Molecular assets on @addgene.bsky.social. Analysis software on @github.com.
There's so much to explore, get out there!!
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.
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.
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.
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.
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...
I wrote a longer essay expanding on this here: hhlee.substack.com/p/building-...
Scientific progress depends less on what problems we prioritize and more on who is allowed to assemble, and under what conditions.
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.
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 🧪
Want to shout out @glebkuz @PierceOgdenJ who recently and to great success used the pharma biobucks model!
x.com/pierceogden...
Synthetic biology / Industrial Biotech could really use some BiBs.
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...
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)
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-...
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-...
I got your waste, fraud, and abuse right here
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.
I am outdated myself but tagging our cracked compbio team @acritschristoph.bsky.social @tylerbarnumphd.bsky.social
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏
www.science.org/doi/10.1126/...
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.
Sure hope so!
Yes, please definitely use the chat feature to give feedback. We are considering giving user direct access to make edits themselves.
Thanks for trying it! Would you like the ability to make suggested updates? We are scoping this feature out.
We will continue to improve this resource and would like your feedback!
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.
(Lab lore) Vnat replicates “SC101” differently depending on what each lab calls SC101. 👎
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.
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).
Looking forward to seeing it!
