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Reposted by Carl de Boer

Mathieu Quesnel-Vallières @rna-ken.bsky.social · 4d

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...

medecine.umontreal.ca

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Reposted by Carl de Boer

Connor Rogerson @doctorconnor.bsky.social · 13d

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...

Postdoctoral Fellow - Gene Regulation and Functional Genomics

Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...

sanger.wd103.myworkdayjobs.com

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Reposted by Carl de Boer

John Ray @jraylab.bsky.social · 19d

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...

Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics

Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...

www.nature.com

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Reposted by Carl de Boer

Alejandro Montenegro @aemonten.bsky.social · Sep 3

"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...

Multiple overlapping binding sites determine transcription factor occupancy - Nature

A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

www.nature.com

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Carl de Boer @carldeboer.bsky.social · Sep 4

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 👇

Madison Chapel @chapelmadison.bsky.social · Sep 3

1/ Why are eukaryotic gene regulatory networks (GRNs) so much more complex than prokaryotic ones?
In our new preprint, we investigated the role that recombination – a key step in eukaryotic reproductive strategies – plays in this problem! www.biorxiv.org/content/10.1...

Evolutionary simulations reveal role for genomic recombination in the evolution of gene regulatory network complexity and robustness

The gene regulatory networks (GRNs) of eukaryotes are dramatically more complex than the GRNs of prokaryotes, but we lack a complete picture of the selective pressures that have shaped this difference...

www.biorxiv.org

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Reposted by Carl de Boer

Francis Lynn 🇨🇦 @nictitate.bsky.social · Sep 2

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

Defence spending must include health spending too

Biotech investment can deliver on Canada’s NATO commitments, protect citizens and drive economic growth

www.theglobeandmail.com

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Reposted by Carl de Boer

Cyntia Taveneau @cyntiat.bsky.social · Sep 2

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...

Code to complex: AI-driven de novo binder design

In this review, Fox et al. discuss how artificial intelligence has transformed our ability to design new-to-nature proteins that bind target proteins with high affinity and specificity. The authors de...

www.cell.com

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Reposted by Carl de Boer

Shaun Mahony @shaunmahony.bsky.social · Aug 23

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...

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution...

www.biorxiv.org

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Reposted by Carl de Boer

Matthew Aguirre @aguirre404.bsky.social · Aug 22

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...

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Reposted by Carl de Boer

Arnaud Krebs @arnaudkr.bsky.social · Aug 18

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👇

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Reposted by Carl de Boer

Tom Ellis @proftomellis.bsky.social · Aug 11

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

https://www.nature.com/articles/s41467-025-62356-y

t.co

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Reposted by Carl de Boer

Eileen Furlong @eileen-furlong.bsky.social · Jul 30

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...

Group Leader - Genome Biology Unit

Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

embl.wd103.myworkdayjobs.com

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Carl de Boer @carldeboer.bsky.social · Jul 11

Thanks for reading! Please let us know what you think, and support GAME by contributing modules!
Preprint: doi.org/10.1101/2025...
GitHub: github.com/de-Boer-Lab/...

GAME: Genomic API for Model Evaluation

The rapid expansion of genomics datasets and the application of machine learning has produced sequence-to-activity genomics models with ever-expanding capabilities. However, benchmarking these models ...

doi.org

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Carl de Boer @carldeboer.bsky.social · Jul 11

GAME was designed in consultation with many functional genomics and ML researchers. Many enthusiastically contributed their models and datasets in GAME modules. Thanks to all the coauthors and colleagues for your support in developing GAME! 🙏

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Carl de Boer @carldeboer.bsky.social · Jul 11

As GAME builds momentum, more models and benchmarks will be created, and, because they’re all inherently cross-compatible, the easiest way to benchmark your model will be to put it in GAME, snowballing further.📈

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Carl de Boer @carldeboer.bsky.social · Jul 11

6) Better estimates of real-world performance (since tasks and models are cleanly separated and uniformly applied)
7) GAME enables continual benchmarking; we anticipate a yearly “state of the field” to be easily produced. Here's an example for gene expression prediction using existing GAME modules.

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Carl de Boer @carldeboer.bsky.social · Jul 11

5) Getting funding 💰and people for long term maintenance of bioinformatics projects is notoriously challenging😱. Our solution is inherently sustainable in the long term because it is distributed: anyone can add their own GAME modules!🔥

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Carl de Boer @carldeboer.bsky.social · Jul 11

3) GAME communicates over TCP/IP sockets, enabling evaluation of even remote/proprietary models (think ChatGPT)🌐
4) Because the Matcher is modular, we can swap it with a better version and nothing will break. 🔄

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Carl de Boer @carldeboer.bsky.social · Jul 11

GAME has many key advantages for genomics model benchmarking:
1) Via the API, all models are inherently compatible with all benchmarks
2) GAME will work across platforms – just get Apptainer installed, and away you go 💻↔️🖥️

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Carl de Boer @carldeboer.bsky.social · Jul 11

Our Matcher containerizes an LLM, which is the basis for matching. It worked surprisingly well almost out of the box, and can match cell/tissue types, species, and molecule types. 🔮

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Carl de Boer @carldeboer.bsky.social · Jul 11

The “Matcher” enables pairing up of the benchmark tasks and things the model can predict. Evaluator wants predictions in heart cells? The Matcher can tell you that your cardiomyocyte model is your best bet. The Matcher and Predictors also communicate via an API!

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Carl de Boer @carldeboer.bsky.social · Jul 11

Benchmarks are containerized as “Evaluators”. We created several, including chromatin conformation, MPRA, and synthetic cis-regulatory variant effects. As new datasets come out, they can be added to GAME to see whether models can predict them.

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Carl de Boer @carldeboer.bsky.social · Jul 11

Models are containerized in “Predictors”. We created DREAM-RNN (K562), Enformer, Orca, DeepBICCN2, and Borzoi Predictors. We anticipate as new models are created, model builders will encapsulate their models, referencing the examples we provide.

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Carl de Boer @carldeboer.bsky.social · Jul 11

GAME uses Application Programming Interfaces, a concept introduced to the genomics model world with Kipoi, to enable uniform application of any benchmark to any model.

Diagram of the GAME modules and how they interact.

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Carl de Boer @carldeboer.bsky.social · Jul 11

Unlike the protein folding code, gene regulation cannot have a single benchmark (e.g. CASP) because the gene regulatory code differs across species, cell types, and conditions. We need a variety of benchmarks to understand model strengths and weaknesses: enter, GAME.

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