Jason Buenrostro @jbuenrostro.bsky.social · 18/07/2026Thank 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! 0239
Reposted by Jason BuenrostroWaggoner 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... 052
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026Can 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 13310
Reposted by Jason BuenrostroSurya Nagaraja @snaga13.bsky.social · 28/03/2026A 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.comEpigenetic memory of colitis promotes tumour growth - NatureColonic 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... 3429
Reposted by Jason BuenrostroWaggoner Lab @labwaggoner.bsky.social · 26/03/2026The 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... 0132
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026It’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.comEpigenetic memory of colitis promotes tumour growth - NatureColonic 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... 16226
Reposted by Jason BuenrostroBroad Institute @broadinstitute.org · 25/03/2026Chronic 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.socialbroad.ioHow inflammation may prime the gut for cancerA 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. 0116
Reposted by Jason BuenrostroGenomeTDCC @genometdcc.org · 17/03/2026Coming 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/ 🧪🧪💻 001
Reposted by Jason BuenrostroBroad Institute @broadinstitute.org · 04/11/2025Broad 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 122
Jason Buenrostro @jbuenrostro.bsky.social · 21/10/2025This is a great opportunity. Apply and join our community! academicjobsonline.org/ajo/jobs/30714academicjobsonline.orgBroad 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 062
Reposted by Jason BuenrostroRyan Flynn @raflynn5.bsky.social · 07/10/2025We’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.orgDNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cellsThe 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 ... 37622
Reposted by Jason BuenrostroÇağrı Çevrim @cagricevrim.bsky.social · 10/10/2025I’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.orgInduction of menstruation in mice reveals the regulation of menstrual sheddingDuring 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... 1423382
Reposted by Jason BuenrostroVijay Ramani @vram142.bsky.social · 09/10/2025Congratulations @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.orgInduction of menstruation in mice reveals the regulation of menstrual sheddingDuring 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... 16621
Reposted by Jason BuenrostroBroad Institute @broadinstitute.org · 30/09/2025Leading 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.ioJason Buenrostro named core institute member at BroadAn 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. 1213
Reposted by Jason Buenrostrosiddhartha jena @epijenatics.bsky.social · 11/09/2025One 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 ❄️🚀🪐🌱9/9 151
Reposted by Jason Buenrostrosiddhartha jena @epijenatics.bsky.social · 11/09/2025Huge 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... 8/9biorxiv.orgEngineered histones reshape chromatin in human cellsHistone 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 ... 2194
Reposted by Jason Buenrostrosiddhartha jena @epijenatics.bsky.social · 11/09/2025Excited 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 18832
Reposted by Jason BuenrostroVinay Kartha @vkartha.bsky.social · 10/07/2025Had 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 061
Reposted by Jason BuenrostroXin Jin @xinjin.bsky.social · 20/06/2025Honored 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.orgThe 2025 Freeman Hrabowski Scholars | HHMIFreeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields. 16778
Reposted by Jason BuenrostroEpigenome Technologies @epigenometech.bsky.social · 05/06/2025Epigenetics 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.combit.lyExpansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulationMicroscopy 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... 0185
Reposted by Jason BuenrostroDi 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 #ExpansionMicroscopyscience.orgExpansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulationMicroscopy 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... 04113
Reposted by Jason BuenrostroBroad Institute @broadinstitute.org · 29/05/2025A 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 0236
Reposted by Jason BuenrostroJulia Belk @juliabelk.bsky.social · 18/04/2025A 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) 162
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 21/02/2025Disease 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.orgDisease diagnostics using machine learning of B cell and T cell receptor sequencesClinical 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 ... 69725
Reposted by Jason BuenrostroSurya Nagaraja @snaga13.bsky.social · 18/02/2025We’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) 041
Reposted by Jason BuenrostroSurya Nagaraja @snaga13.bsky.social · 18/02/2025New 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 (🧵) 16619
Reposted by Jason BuenrostroRoxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 27/01/2025To 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. 41490186
Reposted by Jason BuenrostroRyan Flynn @raflynn5.bsky.social · 25/01/2025"cryoET" ? (h/t Jon Perr in my lab) #CryoET #TeamTomo 2412
Reposted by Jason BuenrostroYan Hu @yanhu97.bsky.social · 23/01/2025Super 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.comMultiscale footprints reveal the organization of cis-regulatory elements - NatureWe 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. 17731
Reposted by Jason BuenrostroNature @nature.com · 13/01/2025A decade in, expansion microscopy is unlocking insights across biology and medicine go.nature.com/4adlNgggo.nature.com‘Expansion microscopy’ turns ten: how a tissue-swelling method brought super-resolution imaging to the massesA decade in, expansion microscopy is unlocking insights across biology and medicine. 18519
Reposted by Jason BuenrostroStirling Churchman @stirlingchurchman.bsky.social · 31/12/2024I’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 3237579
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 25/12/2024Our 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.orgChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variantsDespite 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... 723189
Reposted by Jason BuenrostroBrunetLab @brunetlab.bsky.social · 18/12/2024Thrilled 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.beSpatial transcriptomic clocks reveal cell proximity effects in brain ageingNature - 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... 2230296
Reposted by Jason BuenrostroAndrew 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 616954
Jason Buenrostro @jbuenrostro.bsky.social · 23/11/2024Important piece on the future of a critical US investment www.nature.com/articles/s41...nature.comThe BRAIN initiative: a pioneering program on the precipice - Nature NeuroscienceLaunched 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... 081
Jason Buenrostro @jbuenrostro.bsky.social · 22/11/2024Happy for my former mentor Howard Chang, congratulations Howard!: www.amgen.com/newsroom/pre... 0181
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 21/11/2024If others have ways of getting around the very poor recall of fine mapping methods + their instability across populations, we would love to know. 041
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 20/11/2024Of 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. 051
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 20/11/2024We 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. 131
Reposted by Jason BuenrostroAnshul Kundaje @anshulkundaje.bsky.social · 20/11/2024Yeah 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. 251
Reposted by Jason BuenrostroKaur Alasoo @kauralasoo.bsky.social · 20/11/2024Yes, 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-EBIEMBL-EBI 171
Reposted by Jason BuenrostroKaur Alasoo @kauralasoo.bsky.social · 20/11/2024For 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.orgInsights from complex trait fine-mapping across diverse populationsDespite 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... 2184
Jason Buenrostro @jbuenrostro.bsky.social · 19/11/2024Hey, 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! 106821
Reposted by Jason BuenrostroRazvan 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 2610430
Reposted by Jason BuenrostroRoxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 12/11/2024Another amazing academic/scientic follow: @jbuenrostro.bsky.social (also a MacArthur fellow!).jbuenrostro.bsky.socialJason Buenrostro (@jbuenrostro.bsky.social)Epigenetics & Genomics Harvard University & Broad Institute buenrostrolab.com 162
Jason Buenrostro @jbuenrostro.bsky.social · 16/11/2024Excited 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.comDegradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assayTay 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... 24411
Jason Buenrostro @jbuenrostro.bsky.social · 16/11/2024That time when your Postdoc thinks he runs the place bsky.app/profile/zchi... 020
Reposted by Jason Buenrostrozack chiang @zchiang.bsky.social · 11/11/20247 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/ 714357