Jon Bloom
@MorseCell
Sr Lecturer at MIT Math/ESG, data science & topology. ML @CellarityBio; Institute Scientist, @hailgenetics & MIA @BroadInstitute; math at MIT, Columbia, Harvard
In @NatureGenet we report that base editing of trinucleotide repeats (TNRs) reduces somatic repeat expansions in Huntington’s disease (HD) and Friedreich’s ataxia (FRDA)—in patient-derived cells and in vivo—a collaboration with the Mouro Pinto lab. drive.google.com/file/d/1on7kdy… 1/14
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing @divyanshi91! biorxiv.org/content/10.110…
Excited to share some of the work we're doing at Digital Bio to engineer spatially intelligent medicines. Our MxP platform is designed to identify and validate synergistic targets for multifunctional biologics and combination therapies for solid tumors: digit.bio/products.
Digital Bio unlocked spatial NGS in FFPE patient tissues, at scale. Check us out! digit.bio/products
🥳 Today I was promoted to Senior Lecturer at MIT Math, exactly a decade after my postdoc there. A decade is standard from Lecturer to Principal to Senior. I'm grateful MIT saw the 8 years in genomics, ML, and biotech as an asset. I 🤬 love this job!! 🧑🏫🧮 linkedin.com/feed/update/ur…
Today, we are thrilled to announce that @VerveTx has entered into a definitive agreement to be acquired by @EliLillyandCo From 2018 to 2025, Verve moved a new concept (a one-dose future for the treatment of atherosclerotic cardiovascular disease) and a new medical technology (in…
Alzheimer's disease (AD) is associated with numerous proteome changes. We find large & consistent decrease in the abundance and stoichiometry of 20S proteasome subunits. ⬛️ It leads to abnormal accumulation of 20S substrate proteins. biorxiv.org/content/10.110…
We performed global and systematic proteome analysis of Alzheimer's disease (AD). Our results suggest that decreased ubiquitin-proteasome system capacity and impaired clearance of proteins contribute substantially to proteopathic burden in AD. biorxiv.org/content/10.110…
Our paper on detecting abandoned oil wells with machine learning, led by @pratinavseth, is accepted at ICML 2025! These wells are a major source of emissions (and groundwater pollution). More details in the thread, and preprint here: arxiv.org/abs/2410.09032
I’m happy to share that our paper on detecting oil & gas wells with AI has been accepted to ICML 2025! Millions of such wells exist, leaking methane & other toxins. We show how remote sensing can help find them, using high-resolution, multi-spectral satellite imagery. @icmlconf
I am pleased to announce a new version of my RL tutorial. Major update to the LLM chapter (eg DPO, GRPO, thinking), minor updates to the MARL and MBRL chapters and various sections (eg offline RL, DPG, etc). Enjoy! arxiv.org/abs/2412.05265
Another medical milestone! The first patient treated with a prime edited therapeutic shows positive clinical outcomes consistent with effective rescue of his chronic granulomatous disease (CGD), a debilitating and life-shortening primary immunodeficiency. At least 19 base editing…
Genomes encode biological complexity, which is determined by combinations of DNA mutations across millions of bases In new @arcinstitute work, we report the discovery and engineering of the first programmable DNA recombinases capable of megabase-scale human genome rearrangement
What if we could universally recombine, insert, delete, or invert any two pieces of DNA? In back-to-back @Nature papers, we report the discovery of bridge RNAs and 3 atomic structures of the first natural RNA-guided recombinase - a new mechanism for programmable genome design
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
Can AI enable safe vaccines at scale that last? Can we anticipate immune response? We tested this .. See cell.com/immunity/fullt… and hms.harvard.edu/news/building-… And big thx to @CEPIvaccines for funding
🚨 New in @ImmunityCP ! EVE-Vax, an AI model that anticipates future viral evolution and designs antigens to proactively test vaccines + therapeutics—before variants even emerge. We envision this work will help make future-proofed vaccines and therapeutics. 👇 (1/7)
Researchers have devised a scheme for painting the edges of a graph that’s *almost* as speedy as possible. Steve Nadis reports: quantamagazine.org/the-fastest-wa…
Today I have received by email: one disproof of the Riemann hypothesis, one proof that P =/= NP, one proof of the Riemann hypothesis, and one proof that Peano arithmetic is inconsistent (which follows from the two Riemann hypothesis papers, but this was an independent discovery).
We @navigationfund are looking for proposals on how to move scientific publishing into the future. If you think we can do better, stop complaining and come build by applying AI towards open science os.nav.fund/ai-for-os/
I am pleased to announce that I have updated the online versions of my 2 textbooks (see probml.github.io/pml-book/): I fixed all issues listed on github, added some new references (esp on LLMs), and made a few other small tweaks.
Regulatory sequence ML has been widely applied to predict substitution SNP effects (to promising results!), but most teams have shied away from indels. biorxiv.org/content/10.110…
We developed a new siRNA drug candidate for prion disease, a @broadinstitute / @RTI_UMassChan collaboration. We now have an open IND meaning FDA has given us permission to start first-in-human trials. Work remains before trials can launch. The full update: cureffi.org/2025/04/14/ope…
Last month there was an announcement that I thought was a major advancement in world health, but it got little attention. I thought I would tell you all a little bit about it and why it is so important. 1/25