Vaughn Cooper

Vaughn Cooper

@vscooper.micropopbio.org

Evangelist for the study of evolution in action by everyone. Pitt Prof | ASM President|EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social)| exercise addict ~ swim bike run

8K followers1.5K following1.7K posts

Vaughn Cooper reposted

Simon Roux
@simrouxvirus.bsky.social

New pre-print and tool alert ! This one addressing a long-standing viromics issue: we were missing a tool that can reliably assign broad host categories (e.g. prokaryote vs eukaryote) to novel viruses. VHAMSTeR is now available for this thanks to very talented postdoc @susiegriggo.bsky.social !!

Susie Grigson@susiegriggo.bsky.social

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

biorxiv.orgViral host assignment across the tree of life with VHAMSTeRViruses infect organisms across the tree of life, but many are not associated with a specific host. Here we present VHAMSTeR (Virus Host Assignment Model using Sequence Transformers and Reading-frames...

Vaughn Cooper reposted

Joao Ascensao
@joaoascensao.bsky.social

Now published! doi.org/10.1126/scia...

doi.orgFrequency-dependent fitness effects are ubiquitous in rapidly adapting microbial populationsIn simple microbial populations, the fitness effects of selected mutations are typically assumed to be constant, regardless of mutant frequency. This assumption underpins predictions about evolutionar...
Joao Ascensao@joaoascensao.bsky.social

How common are frequency dependent fitness effects? New preprint out today 👇 doi.org/10.1101/2025...

doi.orgFrequency-dependent fitness effects are ubiquitousIn simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

Vaughn Cooper reposted

Colette Delawalla, PhD
@cdelawalla.bsky.social

The 5-year cancer survival rate is up to 70% SIDS deaths have decreased by over 50% 89% decline in tornado deaths All thanks to federal investment in science and OUR tax dollars at work!

Michael Druker 🇨🇦@mdruker.app

Social media loves talking about how everything is getting worse. But what’s something that you’ve seen get _better_ in your lifetime?

Vaughn Cooper reposted

Richard Lenski
@relenski.bsky.social

@asm.org President Vaughn Cooper and Paul Turner (who gave the Tom Whittam Memorial Lecture) from yesterday's wonderful celebrations with @msumgi.bsky.social

Vaughn Cooper@vscooper.micropopbio.org

Absolutely delighted to be back at MSU to celebrate their recognition as a Milestones in Microbiology site, as @asm.org President. Go Green, Go White! …will post my formal remarks later!

Vaughn Cooper reposted

Pat Schloss
@patschloss.bsky.social

Replying to @vscooper.micropopbio.org

This is great. I think more "live" forms of evaluation are going to have to be more common if we're going to be taking AI generated "science" seriously.

Vaughn Cooper
@vscooper.micropopbio.org

Fantastic paper about the evolution and untapped potential of non-ribosomal peptide synthases. Congrats Georg and team! 👇🏻

georghochberg.bsky.social@georghochberg.bsky.social

Haven't used this is in a while, but a new paper from the group is a good excuse. This is monster of a paper from Sebastian Kaiser about the evolution of non-ribosomal peptides. www.nature.com/articles/s41...

nature.comDrift, selection and recombination bias drive the evolution of a non-ribosomal peptide - Nature Ecology & EvolutionThe structural diversity of non-ribosomal peptides is largely determined by recombination. This study shows that selection, genetic drift and biased recombination rates contribute to the diversity of ...

Vaughn Cooper reposted

georghochberg.bsky.social
@georghochberg.bsky.social

Haven't used this is in a while, but a new paper from the group is a good excuse. This is monster of a paper from Sebastian Kaiser about the evolution of non-ribosomal peptides. www.nature.com/articles/s41...

nature.comDrift, selection and recombination bias drive the evolution of a non-ribosomal peptide - Nature Ecology & EvolutionThe structural diversity of non-ribosomal peptides is largely determined by recombination. This study shows that selection, genetic drift and biased recombination rates contribute to the diversity of ...

Vaughn Cooper reposted

Katie Spoon
@kspoon.bsky.social

Replying to @kspoon.bsky.social

We wanted to understand why academics leave their jobs (doi.org/10.1126/scia...). We asked: “Tell us your story: what needs/needed to be different about your position?” I thought we would get a few hundred responses and I’d learn a bit more about the context of academic retention for myself.

doi.orgGender and retention patterns among U.S. facultyWomen faculty are more likely to leave their jobs than men, most often due to workplace climate, rather than work-life balance.

Vaughn Cooper reposted

Richard Lenski
@relenski.bsky.social

Replying to @vscooper.micropopbio.org

Also, if mirror bacteria ever establish themselves (ie, reach a significant population size outside a lab), one would need to treat many other vertebrate species along with humans. It would be a colossal, even impossible undertaking -- best avoided by never allowing the creation of mirror bacteria

Vaughn Cooper
@vscooper.micropopbio.org

Adding my $.02 to the many quotes in this article: Helen Branswell's reporting on ID epidemiology was always so clear and informative. A cool drink of spring water when everything seemed muddy. A treasure. RIP.

