Vaughn Cooper
@vscooper.micropopbio.org
Evangelist for the study of evolution in action by everyone.
Pitt Prof | EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social) | ASM President-Elect | exercise addict ~ swim bike run
Pitt Prof | EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social) | ASM President-Elect | exercise addict ~ swim bike run
Pinned
Vaughn Cooper
@vscooper.micropopbio.org
· Jan 21
I'm incredibly honored by this opportunity to serve as President-Elect of @asm.org starting this summer. Looking forward to working with the Board, ASM leadership ,and staff to help advance the microbial sciences. I'm also glad to share my Vision statement, please join us!
asm.org/Press-Releas...
asm.org/Press-Releas...
Reposted by Vaughn Cooper
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Vaughn Cooper
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
November 20, 2025 at 8:47 AM
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Reposted by Vaughn Cooper
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Early Career Scientist Awards 2026
Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.
urldefense.com
November 19, 2025 at 8:55 PM
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Reposted by Vaughn Cooper
Please apply for this, and/or encourage your mentees and peers to do so!
Every year #ESEB distinguishes a young evolutionary biologist with the John Maynard Smith Prize! Nominations for the 2026 prize are due by January 15th!
Find out more here: eseb.org/prizes-fundi...
Find out more here: eseb.org/prizes-fundi...
November 19, 2025 at 9:21 AM
Please apply for this, and/or encourage your mentees and peers to do so!
Reposted by Vaughn Cooper
Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin https://www.biorxiv.org/content/10.1101/2025.11.16.688641v1
November 17, 2025 at 8:27 PM
Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
Reposted by Vaughn Cooper
Hard to believe it’s already that time of year!
Our kick-off meeting for the Klebsiella Seminar Series just wrapped up. Stay tuned for more!
@lauraamike.bsky.social @olayarendueles.bsky.social @caityholmes.bsky.social @tomstantonmicro.bsky.social @juanvalenciabacca.bsky.social WenWen Low & Jay V.
Our kick-off meeting for the Klebsiella Seminar Series just wrapped up. Stay tuned for more!
@lauraamike.bsky.social @olayarendueles.bsky.social @caityholmes.bsky.social @tomstantonmicro.bsky.social @juanvalenciabacca.bsky.social WenWen Low & Jay V.
November 18, 2025 at 10:43 PM
Hard to believe it’s already that time of year!
Our kick-off meeting for the Klebsiella Seminar Series just wrapped up. Stay tuned for more!
@lauraamike.bsky.social @olayarendueles.bsky.social @caityholmes.bsky.social @tomstantonmicro.bsky.social @juanvalenciabacca.bsky.social WenWen Low & Jay V.
Our kick-off meeting for the Klebsiella Seminar Series just wrapped up. Stay tuned for more!
@lauraamike.bsky.social @olayarendueles.bsky.social @caityholmes.bsky.social @tomstantonmicro.bsky.social @juanvalenciabacca.bsky.social WenWen Low & Jay V.
Reposted by Vaughn Cooper
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Reposted by Vaughn Cooper
This phrase has been living in my head rent-free all day. Truly perfect
"decision-based evidence-making"
Chilling. Perfect description.
Chilling. Perfect description.
A new profile of RFK Jr offers fresh insights into how he works, the bond he shares with Trump, & how he's moved HHS “from evidence-based decision-making to decision-based evidence-making." Story by @chelseacirruzzo.bsky.social, @caseyross.bsky.social, & me:
www.statnews.com/2025/11/18/r...
www.statnews.com/2025/11/18/r...
November 19, 2025 at 12:41 AM
This phrase has been living in my head rent-free all day. Truly perfect
Reposted by Vaughn Cooper
The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Klebsiella pneumoniae genomics tutorials – KlebNET-GSP
klebnet.org
November 18, 2025 at 8:25 AM
The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Reposted by Vaughn Cooper
US science is under assault like never before, but in response the scientific community can build an alliance for independent science--that can fill gaps left by the decimation of Federal science and reimagine the role of science in policy and society. 🧵 blog.ucs.org/genna-reed/u...
UCS Is Building an Alliance for Independent Science
UCS is working to build a powerful alliance for independent science. Its new web resource hosts information and resources for current and former advisory committee members, current and former federal ...
blog.ucs.org
November 12, 2025 at 3:07 PM
US science is under assault like never before, but in response the scientific community can build an alliance for independent science--that can fill gaps left by the decimation of Federal science and reimagine the role of science in policy and society. 🧵 blog.ucs.org/genna-reed/u...
Great article with solid science about endurance training, underfueling, and thyroid function. By the incomparable Alex Hutchinson www.outsideonline.com/health/train...
Are Low-Carb Habits Quietly Sabotaging Your Training (and Your Health)?
