
Sr Lecturer at MIT Math/ESG, data science & topology. ML @CellarityBio; Institute Scientist, @hailgenetics & MIA @BroadInstitute; math at MIT, Columbia, Harvard
Cambridge, MA
Joined January 2017
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Jon Bloom retweeted
Is single nucleus RNA-seq representative of single-cell transcriptomes and proteomes ?
This comparison shows that:
1⃣ Both scRNA-seq and snRNA-seq correlate weakly to single-cell proteomes.
2⃣ The correlation is much lower for snRNA-seq
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In 2001 George W Bush proposed a partial privatization plan for Social Security so you could put 10% of your SS contribution into the markets.
People rejected this.
We can now see that if it had passed, the 10% that went into the markets would have outperformed the 90% the government managed, the program would be solvent, and the average SS recipient would be receiving 2X what they currently receive.
The worst bet you’ll ever make is betting on government.
Jon Bloom retweeted
❄️ Happy New Year! MIA returns for spring 2026 on Wednesday, February 4 with @muntakim_rafi and @CarldeBoerPhD.
Check out our spring schedule, read abstracts, and watch past videos at broad.io/MIA.
See you soon!
@Schmidt_Center
Jon Bloom retweeted
Excited to share our new work on immune aging! We explored whether the liver could serve as a temporary "factory" to produce immune factors that decline with aging, potentially helping to rejuvenate aged immunity. @mircoscopy.
Jon Bloom retweeted
Real Analysis, The Game (v0.1) is DONE!!
44 Worlds
138 Levels
All your old favorites like Bolzano-Weierstrass and Heine-Borel, Uniform Convergence and Riemann Sums, and the biggest Boss of all, the Intermediate Value Theorem! :)
Play the game here: adam.math.hhu.de/#/g/AlexKon…
Follow along with all the lectures/videos/notes here: alexkontorovich.github.io/20…
Very relieved to have survived this semester, it was a tough one! Here's a sneak preview of where this project is headed next (math as a Scratch game... Let's get 12 year olds doing epsilon-delta proofs!)
Jon Bloom retweeted
I wrote about the challenge of mathematicians explaining mathematics to other mathematicians for @ScienceMagazine's Expert Voices column series:
science.org/doi/10.1126/scie…
Jon Bloom retweeted
Our MIA 10-Year Anniversary Celebration is this Friday, October 17! 🥳
Note that this will be at 300 Binney St. (2110 - Charles) and online, and not in our usual Acadia room. We will NOT have an MIA event this Wednesday, October 15 (tomorrow).
Register:
ericandwendyschmidtcenter.or…
Jon Bloom retweeted
My resignation letter from CDC.
Dear Dr. Houry,
I am writing to formally resign from my position as Director of the National Center for Immunization and Respiratory Diseases at the Centers for Disease Control and Prevention (CDC), effective August 28, 2025, close of business. I am happy to stay on for two weeks to provide transition, if requested.
This decision has not come easily, as I deeply value the work that the CDC does in safeguarding public health and am proud of my contributions to that critical mission. However, after much contemplation and reflection on recent developments and perspectives brought to light by Secretary Robert F. Kennedy Jr., I find that the views he and his staff have shared challenge my ability to continue in my current role at the agency and in the service of the health of the American people. Enough is enough.
While I hold immense respect for the institution and my colleagues, I believe that it is imperative to align my professional responsibilities to my system of ethics and my understanding of the science of infectious disease, immunology, and my promise to serve the American people. This step is necessary to ensure that I can contribute effectively in a capacity that allows me to remain true to my principles.
I am unable to serve in an environment that treats CDC as a tool to generate policies and materials that do not reflect scientific reality and are designed to hurt rather than to improve the public’s health. The recent change in the adult and children’s immunization schedule threaten the lives of the youngest Americans and pregnant people. The data analyses that supported this decision have never been shared with CDC despite my respectful requests to HHS and other leadership. This lack of meaningful engagement was further compounded by a “frequently asked questions” document written to support the Secretary’s directive that was circulated by HHS without input from CDC subject matter experts and that cited studies that did not support the conclusions that were attributed to these authors. Having worked in local and national public health for years, I have never experienced such radical non-transparency, nor have I seen such unskilled manipulation of data to achieve a political end rather than the good of the American people.
It is untenable to serve in an organization that is not afforded the opportunity to discuss decisions of scientific and public health importance released under the moniker of CDC. The lack of communication by HHS and other CDC political leadership that culminates in social media posts announcing major policy changes without prior notice demonstrate a disregard of normal communication channels and common sense. Having to retrofit analyses and policy actions to match inadequately thought-out announcements in poorly scripted videos or page long X posts should not be how organizations responsible for the health of people should function. Some examples include the announcement of the change in the COVID-19 recommendations for children and pregnant people, the firing of scientists from ACIP by X post and an op-ed rather than direct communication with these valuable experts, the announcement of new ACIP members by X before onboarding and vetting have completed, and the release of term of reference for an ACIP workgroup that ignored all feedback from career staff at CDC.
