How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...

Why a synthetic human genome is still worth building

A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

nature.com

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/...

We are hiring a staff member to support various projects in our lab. Please reach out with questions! wd5.myworkdaysite.com/recruiting/u...

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...

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…

sciencedirect.com

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.

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

We are hiring a scientist to lead our 'Build' team at the Seattle Hub for Synthetic Biology. @alleninstitute.org Job posting below: alleninstitute.org/careers/jobs... Please reach out if you have any questions!

Jobs

We are working to solve the biggest mysteries in bioscience.

alleninstitute.org

The nuclear lamina strengthens the nucleus and organizes the genome. So what happens when you acutely degrade it in living cells? Not what we thought! (1/n) www.molbiolcell.org/doi/10.1091/...

Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity | Molecular Biology of the Cell

The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. ...

molbiolcell.org

Excited to share our work with @julietrolle.bsky.social & Jef Boeke. We developed a 'shotgun' method to screen millions of synthetic metabolic pathways to enable mammalian cells to grow without two essential nutrients for the first time in >500 million years! doi.org/10.1101/2025... Thread...

A shotgun approach for highly multiplexed mammalian metabolic engineering

Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

doi.org

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

nature.com

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☺️

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...

A multi-kingdom genetic barcoding system for precise clone isolation - Nature Biotechnology

A barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.

nature.com

Need a site-specific, dox-inducible system for human cells? Low leakage, silencing-resistant, and modular? It’s here in the first paper from my lab, led by Tomoki Yanagi MD, PhD. Bonus: forward programming of TEC-like cells from hiPSCs. tinyurl.com/trunod01

Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing - Journal of Biological Engineering

Background Inducible gene expression circuits enable precise control over target gene activation and are widely used in direct reprogramming. However, their usability is often compromised by DNA methy...

tinyurl.com

We are hiring a person to join our team at the Seattle Hub for Synthetic Biology. Please share the word! Link to apply: alleninstitute.org/careers/jobs...

Jobs

We are working to solve the biggest mysteries in bioscience.

alleninstitute.org

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/

Join us at the Cascadia Advanced Genomic Technologies conference in beautiful Vancouver this summer. Registration is FREE at the link below! de-boer-lab.github.io/CAGT_meeting/

Check out this video explainer of our recent paper on shuffling mammalian genomes. Thanks to Jeremy @genometdcc.bsky.social for putting this together!

GenomeTDCC@genometdcc.org · last yr.

🧪🧬🖥️ #STS @sudpinglay.bsky.social describes how Genome-Shuffle-seq enables multiplex generation, mapping, and characterization of structural variants by leveraging barcoded "shuffle cassettes" with site-specific recombination and novel barcode pairings for genome-wide mapping 📽️ 👇 youtu.be/rW8AFhq1Pys

@science.org Genome recombination on demand | Science www.science.org/doi/10.1126/... a Perspective by @seczmarta.bsky.social Lars Steinmetz @stanford.edu on two studies bit.ly/4hzFRMg + bit.ly/4jyT4Hf that generate large genome rearrangements in mammalian cells @ unprecedented scale #synbio #genome

Genome recombination on demand

Large genome rearrangements in mammalian cells can be generated at scale

science.org

Read thread below, if you want more details on the personal side of this wonderful collaboration.

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Great work and it's very nice to see the studies co-published. Can you say a bit more about how the two teams ended up knowing about each other's work and co-submitting? cc @jshendure.bsky.social @sudpinglay.bsky.social

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/...

Multiplex generation and single-cell analysis of structural variants in mammalian genomes

Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...

science.org

The Chan Zuckerberg Initiative is awarding BBI researchers $1.5 million over two years to “democratize” access to synthetic DNA. We are envisoning complementary technologies that address shortcomings of current systems for manufacturing DNA. brotmanbaty.org/news/chan-zu... @sudpinglay.bsky.social

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

nature.com