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Jonathan Eisen

@phylogenomics.bsky.social

Professor at UC Davis Work: phylogenomics & microbiomes; wildlife and aquatic microbiology; #openscience; Other: #birds; baseball; T1D Lab phylogenomics.me Pics jonathaneisen.smugmug.com Links linktr.ee/jonathaneisen TED go.ted.com/6WPm

2757 Posts32799 Follower5584 Folgt
Ashton Pittman@ashtonpittman.bsky.social · 3d ago

This is such bullshit. During the pandemic, we were down here reporting on how the University of Mississippi Medical Center had to turn its PARKING GARAGE into a makeshift ICU to handle the COVID surges. Lying about history I lived pisses me off. www.mississippifreepress.org/ummc-preppin...

UMMC Prepping Garage For Field Hospital, Requesting Federal Support To Staff It (Updated)

UMMC is clearing out space in a parking garage for a field hospital as the delta wave of COVID-19 continues to batter Mississippi.

mississippifreepress.org

Gabriel Bosslet@gbosslet.bsky.social · 3d ago

RFK Jr said these words today on national television "There were ICUs that were empty all over the country including in New York at the height (of the pandemic)" hahahahahahahahahahahahahahahahahahahahahahahahahahahahaha You are a fucking idiot hahahahahahahahahahahahahahahahaha <sobs silently>

Pável Matos@pavelmatosm.bsky.social · 5d ago

Please share: Full-time PhD position on Butterfly Evolution at High Elevations 🦋⛰️ The project aims to understand the evolution and adaptation of Andean white butterflies using genomics. DEADLINE: September 11, 2026 More info: pavelmatos.wordpress.com/join-us/

Join us

Opportunities Below are the positions currently open in our lab. Open PhD position (full time) Comparative and Population Genomics of Butterflies at High Elevations. The project aims to understand …

pavelmatos.wordpress.com

Jonathan Eisen@phylogenomics.bsky.social · 6d ago

New paper out in mSystems from my collaboration with labs of @maggiesogin.bsky.social, Jay Stachowicz, and Trent Northen. Lead author is Gina Chaput. Microbiota assembly in Zostera marina during early host development across controlled growth experiments See journals.asm.org/doi/10.1128/....

Microbiota assembly in Zostera marina during early host development across controlled growth experiments | mSystems

Using the Fabricated Ecosystem 2.0 (EcoFAB 2.0), we were able to successfully control the microbial environment of eelgrass, Zostera marina, resulting in the reduction of epiphytes and maintaining low...

journals.asm.org

Robert Reich@rbreich.bsky.social · 6d ago

Six congressmen bought between $83,000 to $245,000 in SpaceX stock just before its IPO: -Jared Moskowitz -Gil Cisneros -Dan Meuser -John McGuire -William Timmons -John James Five serve on committees whose work impacts SpaceX's business. We must ban members of Congress from trading stock.

Jonathan Eisen@phylogenomics.bsky.social · 6d ago

New paper out in mSystems from my collaboration with labs of @maggiesogin.bsky.social, Jay Stachowicz, and Trent Northen. Lead author is Gina Chaput. Microbiota assembly in Zostera marina during early host development across controlled growth experiments See journals.asm.org/doi/10.1128/....

Microbiota assembly in Zostera marina during early host development across controlled growth experiments | mSystems

Using the Fabricated Ecosystem 2.0 (EcoFAB 2.0), we were able to successfully control the microbial environment of eelgrass, Zostera marina, resulting in the reduction of epiphytes and maintaining low...

journals.asm.org

Jonathan Howard@joho.bsky.social · 6d ago

Yes

The Covid Amnesia Project and the Plot to Erase 2020

It’s up to those of us who experienced the pandemic in the real-world to make sure that what actually happened in 2020 isn’t deliberately erased by sheltered disinformation agents who experienced

sciencebasedmedicine.org

Bill Grueskin@bgrueskin.bsky.social · 7d ago

Running out of body bags, using forklifts to transfer corpses into makeshift morgues, a mortician conducting 200 funerals in a month when he usually does 30, crematories running at double capacity… And these senators just want to memory-hole it all www.nytimes.com/2020/04/30/n...

