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Henry Lee

@citizenlee.bsky.social
606 followers 719 following 77 posts

CEO at Cultivarium. Technobiologist, starting with microbes.

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Henry Lee @citizenlee.bsky.social · 03/02/2026
Molecular assets on @addgene.bsky.social. Analysis software on @github.com. There's so much to explore, get out there!!
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Henry Lee @citizenlee.bsky.social · 03/02/2026
Today we infer what a gene by computing similarities, whether by sequence or by structure. Incredibly useful for a first pass but not good enough in most cases to understand or engineer biology. You have to modify the genes and measure the consequences to know what they do.
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Henry Lee @citizenlee.bsky.social · 03/02/2026
Over the last decade, biology has learned how to generate genome sequences at extraordinary scale. What hasn’t kept pace is figuring out what those genes actually do.
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Henry Lee @citizenlee.bsky.social · 03/02/2026
So you sequenced a billion+ bases. That don’t impress me much. JERBOA is a toolkit to figure out what genes do at scale. We've used it to unlock 43 non-model microbes across 12 different phyla.
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Henry Lee @citizenlee.bsky.social · 21/01/2026
We scientists were so preoccupied with whether we could send samples out for cheap pooled sequencing, we didn’t stop to think if we should.
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Henry Lee @citizenlee.bsky.social · 20/01/2026
After a few conversations on AI and science this week, I keep coming back to the same point: execution, not ideation, is still the bottleneck. I wrote this up here: open.substack.com/pub/hhlee/p...
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Henry Lee @citizenlee.bsky.social · 12/01/2026
I wrote a longer essay expanding on this here: hhlee.substack.com/p/building-...
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Henry Lee @citizenlee.bsky.social · 12/01/2026
Scientific progress depends less on what problems we prioritize and more on who is allowed to assemble, and under what conditions.
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Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Figure 2. PET screen results and RB-TnSeq gene fitness results
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Stu Cantrill @stuartcantrill.com · 07/11/2025
Nov 7th is the birthday of both Lise Meitner & Marie Curie. Of the 13 chemical elements named directly after real people (not mythological figures) only two are named after women: meitnerium and curium (the latter of which is named in honour of both Marie & her husband) #chemsky 🧪
A black & white picture of Lise Meitner sat on a chair while holding a book. There is a bookcase in the background A black & white picture of Marie Curie
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Henry Lee @citizenlee.bsky.social · 04/11/2025
Want to shout out @glebkuz @PierceOgdenJ who recently and to great success used the pharma biobucks model! x.com/pierceogden...
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Henry Lee @citizenlee.bsky.social · 04/11/2025
Synthetic biology / Industrial Biotech could really use some BiBs.
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Henry Lee @citizenlee.bsky.social · 04/11/2025
Whether you want to industrialize biology or biologize industry, we could use new financing structures. I propose BiBs (Bioindustrial Bucks). www.genengnews.com/industry-ne...
genengnews.com
Bring on the BioIndustrial Bucks: Growing America’s Bioeconomy
Synthetic biology is ready for the next developmental milestone and America’s leadership depends on getting the financing right.
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Viv Goosens @candiedgoose.bsky.social · 25/04/2025
Register for free (www.cultivarium.org/portal) to access their fantastic work and engage with their growing community. Let's diversify our biological models for deeper understanding! (2/2)
cultivarium.org
Portal — Cultivarium
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Viv Goosens @candiedgoose.bsky.social · 25/04/2025
I'm thrilled to finally share that @wellcometrust.bsky.social funding @cultivarium.bsky.social to expand their portal an include more #fungi & #archaea. Already a go-to for bacteria research, as a hub to find info on how to grow and manipulate microbes. (1/2) blog.cultivarium.org/p/fungi-and-...
blog.cultivarium.org
Filaments of the Future
Over the next three years, Cultivarium will weave fungi and archaea into the fabric of a healthier, cleaner, and more resilient world.
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Cultivarium @cultivarium.bsky.social · 24/04/2025
We're gearing up to tackle new kingdoms of life, thanks to generous support from @wellcometrust.bsky.social. Get in touch! Read more on our blog: cultivarium.substack.com/p/fungi-and-...
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Stacey Burns @wentrogue.bsky.social · 08/03/2025
I got your waste, fraud, and abuse right here

