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Jason Buenrostro

@jbuenrostro.bsky.social
2.1K followers 166 following 36 posts

Epigenetics & Genomics Harvard University & Broad Institute www.macfound.org/fellows/class-of-2… buenrostrolab.com

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Jason Buenrostro @jbuenrostro.bsky.social · 18/07/2026
Thank you Broad Institute of MIT and Harvard for this profile. The last 2 years have been an extraordinary moment of creativity and inspiration. If you’re interested in joining us, PM me! We’re building new methods, models and ML tools - we’re recruiting at all levels!
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Waggoner Lab @labwaggoner.bsky.social · 06/05/2026
@biorxivpreprint.bsky.social RUNX is a "master collaborator" in T cells, where RUNX2:KLF2 interactions specify exhaustion, which can be perturbed by mutating the RUNX2:KLF2 interface or amp'ed by synthetic tethering of RUNX2 to KLF2 @jbuenrostro.bsky.social @harvard.edu doi.org/10.64898/202...
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Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
Can we control cells by forcing TFs to collaborate? Interested? Read our preprint! An awesome collaboration with @cgersbach.bsky.social, @igvfconsortium.bsky.social, Christian McRoberts Amador, @rachel-savage.bsky.social: www.biorxiv.org/content/10.6... 🧵
biorxiv.org
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Surya Nagaraja @snaga13.bsky.social · 28/03/2026
A little late to Bluesky but my postdoc work w/ @jbuenrostro.bsky.social now out in @nature.com "Epigenetic memory of colitis promotes tumour growth" www.nature.com/articles/s41... We wanted to understand how transient inflammation can create an increase in cancer risk, even after full recovery 🧵
nature.com
Epigenetic memory of colitis promotes tumour growth - Nature
Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...
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Waggoner Lab @labwaggoner.bsky.social · 26/03/2026
The epigenome "remembers" inflammation and primes stem cells for cancer @snaga13.bsky.social @nature.com @jbuenrostro.bsky.social @harvard.edu www.nature.com/articles/s41... www.nature.com/articles/d41...
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Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
It’s well known that inflammation increases cancer risk, but how? The answer: the epigenome "remembers" inflammation and primes stem cells for cancer. Here is our paper: nature.com/articles/s41... And a special shoutout to the lead author @snaga13.bsky.social A 🧵
nature.com
Epigenetic memory of colitis promotes tumour growth - Nature
Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...
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Broad Institute @broadinstitute.org · 25/03/2026
Chronic gut inflammation leaves behind “molecular scars” that may raise the risk for developing cancer, according to a new study showing that epigenetic memory of colitis, along with a cancer-promoting mutation, can accelerate tumor growth in mice. @jbuenrostro.bsky.social
broad.io
How inflammation may prime the gut for cancer
A study in mice suggests that even intestinal cells that appear healthy may hold epigenetic “memories” of earlier bouts of inflammation that can promote colon cancer later in life.
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GenomeTDCC @genometdcc.org · 17/03/2026
Coming Soon: March 31 @2pm ET. 📅 Charting Cellular Futures: Lineage Recording & Regulatory Network Insights. Free webinar featuring @jshendure.bsky.social and @jbuenrostro.bsky.social. Register www.jax.org/GenomeTechDev26/ 🧪🧪💻
Free webinar featuring Jay Shendure and Jason Buenrostro. Charting Cellular Futures: Lineage Recording & Regulatory Network Insights. March 31 2pm ET. Register www.jax.org/GenomeTechDev26/
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Broad Institute @broadinstitute.org · 04/11/2025
Broad has launched the Biology of Adversity Project, led by @jbuenrostro.bsky.social a 2023 @macfound.org fellow, to uncover how adverse life experiences can inflict molecular “scars” in the genome and body and increase risk of heart disease and other disorders. Learn more: broad.io/BAP
Jason Buenrostro stands behind a podium speaking to an audience.
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Jason Buenrostro @jbuenrostro.bsky.social · 21/10/2025
This is a great opportunity. Apply and join our community! academicjobsonline.org/ajo/jobs/30714
academicjobsonline.org
Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center
Job #AJO30714, Postdoctoral Associate, Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, US
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Ryan Flynn @raflynn5.bsky.social · 07/10/2025
We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...
biorxiv.org
DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells
The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...
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Çağrı Çevrim @cagricevrim.bsky.social · 10/10/2025
I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉 @karalmckinley.bsky.social We built the first transgenic model of menstruation in mice. We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪 www.biorxiv.org/content/10.1... 🧵
biorxiv.org
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
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Vijay Ramani @vram142.bsky.social · 09/10/2025
Congratulations @karalmckinley.bsky.social & lab on their groundbreaking recent preprint establishing + characterizing a chemically inducible model of menstruation in mouse: www.biorxiv.org/content/10.1... My jaw dropped when I heard this presented earlier this year. Incredible.
biorxiv.org
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
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Broad Institute @broadinstitute.org · 30/09/2025
Leading epigenetics researcher and longtime Broad member @jbuenrostro.bsky.social has been named core institute member of the Broad. His lab will study how cells change in response to life experiences, and how those alterations affect health and disease.
broad.io
Jason Buenrostro named core institute member at Broad
An expert in epigenetics and longtime member of the Broad community, Buenrostro will focus on how life experiences can alter the epigenome and increase risk of disease.
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
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
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
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
biorxiv.org
Engineered histones reshape chromatin in human cells
Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
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
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Vinay Kartha @vkartha.bsky.social · 10/07/2025