J. Emory Parker 🏳️‍🌈@jaspar.bsky.social

I’m afraid I have terrible news to share 💔 www.statnews.com/2026/10/13/h...

statnews.comHelen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.
Vaughn Cooper
@vscooper.micropopbio.org

HOLY S*@#$ I SPOKE TOO SOON! TAYLOR KNIBB IS IRONMAN WORLD CHAMPION🇺🇸! She threw up, got passed by the 2025 champ Lovseth, walked, pulled it together, and held steady. When Lovseth faltered dramatically with 1K to go, she passed for the win!

Vaughn Cooper@vscooper.micropopbio.org

Amazing race, congrats Vincent Luis🥇, Gustav Iden🥈 and Matthew Marquardt🇺🇸🥉, a med student at OSU! And hang in there Taylor Knibb, you'll win this soon, fabulous race by the women, finishing soon!

Vaughn Cooper
@vscooper.micropopbio.org

Amazing race, congrats Vincent Luis🥇, Gustav Iden🥈 and Matthew Marquardt🇺🇸🥉, a med student at OSU! And hang in there Taylor Knibb, you'll win this soon, fabulous race by the women, finishing soon!

Vaughn Cooper@vscooper.micropopbio.org

Ironman Hawaii World Champs is on and for once the swim is an adventure! Huge swell, fun to watch. I would have loved these conditions

Vaughn Cooper
@vscooper.micropopbio.org

OTOH the crazy humidity following the rainstorms in town would have been brutal to run in. Amazing race, congrats Vincent Luis🥇, Gustav Iden🥈 and Matthew Marquardt🇺🇸🥉, a med student at OSU!

Vaughn Cooper reposted

Evgenii Protasov
@evgenii-protasov.bsky.social

The archaeon Sukunaarchaeum mirabile, associated with dinoflagellates, has a genome of only 238 kbp🧬🤯 #archaea #symbiosis #eukaryotes #protists #MicroSky @currentbiology.bsky.social www.cell.com/current-biol...

cell.comA hidden archaeal lineage with an ultra-reduced genome retaining only its replicative coreHarada et al. describe an archaeon, recovered from a single marine plankton cell, whose 238-kb genome is the smallest known for the domain. It has lost nearly all metabolism but keeps the machinery to...

Vaughn Cooper reposted

Ryan Hisner
@ryanhisner.bsky.social

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

Vaughn Cooper
@vscooper.micropopbio.org

Pitt has never been more popular, and yet, our graduate enrollment declined 2.8%. 🤔 hmm, what would have caused this? ...the ultimate own-goal in our research leadership

Vaughn Cooper reposted

Eric Topol
@erictopol.bsky.social

New @science.org A breakthrough in understanding why do we get fever and an inflammation response to vaccines. The gut microbiome chronic production of flagellin Paves the way to potentially prevent these acute phase side-effects in the future www.science.org/doi/10.1126/...

science.orgThe human gut microbiome primes fever after vaccinationFever is a common adverse reaction to vaccination, contributing to vaccine hesitancy and reduced uptake. To understand variation in fever risk, we longitudinally profiled fecal microbiota, oral temper...

Vaughn Cooper reposted

Will Ratcliff
@wcratcliff.bsky.social

Replying to @wcratcliff.bsky.social

Challenge 2: the Darwinian threshold. Groups need a life cycle before they can evolve one, a classic chicken-and-egg problem. The way out: life cycles can be scaffolded "for free," either by the environment (e.g., floods dispersing cells) or by physics (packing stress fracturing snowflake yeast).

Vaughn Cooper reposted

Will Ratcliff
@wcratcliff.bsky.social

Replying to @wcratcliff.bsky.social

Challenge 1: forming groups. Across yeast, algae, bacteria and holozoans, lab evolution shows group formation arises fast (within 100–750 generations) and convergently, often through simple mutations like loss of ACE2 in snowflake yeast.

Vaughn Cooper reposted

Joshua Weitz
@joshuasweitz.bsky.social

Thoughts on the intersection of findings that the administration diverted $1.4B in NSF funds away from investigator-initiated research and today's New Golden Age of Science Summit showcasing the White House's preferred political priorities of what constitutes 'science'.

joshuasweitz.substack.comA Compromised Mission at the National Science FoundationRhetoric heralding a New Golden Age of Science obscures what is evident: the White House is undermining capacity for investigator-led basic research.

