join for both parts of the event or just one. Register now: ubc.ca1.qualtrics.com/jfe/form/SV_...

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

Join us for the first edition of the Cascadia Advanced Genomic Technologies meeting! We aim at fostering collaborations to tackle critical challenges in mammalian genomics. Info and registration link below 👇

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/

Cool preprint exploring the dynamics of transcriptional activation between homologous promoters in 🪰! Promoters are in physical proximity when simultaneously activated and a single active promoter produces more RNA. Competition for transcriptional resources between promoters? doi.org/10.1101/2025...

A though provocative read genome.cshlp.org/content/35/3.... While estrogen response triggers transcriptional and 3D chromatin changes, only a select few structural shifts are likely to subtly contribute to transcriptional regulation 🤔

In this study, Huang et al. demonstrate how a single enhancer independently controls the expression of two distal and functionally unrelated genes. Learn more here: ➡️ tinyurl.com/gd352235

Proliferation history and transcription factor levels drive direct conversion to motor neurons: Cell Systems www.cell.com/cell-systems... 🧪

Excited to share the peer-reviewed version of our paper on predicting the chromatin response to TF dosage using transfer learning www.cell.com/cell-genomic...

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 🧬

🎆Next #FragileNucleosome meeting is less than a week away! We are delighted to host @manucazottes.bsky.social, @robertadolling1.bsky.social & @leandrosboukas.bsky.social ! We will discuss evolution of XIST regulatory network, cancer epigenetics, and MDEMs! 🗓️ us06web.zoom.us/webinar/regi...

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 online! Intrinsically disordered regions as facilitators of the transcription factor target search

Ling Liu’s beautiful PhD work on modeling transcriptional elongation and its genomic and epigenomic determinants is now published. A technical tour de force with a number of interesting biological observations academic.oup.com/nar/article/...

How can we improve gene regulatory network inference from noisy scRNA-seq data? Our new review in @molsystbiol.org explores the latest methods integrating prior knowledge to enhance reliability. Plus, some suggestions on how to improve benchmarking! www.embopress.org/doi/full/10....

Despite the trying times, thrilled to share our @natprot.bsky.social Nature Protocols on massively parallel in vivo Perturb-seq: www.nature.com/articles/s41... Grateful for the excellent primer by Christopher Bock and Eugenia Pankevich: www.nature.com/articles/s41...

new paper: "Evolution and the Knightian Blindspot of Machine Learning" Our ever-changing world bubbles with surprise and complexity. General AI must include handling unforeseen situations with grace. Yet this issue largely lies outside AI's formalisms: a blind spot. (1/n)

[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: June 1 More details: mlcb.github.io Help spread the word—please RT! #MLCB2025

Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com

In our new paper, we uncover a damaged chromatin marking mechanism that drives the non-random segregation of UV damage through mitosis. Chromatin alterations impinge on genome stability by controlling DNA damage segregation See Ferrand*, Dabin* et al., Nat Commun 2025.

Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin? By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient! #chromatin #3Dgenome #generegulation www.science.org/doi/10.1126/... 👇

Hello, Bluesky!👋 We are excited to connect with you!🌟 Europe PMC is an open database of global life science research - discover articles, preprints, theses, grants, and more. We talk about scholarly communication, open science, bioinformatics, and meta research. Follow us and join the conversation!

The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification. www.biorxiv.org/content/10.1...

Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment. www.science.org/doi/10.1126/...

www.biorxiv.org/content/10.1... Might explain some of the discrepancies between QTL effect & personalized gene expression prediction performance by S2F models

0/ Essential reading for anyone training or using sequence-function models trained on genomic sequences! 🚨 In our new preprint, we explore the ways homology within genomes can cause leakage when training sequence-based models and ways to prevent it

Excited to present the results of my 20% project in collaboration with @broadinstitute.org and @danafarber.bsky.social . In our new paper we demonstrate a long-range model capable of detecting regulatory elements at distances beyond a million base pairs.

Thermodynamic principles link in vitro transcription factor affinities to singlemolecule chromatin states in cells www.biorxiv.org/content/10.1...