Jonathan Eisen
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phylogenomics.bsky.social
Jonathan Eisen
@phylogenomics.bsky.social

Professor at UC Davis

Work: evolution, ecology, function & phylogenomics of host-microbiome systems; #openscience;
Other: #birds; baseball; T1D

Lab phylogenomics.me
Pics jonathaneisen.smugmug.com
Links linktr.ee/jonathaneisen
TED go.ted.com/6WPm .. more

Jonathan Andrew Eisen is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open access journal PLOS Biology. .. more

Biology 43%
Environmental science 24%
Pinned
Say hello to my little friend #birds

I am a huge fan of Lindsey Vonn and have no problem with her racing after the ACL issue. I do think it would be funny if she trolled everyone and said she was hoping to still compete in some events with a fractured leg.
We are murdering people and it is basically just background noise at this point. www.nytimes.com/2026/02/09/u...
U.S. Boat Strike Kills 2 in Pacific, With One Survivor
www.nytimes.com
🚨BREAKING: Puerto Rico has been part of the United States since 1898, and people still act confused that Puerto Ricans are American.

States that joined after Puerto Rico:
• Oklahoma — 1907
• New Mexico — 1912
• Arizona — 1912
• Alaska — 1959
• Hawaii — 1959

Yet somehow this is still news to folks.

Reposted by Jonathan A. Eisen

We already did it for chimpanzees. And it was long overdue. We should have immediately moved the conversation to retiring other primates, but there’s been major hindrances to those efforts.

Reposted by Jonathan A. Eisen

I don’t have the energy to read the details about plans to convert the Oregon Primate Center to a sanctuary, but I will say this: we are far overdue for retiring primates used in biomedical research to sanctuaries or other similar retirement care.

Cool - I will send you a DM in a bit

Reposted by Jonathan A. Eisen

We were in no rush and had blocked out the whole day for it, but I think it could easily be done in 3 hours with some pre-planning and streamlined setup. It's nice to be able to have pre-sequenced data on hand so they can see the end product as soon as they 'ship' their samples/finish the protocol.

Reposted by Jonathan A. Eisen

I recently took my undergrads through the process of DNA extraction, PCR, and sample prep for metagenomics. (from soil for fungal metagenomics)

It took them 2 hours to extract the DNA, about 30 minutes to start the PCR, and another hour to purify and QC the product (using previous days run).
Our DHS reform demands are exceedingly reasonable.

We're asking ICE to do nothing more than follow the standards that the vast majority of law enforcement agencies already follow.

Republicans, the ball is in your court. The clock is ticking.

Do you know if that discusses a lab that could be done in 2-3 hours?

I am looking for examples of a 2-3 hour lab activity for a course that would allow college students to get some experience connected to environmental DNA studies (e.g., e-DNA, rRNA/ITS PCR, metagenomics, etc). Ideally this would have some DNA extraction and some follow up processing / analysis.
omg everybody go draw a horse this is what the internet was made for

gradient.horse
gradient.horse
Draw a horse, watch it run!
gradient.horse

Reposted by Jonathan A. Eisen

BREAKING: The Oregon Health & Science University board of directors has voted to begin negotiations with the NIH about potentially transitioning the university’s primate research center to a sanctuary for the animals.

By @callimcflurry.bsky.social

#neuroskyence

bit.ly/4a6mycK
Oregon primate center to negotiate transition to sanctuary
The board of directors at Oregon Health & Science University, which runs the primate center, voted unanimously for the move.
bit.ly

Reposted by Jonathan A. Eisen

Exclusive: Site takes a cut of subscriptions to content that promotes far-right ideology, white supremacy and antisemitism
Revealed: How Substack makes money from hosting Nazi newsletters
www.theguardian.com
Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!
Davis Summer Population Genomics Program
Want to learn population genetics? Please fill out this form to indicate your potential interest in a 2-week intensive online summer population genetics course taught by Jeffrey Ross-Ibarra and Graham...
docs.google.com

Reposted by Jonathan A. Eisen

I don’t understand. He’s actually a very good bunny.
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
www.nature.com
NPR @npr.org · 1d
For most people, the pandemic days of masking are behind us. In certain corners of the Winter Olympics, though, things still look a lot like they did in Covid times. Some athletes are taking extreme measures to stay healthy. n.pr/4akK70l
Olympic Covid restrictions are gone, but some athletes still self-quarantining
For most people, the pandemic days of masking are behind us. In certain corners of the Winter Olympics, though, things still look a lot like they did in Covid times. Some athletes are taking extreme measures to stay healthy.
n.pr
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Missed Bad Bunny’s halftime show? Want to rewatch? (4x and counting for me). The NFL posted the whole performance on YouTube: on pace for 500k views in the first 30 minutes.
Bad Bunny's Apple Music Super Bowl Halftime Show
YouTube video by NFL
youtu.be
The guys behind him in the flat hats are Los Pleneros de la Cresta, a teaching ensemble working to keep traditional plena music alive on the island

They were an integral part of the residency last summer and are on tour with him this year

Reposted by Jonathan A. Eisen

💙💎

Well the halftime show by Bad Bunny - aka Benito Antonio - aka San Benito was phenomenal. I would just like to add that it is fitting he did the show in California as Benitoite is our "State Gem" (this is a pic from street art on the @ucdavis.bsky.social campus).

“Relax your Tight End” could be a microbiome ad

🐰🐇 🐰🐇 🐰🐇 🐰🐇 🐰🐇 🐰🐇 🐰🐇 🐰🐇 🐰🐇
I made a map of 3.4 million Bluesky users - see if you can find yourself!

bluesky-map.theo.io

I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
bluesky-map.theo.io

So - if you need a #SuperbOwl fix - I suggest checking out @inaturalist.bsky.social

www.inaturalist.org/observations...
Observations
Observations of Owls
www.inaturalist.org

Or the Papuan Boobook with 27

Like the iTombwe Owl, with one

I personally like to go through the Species list www.inaturalist.org/observations... and look at the ones with the fewest observations (at the bottom)
Observations
Observations of Owls
www.inaturalist.org