Henry Lee @citizenlee.bsky.social · 03/02/2026Molecular assets on @addgene.bsky.social. Analysis software on @github.com. There's so much to explore, get out there!! 030
Henry Lee @citizenlee.bsky.social · 03/02/2026Today 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. 120
Henry Lee @citizenlee.bsky.social · 03/02/2026Over 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. 130
Henry Lee @citizenlee.bsky.social · 03/02/2026So 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. 183
Henry Lee @citizenlee.bsky.social · 21/01/2026We scientists were so preoccupied with whether we could send samples out for cheap pooled sequencing, we didn’t stop to think if we should. 030
Henry Lee @citizenlee.bsky.social · 20/01/2026After 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... 010
Henry Lee @citizenlee.bsky.social · 12/01/2026I wrote a longer essay expanding on this here: hhlee.substack.com/p/building-... 010
Henry Lee @citizenlee.bsky.social · 12/01/2026Scientific progress depends less on what problems we prioritize and more on who is allowed to assemble, and under what conditions. 130
Reposted by Henry LeeAlex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025Very 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. 57938
Reposted by Henry LeeStu Cantrill @stuartcantrill.com · 07/11/2025Nov 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 🧪 111037
Henry Lee @citizenlee.bsky.social · 04/11/2025Want to shout out @glebkuz @PierceOgdenJ who recently and to great success used the pharma biobucks model! x.com/pierceogden... 010
Henry Lee @citizenlee.bsky.social · 04/11/2025Synthetic biology / Industrial Biotech could really use some BiBs. 110
Henry Lee @citizenlee.bsky.social · 04/11/2025Whether 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.comBring on the BioIndustrial Bucks: Growing America’s BioeconomySynthetic biology is ready for the next developmental milestone and America’s leadership depends on getting the financing right. 151
Reposted by Henry LeeViv Goosens @candiedgoose.bsky.social · 25/04/2025Register 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.orgPortal — Cultivarium 133
Reposted by Henry LeeViv Goosens @candiedgoose.bsky.social · 25/04/2025I'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.orgFilaments of the FutureOver the next three years, Cultivarium will weave fungi and archaea into the fabric of a healthier, cleaner, and more resilient world. 1167
Reposted by Henry LeeCultivarium @cultivarium.bsky.social · 24/04/2025We'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-... 22411
Reposted by Henry LeeStacey Burns @wentrogue.bsky.social · 08/03/2025I got your waste, fraud, and abuse right here 1102377677154
Reposted by Henry LeeJeremy Berg @jeremymberg.bsky.social · 09/03/2025Bluetorial: 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.coma cartoon says hey everybody an old man 's talking while bart simpson looks onALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on 5472146
Henry Lee @citizenlee.bsky.social · 13/02/2025I am outdated myself but tagging our cracked compbio team @acritschristoph.bsky.social @tylerbarnumphd.bsky.social 110
Reposted by Henry LeeCarolyn Bertozzi @carolynbertozzi.bskyverified.social · 09/02/2025Cool paper using LLM to discover a protein sequence code for subcellular localization 👏 www.science.org/doi/10.1126/...science.orgProtein codes promote selective subcellular compartmentalizationCells 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... 623568
Reposted by Henry LeeSri Kosuri @srikosuri.bsky.social · 08/02/2025It’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. 841009846
Henry Lee @citizenlee.bsky.social · 29/01/2025Yes, please definitely use the chat feature to give feedback. We are considering giving user direct access to make edits themselves. 110
Henry Lee @citizenlee.bsky.social · 28/01/2025Thanks for trying it! Would you like the ability to make suggested updates? We are scoping this feature out. 100
Henry Lee @citizenlee.bsky.social · 28/01/2025We will continue to improve this resource and would like your feedback! 021
Henry Lee @citizenlee.bsky.social · 19/01/2025It’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. 100
Henry Lee @citizenlee.bsky.social · 19/01/2025(Lab lore) Vnat replicates “SC101” differently depending on what each lab calls SC101. 👎 100
Henry Lee @citizenlee.bsky.social · 19/01/2025We’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. 100
Henry Lee @citizenlee.bsky.social · 19/01/2025It’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). 240
Reposted by Henry LeeEduardo Rocha @epcrocha.bsky.social · 01/01/2025New 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. 34327
Reposted by Henry LeeGeorge Takei @georgetakei.bsky.social · 30/12/2024I continue to be deeply moved by this statement to the heavens by President Carter. 795322026758
Henry Lee @citizenlee.bsky.social · 30/12/2024Author deposited manuscripts barely crack 900k and are not accounted for in the above statements. 000
Henry Lee @citizenlee.bsky.social · 30/12/2024The available articles are disappointing in number and location. 100
Henry Lee @citizenlee.bsky.social · 30/12/2024Yikes, 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. 110
Henry Lee @citizenlee.bsky.social · 24/12/2024@atinygreencell.bsky.social towards a modern affordable lab… 110
Henry Lee @citizenlee.bsky.social · 24/12/2024Important work that should not be forgotten or diminished. 000
Henry Lee @citizenlee.bsky.social · 20/12/2024I 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”… 120
Reposted by Henry LeeNature Portfolio @natureportfolio.nature.com · 07/12/2024Resistance 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 🧪 722369
Henry Lee @citizenlee.bsky.social · 07/12/2024How about new.nsf.gov/funding/oppo...new.nsf.govBuilding Synthetic Microbial Communities for Biology, Mitigating Climate Change, Sustainability and Biotechnology (Synthetic Communities) 120
Henry Lee @citizenlee.bsky.social · 07/12/2024Now use the spent media to culture a different microbe! 110
Henry Lee @citizenlee.bsky.social · 06/12/2024We’re making it easier for you to figure out exactly what is and is not possible for your most interesting bacteria. 040
Reposted by Henry LeeAxel Visel @axelvisel.bsky.social · 04/12/2024BOOSTER, 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... 38630
Henry Lee @citizenlee.bsky.social · 06/12/2024Mapping 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. 000
Henry Lee @citizenlee.bsky.social · 06/12/2024The maternal brain undergoes sweeping changes (on/off/permanent) throughout pregnancy www.nature.com/articles/s41...nature.comNeuroanatomical changes observed over the course of a human pregnancy - Nature NeuroscienceNeural 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... 100