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Join our team! We’re looking for an exceptional candidate to help us lead our new center. Editor experience is a plus, but not required. Reach out with questions. broadinstitute.avature.net/en_US/careers/…

What's cooking~

This looks so cool!

We wrote a review article for the 2024 edition of Annual Reviews of Biomedical Data Science! In this age of ML 🖥️ and patient data, privacy-enhancing technologies (PETs) are ever more important. We review several modern PETs and highlight use cases in biomedicine for each! (1/n)

Let me tell you a story. It'll end up at the current tech-bio and protein design scene. But the story starts about 25 years earlier. Did you know that, commercially, the human genome project precipitated the end and not the start of a genomics boom? 1/

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/

Just want to add that you should follow/hire all my amazing co-authors! IGS/expansion proof-of-principle - Paul Reginato (now Homeworld Collective) - Andrew Payne (now E11 Bio) ExIGS - Ajay Labade (seeking PI positions in India) - @carolinecomenho (seeking biotech PM positions)

Blown away by the response to our preprint - I always forget one of the best parts of science is seeing others genuinely excited about your work Thought it might be a fun time to repost my 2022 essay on where spatial technologies may go in the future: chianglab.bio/2024/09/26/spa…

Interested in pursuing #machinelearning, #appliedmathematics, #statistics, or #computationalresearch to work on biomedical problems at the Broad Institute? Apply to become a Eric and Wendy Schmidt Center postdoctoral associate: broad.io/ewsc-postdoc

Can we skip genomic Foundation Model pretraining? Our work L2G repurposes language LLMs for genomics via cross-modal transfer, matching fine-tuned genomic FMs. Kudos to Wenduo Cheng & amazing collab w/ Ameet Talwalkar. L2G, language to genome; L2G, life’s too good biorxiv.org/content/10.110…

A troubling incident unfolded at #NeurIPS2024, where a keynote speaker used a slide that perpetuated harmful stereotypes and racial biases against Chinese students and researchers. I wasn't attending the conference, but I watched the talk recording and followed this closely. 1/7

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…

Thrilled to introduce a new single-cell 3D genome analysis tool to our toolkit! Our high-throughput droplet Hi-C (dscHi-C) and dscHi-C-multiome methods use droplet microfluidics to generate tens of thousands of single-cell Hi-C profiles with high sensitivity in a single batch.

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…

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-…

What do you do when grants are cancelled, faculty searches are frozen, and the ability to do the science you believe in is slipping out of reach? I wrote an essay. On efforts to solve aging with reprogramming, the primacy of the epigenome, and the path to rewriting our future:

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:

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…

It's a wrap on my postdoc Harvard University. It's been a privilege to develop ExIGS and contribute to the birth of expansion genomics! Deeply grateful to Jason Buenrostro, my amazing co-authors zack chiang & Caroline Comenho, & colleagues who made Boston feel like home. Goodbye!