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
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Xin Jin @xinjin.bsky.social · 20/06/2025
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...
hhmi.org
The 2025 Freeman Hrabowski Scholars | HHMI
Freeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields.
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Epigenome Technologies @epigenometech.bsky.social · 05/06/2025
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
bit.ly
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...
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Di Jiang @dijiang319.bsky.social · 29/05/2025
@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
science.org
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...
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Broad Institute @broadinstitute.org · 29/05/2025
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
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Julia Belk @juliabelk.bsky.social · 18/04/2025
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)
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Anshul Kundaje @anshulkundaje.bsky.social · 21/02/2025
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/
science.org
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
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Surya Nagaraja @snaga13.bsky.social · 18/02/2025
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)
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Surya Nagaraja @snaga13.bsky.social · 18/02/2025
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 (🧵)
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Roxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 27/01/2025
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.
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Ryan Flynn @raflynn5.bsky.social · 25/01/2025
"cryoET" ? (h/t Jon Perr in my lab) #CryoET #TeamTomo
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Yan Hu @yanhu97.bsky.social · 23/01/2025
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...
nature.com
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
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Nature @nature.com · 13/01/2025
A decade in, expansion microscopy is unlocking insights across biology and medicine go.nature.com/4adlNgg
go.nature.com
‘Expansion microscopy’ turns ten: how a tissue-swelling method brought super-resolution imaging to the masses
A decade in, expansion microscopy is unlocking insights across biology and medicine.
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Stirling Churchman @stirlingchurchman.bsky.social · 31/12/2024
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
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Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
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/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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BrunetLab @brunetlab.bsky.social · 18/12/2024
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 🧵
rdcu.be
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...
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Andrew Payne @andrewcpayne.bsky.social · 03/12/2024
🧪 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
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Jason Buenrostro @jbuenrostro.bsky.social · 23/11/2024
Important piece on the future of a critical US investment www.nature.com/articles/s41...
nature.com
The BRAIN initiative: a pioneering program on the precipice - Nature Neuroscience
Launched in 2013, the BRAIN Initiative (BRAIN) in the United States aimed to unlock the mysteries of the brain and develop new treatments for neurological and neuropsychiatric disorders. The success o...
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Jason Buenrostro @jbuenrostro.bsky.social · 22/11/2024
Happy for my former mentor Howard Chang, congratulations Howard!: www.amgen.com/newsroom/pre...
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Anshul Kundaje @anshulkundaje.bsky.social · 21/11/2024
If others have ways of getting around the very poor recall of fine mapping methods + their instability across populations, we would love to know.
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Anshul Kundaje @anshulkundaje.bsky.social · 20/11/2024
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 20/11/2024
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 20/11/2024
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.
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Kaur Alasoo @kauralasoo.bsky.social · 20/11/2024
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.
ebi.ac.uk
Project < eQTL Catalogue < EMBL-EBI
EMBL-EBI
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Kaur Alasoo @kauralasoo.bsky.social · 20/11/2024
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...
medrxiv.org
Insights from complex trait fine-mapping across diverse populations
Despite the great success of genome-wide association studies (GWAS) in identifying genetic loci significantly associated with diseases, the vast majority of causal variants underlying disease-associat...
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Jason Buenrostro @jbuenrostro.bsky.social · 19/11/2024
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!
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Jason Buenrostro @jbuenrostro.bsky.social · 17/11/2024
go.bsky.app/KWAeJxp
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Razvan Borza @rborza.bsky.social · 16/11/2024
🚨 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
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Roxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 12/11/2024
Another amazing academic/scientic follow: @jbuenrostro.bsky.social (also a MacArthur fellow!).
jbuenrostro.bsky.social
Jason Buenrostro (@jbuenrostro.bsky.social)
Epigenetics & Genomics Harvard University & Broad Institute buenrostrolab.com
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Jason Buenrostro @jbuenrostro.bsky.social · 16/11/2024
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...
cell.com
Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay
Tay et al. demonstrate an antigen-specific assay producing exhausted T cells that reflect those found in human tumors. They identify IKZF1 (IKAROS) as a driver of exhaustion progression and validate t...
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Jason Buenrostro @jbuenrostro.bsky.social · 16/11/2024
That time when your Postdoc thinks he runs the place bsky.app/profile/zchi...
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zack chiang @zchiang.bsky.social · 11/11/2024
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/
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