Scientists weigh in on the underlying causes of relative energy deficiency in sport
www.outsideonline.com
November 18, 2025 at 1:03 AM
Great article with solid science about endurance training, underfueling, and thyroid function. By the incomparable Alex Hutchinson www.outsideonline.com/health/train...
Reposted by Vaughn Cooper
⭐️This person is one of my favorite people to follow. I especially love his passion about sports and the paragraphs like this one where I do NOT UNDERSTAND A SINGLE WORD. The less I get it, the more fun for me. (Not an invitation for anyone to explain it.)
Tua unloading an underthrown deep shot into double coverage after having a full 3.5 seconds to bounce around in the pocket with two underneath guys open is definitely something else
November 16, 2025 at 5:39 PM
⭐️This person is one of my favorite people to follow. I especially love his passion about sports and the paragraphs like this one where I do NOT UNDERSTAND A SINGLE WORD. The less I get it, the more fun for me. (Not an invitation for anyone to explain it.)
Reposted by Vaughn Cooper
🧬 October’s most-read #Genetics paper tracks the global rise of artemisinin resistance using over 100,000 Plasmodium falciparum samples: elifesciences.org/articles/105...
Have a paper people should see? See what our Editors look for: buff.ly/JNOgmOA
Have a paper people should see? See what our Editors look for: buff.ly/JNOgmOA
November 16, 2025 at 11:01 AM
🧬 October’s most-read #Genetics paper tracks the global rise of artemisinin resistance using over 100,000 Plasmodium falciparum samples: elifesciences.org/articles/105...
Have a paper people should see? See what our Editors look for: buff.ly/JNOgmOA
Have a paper people should see? See what our Editors look for: buff.ly/JNOgmOA
Reposted by Vaughn Cooper
NSF is open again!
A few comments:
*Please be patient.
During a shutdown NSF employees cannot open computers or respond to emails.
*Merit review will continue. However panels won’t resume until after Dec 8th.
*POs remain excited and committed to advancing science and the scientific workforce.
A few comments:
*Please be patient.
During a shutdown NSF employees cannot open computers or respond to emails.
*Merit review will continue. However panels won’t resume until after Dec 8th.
*POs remain excited and committed to advancing science and the scientific workforce.
November 13, 2025 at 5:58 PM
NSF is open again!
A few comments:
*Please be patient.
During a shutdown NSF employees cannot open computers or respond to emails.
*Merit review will continue. However panels won’t resume until after Dec 8th.
*POs remain excited and committed to advancing science and the scientific workforce.
A few comments:
*Please be patient.
During a shutdown NSF employees cannot open computers or respond to emails.
*Merit review will continue. However panels won’t resume until after Dec 8th.
*POs remain excited and committed to advancing science and the scientific workforce.
Reposted by Vaughn Cooper
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.
A bit of a video explainer here: 1/ 🧪
A bit of a video explainer here: 1/ 🧪
November 13, 2025 at 10:31 PM
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.
A bit of a video explainer here: 1/ 🧪
A bit of a video explainer here: 1/ 🧪
Reposted by Vaughn Cooper
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes www.nature.com/articles/s41... #jcampubs
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes - Nature Methods
By developing a strategy of metagenomic coassembly and prioritizing divergent marker gene sequences, Bin Chicken efficiently recovers more than 77,000 microbial genomes with high novel diversity, ther...
www.nature.com
November 13, 2025 at 7:46 PM
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes www.nature.com/articles/s41... #jcampubs
Reposted by Vaughn Cooper
If you are #ASMBiofilms and would like a science friendship bracelet come find me! I have a variety of colors and special Biofilms 2025 bracelets! I'll be doing the 5K walk and at the poster session!
November 12, 2025 at 7:49 PM
If you are #ASMBiofilms and would like a science friendship bracelet come find me! I have a variety of colors and special Biofilms 2025 bracelets! I'll be doing the 5K walk and at the poster session!
Reposted by Vaughn Cooper
When I was in graduate school my life and carreer were completely transformed by a seminar I attended at Stanford by Dr. Hamilton Smith. In the talk he discussed how TIGR was sequencing whole genomes of organisms. Here is a scan of P1 of my notes. 1/n
November 11, 2025 at 5:42 AM
When I was in graduate school my life and carreer were completely transformed by a seminar I attended at Stanford by Dr. Hamilton Smith. In the talk he discussed how TIGR was sequencing whole genomes of organisms. Here is a scan of P1 of my notes. 1/n
Reposted by Vaughn Cooper
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The eds-and-meds economy that reshaped Pittsburgh after the collapse of steelmaking relies on skilled H-1B visa holders.
The administration’s disruption of these visas pose challenges for Pitt, the area’s largest employer of H-1B workers, and many others
www.publicsource.org/h1b-visa-app...
The administration’s disruption of these visas pose challenges for Pitt, the area’s largest employer of H-1B workers, and many others
www.publicsource.org/h1b-visa-app...
