What if we could locate, sequence, and identify every protein in a cell? This would unlock a transformative way to study biology and disease. That question shaped my PhD, and I’m excited to share our new preprint on the Principles of In Situ Protein Sequencing, now live on bioRxiv.

bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 6mo ago

Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition https://www.biorxiv.org/content/10.64898/2026.01.29.702630v1

New preprint out! www.biorxiv.org/content/10.6... One of the most salient lessons I learned in all my adventures with screening and protein engineering is the importance of context. The context in which you test a gene or protein determines what function it has.

bioRxiv Bioengineering@biorxiv-bioeng.bsky.social · 6mo ago

Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes https://www.biorxiv.org/content/10.64898/2026.01.30.702415v1

In a new blog (uniconq.substack.com), Denisa Lepǎdatu and I propose a playful, and perhaps useful, framing of fundamental science that goes for the ground truth - namely, as universe conquering, the confrontation of the foundational unknowns and challenges of existence.

Universe Conquering | Substack

A blog about how to overcome the limits of human existence, through ground truth-oriented understanding. Click to read Universe Conquering, a Substack publication. Launched 12 days ago.

uniconq.substack.com

Amid a tumultuous year, researchers opined on policy changes, funding uncertainty, scientific trends and AI’s impact. Read essays by @tuthill.bsky.social, @bingbrunton.bsky.social, @kordinglab.bsky.social, @eboyden3.bsky.social, @docbecca.bsky.social, and Tim Requarth. #neuroskyence bit.ly/44NL9jy

The Transmitter’s favorite essays of 2025

Throughout a tumultuous year in science, researchers opined on policy changes and funding uncertainty, as well as scientific trends and the impact of artificial-intelligence tools on the field.

bit.ly

We are hiring a lab manager, for our research group, the Synthetic Neurobiology group (aka Boyden Lab) at MIT/HHMI (on the MIT campus, Cambridge, MA)! Please apply if you're qualified and interested, and spread the word! hhmi.wd1.myworkdayjobs.com/External/job...

Laboratory Manager II - Boyden Lab

Primary Work Address: 77 Massachusetts Avenue, Cambridge, MA, 02139 Current HHMI Employees, click here to apply via your Workday account. The Synthetic Neurobiology Group (Boyden Lab) at the MIT McGov...

hhmi.wd1.myworkdayjobs.com

I’m so excited to share my first-author PhD paper, out today in Neuron as a NeuroResource! A huge thanks to all of my co-authors, and of course to my wonderful mentors Guoping Feng, @fennak.bsky.social and @eboyden3.bsky.social. www.cell.com/neuron/fullt...

A transcriptomic atlas of astrocyte heterogeneity across space and time in mouse and marmoset

In this NeuroResource, Schroeder et al. present a transcriptomic atlas across brain regions and developmental time points in mouse and marmoset. Detailed analysis focused on astrocytes revealed that t...

cell.com

Diatoms – microscopic algae found almost everywhere there’s water – make up ~25% of Earth’s annual oxygen production.🌎 EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬 www.cell.com/current-biol...

Just posted, "The Tiling Tree Method, Part 2: Common Pitfalls and How to Overcome Them" a follow-up to our previous essay on the "tiling tree" method for thinking of all the possible solutions to a problem, by Claire Wang, Nina Khera, and myself. engineeringx.substack.com/p/the-tiling...

The Tiling Tree Method, Part 2: Common Pitfalls and How to Overcome Them

How to really think of every way of solving a problem

engineeringx.substack.com

It was fun writing this essay, about bottom-up neuroscience and how we might simulate entire brains, using data collected via new technologies (expansion microscopy, optogenetics, whole brain voltage imaging, and more), with @kordinglab.bsky.social!

The Transmitter @thetransmitter.bsky.social · 10mo ago

Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology, and how neurons generate behavior, write @kordinglab.bsky.social and @eboyden3.bsky.social. #neuroskyence bit.ly/48EzEO8

Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology, and how neurons generate behavior, write @kordinglab.bsky.social and @eboyden3.bsky.social. #neuroskyence bit.ly/48EzEO8

Whole-brain, bottom-up neuroscience: The time for it is now

Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology and how neurons work together to generate…

bit.ly

Wonderful to collaborate with, and to support as an advisor, E11 Bio - and to announce PRISM, a technology for mapping brains in a self-correcting way, by barcoding neurons followed by expansion microscopy! Thread below by E11 Bio CEO Andrew Payne, with preprint at, www.biorxiv.org/content/10.1...

Andrew Payne@andrewcpayne.bsky.social · 10mo ago

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. Read more: e11.bio/blog/prism

Kicking off #GEF25, the Morning Presidential Lecture features @eboyden3.bsky.social on the origins and mission of the event, who calls it 'the first conference of its kind'.

What if you could think of every possible solution to a problem? Then you might be able to simply pick the best one - even if it was highly nonobvious. With the “tiling tree” method, you can learn, and practice, the skill of doing just that: engineeringx.substack.com/p/the-tiling...

The Tiling Tree Method

How to think of every way of solving a problem

engineeringx.substack.com

Just posted, by Nina Khera, @clairebookworm.bsky.social, and myself: “Involuntary collaboration: a strategy for decentralized science”! Discussing the "invent-deploy-discover-design" model, and why the Bell Labs of the 21st century might be the whole earth. engineeringx.substack.com/p/involuntar...

