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Introducing IN SITU GENOME SEQUENCING, a new technology to resolve DNA sequence🧬 and structure🔬 A team effort with Andrew Payne, Paul Reginato, Ed Boyden, Jason Buenrostro, and Fei Chen science.sciencemag.org/content/early/… This is how it works: (1/8)

Check out the full preprint for more details and insights biorxiv.org/content/10.110…, and the repo github.com/gagneurlab/sco…! Big thanks to Alexander Karollus trevor manz Jason Buenrostro, and Fabian Theis for their contributions to this work! It was a very fun joint effort!

7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies Today, we (Ajay Labade, @carolinecomenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/

Unveiling Expansion in situ genome sequencing: a revolutionary leap in spatial genomics! ExIGS enables simultaneous nanoscale mapping of gDNA and proteins in single cells. It's been an incredible journey co-leading this work with zack chiang , Caroline Comenho , Jason Buenrostro

So excited to finally share ExIGS, a new tech we (zack chiang Ajay Labade Jason Buenrostro) developed to combine spatial genomics with expansion microscopy

This is phenomenal!! ExIGS: Expansion in situ Genome Sequencing!! —> Enabling genomic DNA sequencing and superresolution localization of nuclear proteins in single cells!! By zack chiang Ajay Labade Jason Buenrostro & co biorxiv.org/content/10.110…

Thrilled to see our ExIGS tool featured! A true testament to the power of collaboration. Huge congrats to the team for their hard work! 🧬Ajay Labade zack chiang Caroline Comenho nature.com/articles/d4158…

Excited to share our latest work, where we develop TDAC-seq to simultaneously map CRISPR-induced genetic variants & chromatin accessibility at targeted genomic loci by leveraging a dsDNA cytidine deaminase, DddA. Highlights below: 1/11 biorxiv.org/content/10.110…

Super excited to share our new study from the Jason Buenrostro Lab in nature! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: nature.com/articles/s4158…

Nature research paper: Multiscale footprints reveal the organization of cis-regulatory elements go.nature.com/40jyD88

Gene regulation is complex, with ~2,000 TFs interacting with ~1M CREs. Yan Hu, Max Horlbeck (Jason Buenrostro), Ruochi Zhang (Eric and Wendy Schmidt Center) unveil PRINT & seq2PRINT: tools decoding TF/CRE binding at single-cell resolution. Broad Institute nature ericandwendyschmidtcenter.org/updates/print-…

“Biology and AI form a two-way street—the diverse expertise within our team provides different perspectives on the problem and motivates innovative approaches for investigation,” said Ruochi Zhang. ericandwendyschmidtcenter.org/updates/print-… Yan Hu Jason Buenrostro Broad Institute nature

I’m excited to share my work over the last few years with Jason Buenrostro! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagaraj…. Here’s a walkthrough of what we found (🧵)

We’d like to thank our collaborators in the Omer Yilmaz and Breault labs, and PROSPECT Cancer Research UK National Cancer Institute for their support. Find out about binding partners, drugging AP-1, the new tools we made and more here at our pre-print: tinyurl.com/ColitisNagaraj…

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation science.org/doi/10.1126/sc… Science Magazine Jason Buenrostro Ajay Labade Caroline Comenho

The peer-reviewed version of expansion in situ genome sequencing is now out in Science! The news is bittersweet – when we first revealed this last September, I never guessed it would be my final paper in academia, but a lot has changed. A few parting thoughts:

A new combination technique enables DNA sequencing and high-resolution imaging in intact cells — offering new insights into progeria and aging. broad.io/expansion-in-s… Jason Buenrostro Fei Chen Lab Ajay Labade Caroline Comenho zack chiang Science Magazine

Thrilled to announce that our work on Expansion In Situ Genome Sequencing (ExIGS) is now published in Science Magazine! ExIGS allows us to sequence DNA and image proteins with super-resolution directly within single cells. science.org/doi/10.1126/sc…