Vaughn Cooper reposted

Dave Baltrus 🦦
@surtlab.bsky.social

PSA for those submitting genome assemblies to NCBI… Had a complete bacterial genome submitted and stuck at “processing” since April. It took one email and it’s being released soon. Know I’m not the only one in that boat

Vaughn Cooper reposted

George O'Toole (he/him/his)
@geiselbiofilm.bsky.social

Pls share:The Department of Microbiology at the University of Georgia invites applications for a tenure track Associate or Full professor position in Medical Mycology, beginning August 1, 2027. www.ugajobsearch.com/postings/508...

ugajobsearch.comAssociate Professor or Professor of Microbiology in Medical MycologyThe Department of Microbiology at the University of Georgia invites applications for a nine-month, tenure-track position in Medical Mycology at the rank of Associate or Full Professor, with an anticip...

Vaughn Cooper reposted

Pittsburgh Phage Program
@pghphageprogram.bsky.social

Meet the Pittsburgh Phage Program (P3)! Our new video takes you behind the scenes—from patient isolates and phage research in the lab to the physicians and patients at the center of clinical care! #PhageTherapy #Bacteriophage #P3 #pittsburghphageprogram

Vaughn Cooper reposted

Daniel Bolnick
@danielbolnick.bsky.social

Not sure I’ve ever seen an essay that so precisely hits the mark as this. Read it. Share it.

McSweeney's@mcsweeneys.net

"I don’t know what every person in that group saw or knew. But I am raising one of the others. The boy who might someday be in the room. Or holding the phone. The boy who didn’t do it. The boy who could therefore spend the rest of his life explaining that he didn’t do anything." buff.ly/z7yWbR2

buff.lyAn Open Letter to Cornell University from the Mother of a Prospective Male Student“Seven former Cornell students are accused in a civil lawsuit of sexually assaulting another Cornell student who says she was incapacitated. Messages alleged...

Vaughn Cooper reposted

Coalition for Life Sciences
@c4lifesciences.bsky.social

$1.4 billion in research funding was redirected from the NSF in the latest move by the Trump administration to reshape how federal research dollars are allocated. Use the link below to share the importance of science funding!

Vaughn Cooper reposted

Vaughn Cooper
@vscooper.micropopbio.org

“If there’s one personal accomplishment I’m very proud of, it’s being able to work from a freaking Subaru,” Agnes said. “I’m a master at that.” 💪🏻 -Mother of Julian Hall, 18y old US striker www.nytimes.com/athletic/764...

nytimes.comMeet Julian Hall, the USMNT breakout star who’s just getting started: ‘A lot more to come’The Red Bull New York product became the youngest player in USMNT history to score in each of his first two caps.
Vaughn Cooper
@vscooper.micropopbio.org

Interesting “resurrection experiment” with flowers by @gbaucom.bsky.social and colleagues shows emergent constraint and environmental mismatch over a decade. Their conclusion: not great for climate adaptation academic.oup.com/evlett/artic...

academic.oup.comA resurrection experiment reveals reduced adaptive potential in a common agricultural weedAdaptive evolution is essential for populations facing rapid anthropogenic change, yet realized evolutionary responses often fall short of expectations. Us
Vaughn Cooper
@vscooper.micropopbio.org

“If there’s one personal accomplishment I’m very proud of, it’s being able to work from a freaking Subaru,” Agnes said. “I’m a master at that.” 💪🏻 -Mother of Julian Hall, 18y old US striker www.nytimes.com/athletic/764...

nytimes.comMeet Julian Hall, the USMNT breakout star who’s just getting started: ‘A lot more to come’The Red Bull New York product became the youngest player in USMNT history to score in each of his first two caps.

Vaughn Cooper reposted

Alisa Bokulich
@alisabokulich.bsky.social

History Dept @ University of Texas Austin invites applications for a TT assistant professor, specializing in modern history of science, technology, & medicine. Committee will consider applicants who specialize in any scientific practice in any part of the world since 1600. Deadline Nov 30 #HPS

networks.h-net.orgThe University of Texas at Austin - Assistant Professor (TT) – History of Science, Technology, and Medicine | H-NetPreferred qualifications include research and teaching records that will complement one or more of the department’s strengths including: African History, Asian History, British History, Digital Humanities, Latin American History, U.S. History, and related fields.

Vaughn Cooper reposted

Nigel Goldenfeld
@nigelgoldenfeld.bsky.social

🧪 "Mr. Trump’s science adviser, Michael Kratsios, has criticized the agency’s system for deciding which grants to fund ... He also argued the N.S.F. should ... bypass external review panels.” Kratsios lost 90% of assets while CFO of Clarium Capital. Do you trust him with the US science portfolio?

nytimes.comNational Science Foundation Diverted $1.4 Billion in Science Funds Mandated by CongressThe move, affecting about one-fifth of the National Science Foundation’s primary research budget, is the latest sign of how the White House is asserting more control over grants.