Trump change in visa fee could curb hiring by Pitt, BNY, UPMC and others
A new $100,000 fee on H-1B visa applications may deter hires of international talent, and could discourage skilled foreign workers from staying here.
www.publicsource.org
November 11, 2025 at 5:03 PM
The eds-and-meds economy that reshaped Pittsburgh after the collapse of steelmaking relies on skilled H-1B visa holders.
The administration’s disruption of these visas pose challenges for Pitt, the area’s largest employer of H-1B workers, and many others
www.publicsource.org/h1b-visa-app...
The administration’s disruption of these visas pose challenges for Pitt, the area’s largest employer of H-1B workers, and many others
www.publicsource.org/h1b-visa-app...
Reposted by Vaughn Cooper
The Long-Term Evolution Experiment has returned home. Led by Professors Richard Lenski (@relenski.bsky.social) and Jeffrey Barrick, this groundbreaking work continues to reveal how bacteria evolve in real time. 12 flasks. 1 legacy.
🔗https://tinyurl.com/f6vjyjvr
🔗https://tinyurl.com/f6vjyjvr
November 10, 2025 at 3:25 PM
The Long-Term Evolution Experiment has returned home. Led by Professors Richard Lenski (@relenski.bsky.social) and Jeffrey Barrick, this groundbreaking work continues to reveal how bacteria evolve in real time. 12 flasks. 1 legacy.
🔗https://tinyurl.com/f6vjyjvr
🔗https://tinyurl.com/f6vjyjvr
Reposted by Vaughn Cooper
We don’t talk enough about how Operation Warp Speed saved many lives in spite of Trump, nor how many people died because of his failure of leadership. Great piece from my great colleague @maciekboni.bsky.social
open.substack.com/pub/maciekbo...
open.substack.com/pub/maciekbo...
COVID’s leadership failures
Two moments that were too big for us, and the unfixable chain of mistakes that was set off after November 2020
open.substack.com
November 9, 2025 at 1:34 PM
We don’t talk enough about how Operation Warp Speed saved many lives in spite of Trump, nor how many people died because of his failure of leadership. Great piece from my great colleague @maciekboni.bsky.social
open.substack.com/pub/maciekbo...
open.substack.com/pub/maciekbo...
Reposted by Vaughn Cooper
See below for less subtlety.
More folks will have to ask groups like @scholars.org that uncritically amplify the arguments of In Covid's Wake precisely what they are doing. Is it that they didn't read what the authors wrote, actually agree, or are just 'getting along'?
bsky.app/profile/josh...
More folks will have to ask groups like @scholars.org that uncritically amplify the arguments of In Covid's Wake precisely what they are doing. Is it that they didn't read what the authors wrote, actually agree, or are just 'getting along'?
bsky.app/profile/josh...
"COVID Revisionism Has Gone Too Far"
Ya think?
www.theatlantic.com/ideas/archiv...
Fascinating given that "In Covid's Wake" is unable to grapple with (i) the extent of COVID mortality and morbidity; (ii) lives saved due to interventions; (iii) missed opportunities to align health + the economy.
Ya think?
www.theatlantic.com/ideas/archiv...
Fascinating given that "In Covid's Wake" is unable to grapple with (i) the extent of COVID mortality and morbidity; (ii) lives saved due to interventions; (iii) missed opportunities to align health + the economy.
COVID Revisionism Has Gone Too Far
If the center and left succumb to the view that “nothing worked,” no one will remain to defend sensible public-health measures the next time a pandemic comes around.
www.theatlantic.com
November 7, 2025 at 11:08 PM
See below for less subtlety.
More folks will have to ask groups like @scholars.org that uncritically amplify the arguments of In Covid's Wake precisely what they are doing. Is it that they didn't read what the authors wrote, actually agree, or are just 'getting along'?
bsky.app/profile/josh...
More folks will have to ask groups like @scholars.org that uncritically amplify the arguments of In Covid's Wake precisely what they are doing. Is it that they didn't read what the authors wrote, actually agree, or are just 'getting along'?
bsky.app/profile/josh...
Reposted by Vaughn Cooper
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Vaughn Cooper
Every cubic meter of air contains anywhere from 10 to 10 million microbes, depending on the altitude, location, season and time of day. At an observatory Watop Puy de Dôme, a 4,800-foot inactive volcano in France, microbiologists sample the aeromicrobiome.
Microbes Also Change the Climate. Could That Help Us? | Quanta Magazine
A collection of short dispatches from the field of climate microbiology conveys the contributions that single-celled life forms make to our climate system, and how we can work with them to address…
www.quantamagazine.org
November 7, 2025 at 4:46 PM
Every cubic meter of air contains anywhere from 10 to 10 million microbes, depending on the altitude, location, season and time of day. At an observatory Watop Puy de Dôme, a 4,800-foot inactive volcano in France, microbiologists sample the aeromicrobiome.