The recent term of reference for the COVID vaccine work group created by this ACIP puts people of dubious intent and more dubious scientific rigor in charge of recommending vaccine policy to a director hamstrung and sidelined by an authoritarian leader. Their desire to please a political base will result in death and disability of vulnerable children and adults. Their base should be the people they serve not a political voting bloc.
I have always been first to challenge scientific and public health dogma in my career and was excited by the opportunity to do so again. I was optimistic that there would be an opportunity to brief the Secretary about key topics such as measles, avian influenza, and the highly coordinated approach to the respiratory virus season. Such briefings would allow exchange of ideas and a shared path to support the vision of “Making America Healthy Again.” We are seven months into the new administration, and no CDC subject matter expert from my Center has ever briefed the Secretary. I am not sure who the Secretary is listening to, but it is quite certainly not to us. Unvetted and conflicted outside organizations seem to be the sources HHS use over the gold standard science of CDC and other reputable sources. At a hearing, Secretary Kennedy said that Americans should not take medical advice from him. To the contrary, an appropriately briefed and inquisitive Secretary should be a source of health information for the people he serves. As it stands now, I must agree with him, that he should not be considered a source of accurate information.
The intentional eroding of trust in low-risk vaccines favoring natural infection and unproven remedies will bring us to a pre-vaccine era where only the strong will survive and many if not all will suffer. I believe in nutrition and exercise. I believe in making our food supply healthier, and I also believe in using vaccines to prevent death and disability. Eugenics plays prominently in the rhetoric being generated and is derivative of a legacy that good medicine and science should continue to shun.
The recent shooting at CDC is not why I am resigning. My grandfather, who I am named after, stood up to fascist forces in Greece and lost his life doing so. I am resigning to make him and his legacy proud. I am resigning because of the cowardice of a leader that cannot admit that HIS and his minions’ words over decades created an environment where violence like this can occur. I reject his and his colleagues’ thoughts and prayers, and advise they direct those to people that they have not actively harmed.
For decades, I have been a trusted voice for the LGBTQ community when it comes to critical health topics. I must also cite the recklessness of the administration in their efforts to erase transgender populations, cease critical domestic and international HIV programming, and terminate key research to support equity as part of my decision.
Public health is not merely about the health of the individual, but it is about the health of the community, the nation, the world. The nation’s health security is at risk and is in the hands of people focusing on ideological self-interest.
I want to express my heartfelt gratitude for the opportunities for growth, learning, and collaboration that I have been afforded during my time at the CDC. It has been a privilege to work alongside such dedicated professionals who are committed to improving the health and well-being of communities across the nation even when under attack from within both physically and psychologically.
Thank you once again for the support and guidance I have received from you and previous CDC leadership throughout my tenure. I wish the CDC continued success in its vital mission and that HHS reverse its dangerous course to dismantle public health as a practice and as an institution. If they continue the current path, they risk our personal well-being and the security of the United States.
Sincerely,
Demetre C. Daskalakis MD MPH (he/his/him)
Jon Bloom retweeted
Scaling DNA sequencing is a notable success story.
Scaling protein analysis is harder since the proteome is a much taller mountain: nature.com/articles/s41592-0…
@AsimovPress writes about @ParallelSqTech's approach to scale up proteomics.
Jon Bloom retweeted
Teenager Hannah Cairo's recent proof of a major problem in harmonic analysis is the most amazing—and moving—story I've covered in more than a decade as a math journalist.
Earlier this year, a 17-year-old high school student named Hannah Cairo solved a 40-year-old mystery about how waves behave, surprising and exciting mathematicians. @KSHartnett reports: quantamagazine.org/at-17-han…
Jon Bloom retweeted
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/10.1101/…
Jon Bloom retweeted
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.
Jon Bloom retweeted
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/urn…
Jon Bloom retweeted
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 vivo base editing) to positive initial data in patients, recently showing that our lead asset – VERVE-102 targeting PCSK9 – has the potential to deeply and durably lower blood low-density lipoprotein cholesterol after a single intravenous infusion.
Now, we have an opportunity to take the next phase of this journey for VERVE-102 (further clinical development in Phase 2 and Phase 3 clinical trials, regulatory approval and ultimately, commercialization) as well as the rest of our pipeline with an ideal strategic partner in Lilly.
Lilly shares our vision and we believe their global research, clinical, regulatory and commercial capabilities will help accelerate the development of our novel class of single-course gene editing medicines that will change the treatment paradigm for the millions of patients worldwide living with cardiovascular disease.
My deepest thanks to the entire Verve team for their expertise, creativity and grit. We are grateful to the investigators and patients who have contributed to the success of our clinical trials so far.
@VerveTx + @EliLillyandCo should emerge as a powerful combination, given their complementary cardiometabolic health capabilities, to create a novel class of single-course gene editing medicines that make life better for people around the world.
Details of transaction here: investor.lilly.com/news-rele…
$VERV $LLY
Jon Bloom retweeted
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/10.1101/…
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/10.1101/…
Jon Bloom retweeted
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/1on7…
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