- @ZachinBoston, for @mit.edu News, on the story of Convergent Research and our FROs feat. @eboyden3.bsky.social, @adammarblestone.bsky.social, @andrewcpayne.bsky.social, @sgrodriques.bsky.social, Tom Kalil, @anastasiag.bsky.social... news.mit.edu/2025/former-...

Former MIT researchers advance a new model for innovation

Developed by former MIT researchers, focused research organizations (FROs) undertake large research efforts and have begun to contribute to scientific advances.

news.mit.edu

MIT News reports on focused research organizations (FROs), non-profit startups, developed by some of our group members and alumni. FROs can work on problems that are a poor fit for academia or the for-profit startup world. news.mit.edu/2025/former-...

Former MIT researchers advance a new model for innovation

Developed by former MIT researchers, focused research organizations (FROs) undertake large research efforts and have begun to contribute to scientific advances.

news.mit.edu

Down to my last few post-it notes, that my group members made for me in 2014, after I got tenure at MIT. Each post-it note contains something that I said often enough, that my group members thought it would save me time, to simply hand out a post-it note, whenever the wisdom was needed :)

Just posted, “Engineering Serendipity,” a lightly edited (to accommodate the transition from spoken to written form) version of the commencement speech I gave at my high school, the Texas Academy of Mathematics and Science, May 8, 2025: engineeringx.substack.com/p/engineerin...

Engineering Serendipity

Three Short Stories About How to Increase Luck Through Skill

engineeringx.substack.com

Just published, expansion in situ genome sequencing, where you can sequence DNA while still inside the cell, mapping its organization relative to proteins and other markers, with the help of expansion microscopy! Led by @jbuenrostro.bksy.social. www.science.org/doi/10.1126/...

New op-ed in @nature.com: The Trump administration's assault on freedoms and the rule of law is an existential threat to US science. We urge scientists to speak out in defense of freedoms, not just funding. With Andrea Liu @upenn.edu and Sidney Nagel of UChicago! www.nature.com/articles/d41...

US researchers must stand up to protect freedoms, not just funding

Curtailment of freedoms and disregard for the rule of law in the United States is destroying the ability of science to serve the nation’s, and the world’s, interests. Researchers can take action.

nature.com

"In Down syndrome mice, 40Hz light and sound improve cognition, neurogenesis, connectivity." MIT News: news.mit.edu/2025/in-down... Paper: journals.plos.org/plosone/arti...

Congrats to Lisa Yang - who founded so many visionary centers at MIT, and other places, to do daring and creative research with huge amounts of real-world impact - for being named to the TIME 100 Philanthropy list, for 2025! Grateful to be part of the Yang Tan Collective. time.com/collections/...

TIME100 Philanthropy: K. Lisa Yang

Find out why K. Lisa Yang is on the TIME100 Most Influential People in Philanthropy 2025 list.

time.com

New blog at "Engineering {X}," where X = serendipity, understanding, or existence! @clairebookworm.bsky.social, Nina Khera, and I are co-editors. Our first post, "The Dropout Curriculum," asks: what should you learn, to disrupt fields from the outside? engineeringx.substack.com/p/the-dropou...

The Dropout Curriculum

How do you plan what to learn, to solve the problems you care about?

engineeringx.substack.com

Honored to give the 2025 commencement speech for my amazing high school, the Texas Academy of Mathematics and Science (TAMS) at the University of North Texas (students skip years of high school, and go straight to college). My topic - how to engineer serendipity: www.youtube.com/live/nVknJwk...

Join me May 20 @ 11 AM ET for a webinar with Bio-protocol! I'll walk through our single-shot 20-fold expansion microscopy (20ExM) method + share the full protocol so you can try it too.

Bio-protocol@bio-protocol.bsky.social · last yr.

📢 Bio-protocol Webinars present: Next-generation expansion microscopy: 20× magnification in one step 🔗Register now! Join us on: 🗓 Date: May 20, 2025 ⏰ Time: 11:00 AM EST Speaker: Shiwei Wang #Webinar #LifeSciences #Microscopy

📹 Revisit the discussion on the intricate complexity of brain circuitry with @eboyden3.bsky.social, renowned MIT professor and director of the Synthetic Neurobiology Group, as he seeks to understand human existence.

Technologies for Stimulating and Simulating the Brain | Ed Boyden

YouTube video by Protocol Labs

youtube.com

Fun with worms on @WIRED www.wired.com/story/openwo... We've been thinking about how #celegans can revolutionize science again, together with @kordinglab.bsky.social @eboyden3.bsky.social @wormsense.bsky.social and many other (also find our preprint on #arXiv)

The Worm That No Computer Scientist Can Crack

One of the simplest, most over-studied organisms in the world is the C. elegans nematode. For 13 years, a project called OpenWorm has tried—and utterly failed—to simulate it.

wired.com

MIT’s Ed Boyden is pioneering methods like expansion microscopy to create detailed 3D maps of neural structures, enhancing our understanding of the brain's networks to maybe even fathom life's meaning. 🧠

What if we could understand the meaning of life?

YouTube video by Protocol Labs

youtube.com

Expansion microscopy (ExM) of the entire mouse body (pubs.acs.org/doi/10.1021/...), developed by the labs of Profs. Jae-Byum Chang and Young-Gyu Yoon (former SynthNeuro postdocs running labs at KAIST), could empower studies of how multiple systems (nervous, immune, etc.) interact across scales.