CDC plans to study autism, vaccines
Move comes despite strong evidence finding no link between them.
By LENA H. SUN and LAUREN WEBER • The Washington Post
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Jeremy Berg @jeremymberg.bsky.social · 09/03/2025
Bluetorial: Women, courage, and leadership What follows will include some generalizations based on population averages of what I have experienced over the course of my career. There are, of course, exceptions in every group who are substantially more to one extreme or the other.
media.tenor.com
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
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Henry Lee @citizenlee.bsky.social · 13/02/2025
I am outdated myself but tagging our cracked compbio team @acritschristoph.bsky.social @tylerbarnumphd.bsky.social
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 09/02/2025
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏 www.science.org/doi/10.1126/...
science.org
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
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Sri Kosuri @srikosuri.bsky.social · 08/02/2025
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
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Henry Lee @citizenlee.bsky.social · 30/01/2025
Sure hope so!
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Henry Lee @citizenlee.bsky.social · 29/01/2025
Yes, please definitely use the chat feature to give feedback. We are considering giving user direct access to make edits themselves.
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Henry Lee @citizenlee.bsky.social · 28/01/2025
Thanks for trying it! Would you like the ability to make suggested updates? We are scoping this feature out.
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Henry Lee @citizenlee.bsky.social · 28/01/2025
We will continue to improve this resource and would like your feedback!
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Henry Lee @citizenlee.bsky.social · 19/01/2025
It’s an example of why referring to the exact sequence >>> using an easy to name, even with naming conventions. In this era of sequence and synthesize “anything” and “OMG REPRODUCIBILITY CRISIS”, let’s just get down to bottom of it = nucleotides.
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Henry Lee @citizenlee.bsky.social · 19/01/2025
(Lab lore) Vnat replicates “SC101” differently depending on what each lab calls SC101. 👎
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Henry Lee @citizenlee.bsky.social · 19/01/2025
We’d probably all agree that if we had to learn nomenclature, it’d ideally be useful still. And that convenience is when you know what you put into your experiment so you can troubleshoot.
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Henry Lee @citizenlee.bsky.social · 19/01/2025
It’d be more informative for all if all plasmid identities moved to specific sequence definitions (ie Sequence Object Identifier like DOI) instead of taxonomic and self-important naming schemes (ie using our own initials).
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Henry Lee @citizenlee.bsky.social · 03/01/2025
Looking forward to seeing it!
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Henry Lee @citizenlee.bsky.social · 03/01/2025
Very cool! Where will you store this info?
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Eduardo Rocha @epcrocha.bsky.social · 01/01/2025
New preprint. Large genomes vibriophages have it all: multiple functions, autonomy (full set of tRNA genes!), anti-defenses, broad host range. Yet, they remain rare, pinpointing the limits of generalists. Great collaboration with @fredoleroux.bsky.social led by Charles Bernard in our lab.
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George Takei @georgetakei.bsky.social · 30/12/2024
I continue to be deeply moved by this statement to the heavens by President Carter.
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Henry Lee @citizenlee.bsky.social · 30/12/2024
Author deposited manuscripts barely crack 900k and are not accounted for in the above statements.
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Henry Lee @citizenlee.bsky.social · 30/12/2024
The available articles are disappointing in number and location.
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Henry Lee @citizenlee.bsky.social · 30/12/2024
Yikes, only ~11% of all PubMed-indexed articles are open-access (~4M out of 37M). Guess all those AGI/ASI BioLLMs and All Pipetting self-driving labs (APSDls - coined it here first) will belong to journals or…knowledge pirates.
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Patrick Monahan @pattymo.com · 24/12/2024
The orc from Return of the King saying “The age of men is over. Now the Jingle Hop has begun.” He is wearing a Santa hat
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Henry Lee @citizenlee.bsky.social · 24/12/2024
@atinygreencell.bsky.social towards a modern affordable lab…
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Henry Lee @citizenlee.bsky.social · 24/12/2024
Important work that should not be forgotten or diminished.
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Henry Lee @citizenlee.bsky.social · 22/12/2024
It’s the best thing out there.
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Henry Lee @citizenlee.bsky.social · 20/12/2024
I meant the content of the paper, I’m stoked about a new wave of lab work and automation. @acritschristoph.bsky.social is having a go at me for my disdain for prefixing “towards”…
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Henry Lee @citizenlee.bsky.social · 20/12/2024
Love it
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Nature Portfolio @natureportfolio.nature.com · 07/12/2024
Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. A study in Nature Microbiology presents an approach to systematically discover and understand such antibiotic relationships. go.nature.com/49of3Mk 🧪
This is figure 4, which shows collateral sensitivity and cross-resistance interactions between and within antibiotic classes.
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Henry Lee @citizenlee.bsky.social · 07/12/2024
How about new.nsf.gov/funding/oppo...
new.nsf.gov
Building Synthetic Microbial Communities for Biology, Mitigating Climate Change, Sustainability and Biotechnology (Synthetic Communities)
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Henry Lee @citizenlee.bsky.social · 07/12/2024
Abracadabra all the microbial community grants.
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Henry Lee @citizenlee.bsky.social · 07/12/2024
Now use the spent media to culture a different microbe!
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Henry Lee @citizenlee.bsky.social · 06/12/2024
We’re making it easier for you to figure out exactly what is and is not possible for your most interesting bacteria.
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Axel Visel @axelvisel.bsky.social · 04/12/2024
BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse) To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜 Paper: www.cell.com/developmenta...
Figure from the paper, showing BOOSTER-overexpressing poplar plants that are about twice as tall as the negative controls.  Googly eyes (not from original paper) look at the taller plants.
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Henry Lee @citizenlee.bsky.social · 06/12/2024
Mapping brain connections or stimulating regions with electric fields (spikes or not) is very cool and sexy tech machismo… but functionally the brains are similar. We typically learn the most biology when we can study systems that change a lot.
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Henry Lee @citizenlee.bsky.social · 06/12/2024
The maternal brain undergoes sweeping changes (on/off/permanent) throughout pregnancy www.nature.com/articles/s41...
nature.com
Neuroanatomical changes observed over the course of a human pregnancy - Nature Neuroscience
Neural changes in pregnancy are not well understood. Here Pritschet et al. present an open-access precision brain imaging resource, mapping neuroanatomical change in an individual from preconception t...
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