Seth L. Sanders@nabalkattu.bsky.social · last wk.

Film criticism aside, Emily Wilson's review of the Odyssey concerned me because it misrepresents Late Bronze Age history and reinforces an old Eurocentric pattern of dismissing the experiences--and reality--of ancient peoples other than the Greeks.

Nolan’s other major addition to Homer’s narrative is the repeated reference to threats to ‘our civilisation’ from ‘the sea peoples’ – a now debunked 19th-century theory about maritime tribes who were thought to have attacked Egypt around 1200 BCE and to have also been responsible for the roughly coeval collapse of Mycenaean Greek culture. ‘Our civilisation is under attack,’ Penelope wails. Odysseus comforts her by saying that ‘Bronze Age civilisation’, including literacy, will rise again from the ashes. The current consensus, as Nolan clearly knows, is that there was no such thing as ‘the sea peoples’, and that the Greek-speaking world’s shift away from the more centralised, literate palace culture of the Mycenaeans in the 11th century BCE towards the fragmented social formations of the early Greek Iron Age was caused by a range of factors, including climate change, earthquakes and internal unrest. Nolan uses these competing historical theories to create a characteristic narrative twist about the identity of ‘the sea peoples’, which I will not spoil, though you can probably guess it.
Dr. Lauren E. Fuess@laurenfuess.bsky.social · last wk.

Thanks to this grant we will be hiring!! Our grad position ad is already live with more opportunities forthcoming. But if you’re interested in postdoc or technician positions, please reach out! fuesslab.wp.txstate.edu/opportunities/

opportunities – Symbiommunity Lab

fuesslab.wp.txstate.edu

Dr. Lauren E. Fuess@laurenfuess.bsky.social · last wk.

Alright now that I’m home I guess it’s time to officially announce some really good news: I have received an NIH R35 MIRA!! This award will fund five years of research in my group using Aiptasia to study context dependency and GxGxE interactions in animal-microbe symbioses!

Screenshot of NIH status page, stating the project titled: “Mechanisms of Intergenomic Epistasis and Environmental Context in Animal-Microbe Symbioses” has been awarded with PI Lauren Fuess
MaizeGDB@maizegdb.bsky.social · last wk.

We are deeply saddened to share that Michael Freeling passed away on 7/20/2026 after a year-long battle with cancer. Our deepest condolences go to his family, friends, colleagues, and the many students he inspired. We will share additional memorial information soon.

We are very sorry to share the sad news that Michael Freeling passed away on 7/20/2026 after a year long battle with esophageal cancer. Mike was a long-time faculty member in the Plant and Microbiology Department at University of California-Berkeley, a groundbreaking plant geneticist, and an inspiring teacher and mentor to over two dozen Ph.D. students, four dozen postdocs, and countless undergraduates. He was best known for pioneering work on maize anaerobic metabolism and gene regulation, transposon biology, developmental genetics of the maize ligule, and the discovery of biased gene retention following whole-genome duplications in plants. Mike was hired by UC-Berkeley as an assistant professor straight out of graduate school in 1973, and he was promoted to Associate Professor in 1979 and to full professor in 1984. He was selected as a Guggenheim Fellow in 1980, elected to the National Academy of Sciences in 1994, and won the McClintock Prize for Plant Genetics and Genome Studies in 2017. Mike taught genetics, comparative genomics and scientific reasoning to our graduate students, and he also taught a popular genetics course for non-majors that had various titles over the years but was affectionately known as “Genetics for Poets.” Our deepest condolences go out to his family, friends and many colleagues.
Joanna Masel@joannamasel.bsky.social · last wk.

Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

M. David Ruff@mdavidruff.bsky.social · last wk.

As someone who has voted in every election, donated to numerous campaigns, and knocked on hundreds of doors, it’s really frustrating when I have to spend ten minutes a day unsubscribing to spam candidate fundraising emails I never signed up for.