One last thing - I am on the job market! My lab will extend this approach to decode resilient chromatin: adaptations in proteins/DNA that allow for survival in harsh environments. These hold the 🔑 to designing cells that thrive under stress, esp. as we push the limits of where we take them ❄️🚀🪐🌱9/9

Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

Had a super week filled with great science, curiosity and discussions at this year's Gordon Research Conference on Human genetics and genomics. Also fun when you get to give a talk the same day as your postdoc advisor @jbuenrostro.bsky.social

Honored to be an HHMI FHS! Grateful to brilliant colleagues who push me to think deeply, and to my students whose curiosity & energy make the lab a joy. My grad advisor said in genetic screens, you don’t get what you want—you get what you deserve. Hope we are deserving www.hhmi.org/programs/fre...

Epigenetics Update - Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation bit.ly/4jtXApb Jason D. Buenrostro (MIT/Harvard) reporting in Science #Epigenetics #Chromatin --- Gain deeper insights into gene regulation; epigenometech.com

@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/... @jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu #ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy

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-situ @jbuenrostro.bsky.social

A lot of fun teaming up with Hsin and Howard on this, with key contributions from @ruochiz.bsky.social, @zchiang.bsky.social, and @jbuenrostro.bsky.social on the tech dev and @mattjones.bsky.social, Natasha Weiser, and Paul Mischel on the ecDNA analysis. (5/5)

Disease diagnostics using machine learning of B cell and T cell receptor sequences www.science.org/doi/10.1126/... TL;DR: BCRs ARE ALL YOU NEED! (Well actually .... keep reading) 1/

We’d like to thank our collaborators in the Yilmaz and Breault labs, and PROSPECT @cancerresearchuk.org / NCI 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/ColitisNagar... (14/14)

New to bluesky, but I’m excited to share my work over the last few years with @jbuenrostro.bsky.social! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagar.... Here’s a walkthrough of what we found (🧵)

To help people understand the importance of NIH, share what you’ve used their funding for (in easily understandable terms). I’ll start: my NIH postdoc funding helped me develop and test AI tools that could identify skin cancer across diverse skin tones.

"cryoET" ? (h/t Jon Perr in my lab) #CryoET #TeamTomo

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: www.nature.com/articles/s41...

A decade in, expansion microscopy is unlocking insights across biology and medicine https://go.nature.com/4adlNgg

I’m celebrating tonight with my father in law, Jack Strominger, who is about to enjoy his 100th New Years! He wants to know whether any other scientist has published in their 100th year. He’s proud to have a paper in the works. I told him you all would know! Please RT

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

Thrilled to see this paper out!! 🧪 Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors! Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social! rdcu.be/d33uQ 🧵

🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains. Read more: e11.bio/news/roadmap

Important piece on the future of a critical US investment www.nature.com/articles/s41...

Happy for my former mentor Howard Chang, congratulations Howard!: www.amgen.com/newsroom/pre...

If others have ways of getting around the very poor recall of fine mapping methods + their instability across populations, we would love to know.

Of course GWAS causal variants can affect RNA processing/ translation in which case they won't be found in coding or transcriptional regulatory elements but rather 5', 3'UTRs and splice sites. But a large proportion do enrich in open chromatin but fine mapping methods are quite terrible.

We have good evidence that for caQTLs just using the variants that fall in the peaks in the caQTL cohort that are influenced by the locus, dramatically enriches for likely causal variants which strongly align with predictions from predictive models.

Yeah most fine mapping results appear to be super wonky. You either have to set the posterior prob. high (> 0.9) in which case you barely pick up any variants or if u relax the thresholds u get false positives.

Yes, I agree! Fine mapping with individual-level data or in-sample LD works reasonably well, but is not perfect. For the eQTL Catalogue fine mapping (www.ebi.ac.uk/eqtl/), we've found that if the same variant is fine mapped in at least two indepedent datasets then these are very likely to be causal.

For an idea of how well fine mapping results replicate between biobanks, I would really recommend checking out this preprint from @masakanai.bsky.social www.medrxiv.org/content/10.1...

Hey, a question for the genetics community. Does genetic fine-mapping work well? How often does it miss? We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!

🚨 I want to gather all artists working in Biology, Cell Biology, or Molecular Biology illustration If you know any artists who create this kind of work, let me know so I can add them here. Drop a comment to join! 💬 go.bsky.app/KWAeJxp

Another amazing academic/scientic follow: @jbuenrostro.bsky.social (also a MacArthur fellow!).

Excited to see our T-cell exhaustion preprint published! This work is led by Tristan Tay and collaborators at AstraZeneca. See the sub-thread (reformatted for bluesky) originally composed and posted by the newly minted Dr. Tay www.cell.com/cell-reports...

That time when your Postdoc thinks he runs the place bsky.app/profile/zchi...

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, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/