Carl de Boer

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/...

Canada’s great American breakup: Most now see U.S. as a risk, not an ally, poll finds Findings suggest a profound level of distrust after U.S. President Donald Trump’s first year back in office

Congrats to the USA on this milestone www.theglobeandmail.com/gift/2109fef...

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

Preventing premature deaths through polygenic risk scores - Nature Communications Via an integrative modelling approach that combines population and clinical trial data, the authors find that polygenic risk score-based screening would reduce premature mortality across seven commonl...

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

Remodeling of XIST regulatory landscape during primate evolution How gene regulation strategies rapidly evolve across short evolutionary timescales is explored.

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 👇

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

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...

Living in a Society 101

Unit 2: other people exist. They are just as important as you. Your actions can affect them.

Mammalian genome writing: Unlocking new length scales for genome engineering The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…

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...

Systems Biology: Global Regulation of Gene Expression Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

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!

Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing - Nature Biotechnology Metabolites can be quantified using a combination of aptamers and DNA barcodes.

Metabolites can be quantified using a combination of aptamers and DNA barcodes go.nature.com/42BbXTQ
rdcu.be/eZ8BP

Indeed I am. Then I can constructively review your constructive reviewing constructive review to give you constructive feedback on your constructive reviewing constructive review's constructive review implementation.

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

One final note about NATO: The only time mutual protection (Article 5) was triggered was actually in defense of the USA after the September 11, 2001 attacks.

If we change course now, there’s still time to prevent the worst. But time is running out and there may soon be no turning back.

Not American? Let your American friends and colleagues know what you think. That's why I'm here. Unfortunately, I think that's about all we can do since the US government doesn't care what we think.

What can you do? Organize. Convince others to help, multiplying your efforts. Convince this government’s supporters that this path will only lead to a less secure and prosperous America and get them to speak up too. Talk to your elected representatives at all levels.

Map of NATO which, notably, includes Greenland already.

NATO is a major reason for the relative peace and prosperity of the last 77 years. If your government annexes Greenland, NATO will be destroyed. A year ago, another world war seemed like an impossibility. Now, there is a clear path to war and we keep edging closer.