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...

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 🧪

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.

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.

We will continue to improve this resource and would like your feedback!

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).

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.

I continue to be deeply moved by this statement to the heavens by President Carter.

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.

Important work that should not be forgotten or diminished.

It’s the best thing out there.

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. https://go.nature.com/49of3Mk 🧪

We’re making it easier for you to figure out exactly what is and is not possible for your most interesting bacteria.

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...

Are there any large scale efforts to use pregnancy brain for connectomics and/or remodeling with hormonal programming?

What’s the best way to pellet cells in deep 96-well plates WITHOUT a giant 3k rcf centrifuge? Mega bonus points if you don’t have to spin… cc @atinygreencell.bsky.social

RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...

Can’t wait to read this

Why did sheaths need to arise? 🤔

Unfortunate, but we need to know.

💯

One must also consider that all DNA-based life forms are already other being’s dank memes.

Wake up baby, the 1000 page manifesto on naming fungi just dropped, 2024 edition.

Looking forward to learning the latest on this!

Growth is so incredible!

I didn’t open this PDF so what if this preprint is also a hoax?

Asking for a friend.

So are we going to discuss abolishing the NIH here or is that type of content strictly for the other platform?

Fun! Intriguing that transposons are not depleted in plants. When will someone use plants as a bacterial genome minimization tool?

It’s time to map the holobiomes

tagging #PhageSky

Normalize the drugs