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...
A tour de force in
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.
Congrats Zam and Viridian team on this tremendous resource!
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.
Congrats Zam and Viridian team on this tremendous resource!
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)
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
February 9, 2026 at 3:30 PM
A tour de force in
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.
Congrats Zam and Viridian team on this tremendous resource!
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.
Congrats Zam and Viridian team on this tremendous resource!
Reposted by Vaughn Cooper
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)
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
February 9, 2026 at 3:16 PM
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)
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)
Reposted by Vaughn Cooper
Huh. Green Day skipping the part of "American Idiot" about "I'm not a part of a redneck agenda/Now everybody, do the propaganda."
But, shit, Green Day is playing the damn Super Bowl so I'm happy.
But, shit, Green Day is playing the damn Super Bowl so I'm happy.
February 8, 2026 at 11:09 PM
Huh. Green Day skipping the part of "American Idiot" about "I'm not a part of a redneck agenda/Now everybody, do the propaganda."
But, shit, Green Day is playing the damn Super Bowl so I'm happy.
But, shit, Green Day is playing the damn Super Bowl so I'm happy.
One more @washingtonpost.com casualty: the podcast Post Reports. This was a good program 😮💨
February 7, 2026 at 8:31 PM
One more @washingtonpost.com casualty: the podcast Post Reports. This was a good program 😮💨
Reposted by Vaughn Cooper
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research
The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...
research.pasteur.fr
January 28, 2026 at 11:19 AM
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
Reposted by Vaughn Cooper
We had devastating cuts to @washingtonpost. Our health team of 14 lost 9 reporters yesterday despite it being listed as part of the Post’s new focus.
But I still have my job. Along w/a core team, we are still dedicated to covering public health, holding the powerful to account.
But I still have my job. Along w/a core team, we are still dedicated to covering public health, holding the powerful to account.
February 5, 2026 at 7:16 PM
We had devastating cuts to @washingtonpost. Our health team of 14 lost 9 reporters yesterday despite it being listed as part of the Post’s new focus.
But I still have my job. Along w/a core team, we are still dedicated to covering public health, holding the powerful to account.
But I still have my job. Along w/a core team, we are still dedicated to covering public health, holding the powerful to account.
Reposted by Vaughn Cooper
Genomic clues to the origin of eukaryotic cells www.nature.com/articles/d41...
Genomic clues to the origin of eukaryotic cells
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.
www.nature.com
February 6, 2026 at 9:55 AM
Genomic clues to the origin of eukaryotic cells www.nature.com/articles/d41...
Founded in 1950, NSF's mission is "To promote the progress of science; to advance the national health, prosperity, & welfare; & to secure the national defense; and for other purposes."
NSF discoveries underpin most modern technology from the US.
That scientific progress is ending. Tell your reps!
NSF discoveries underpin most modern technology from the US.
That scientific progress is ending. Tell your reps!
But, as they say, there is no time like the present
[OK, maybe the 1930s if you want to nitpick]
But, with some data wrangling, my first NSF Funding Curves!
2/3
[OK, maybe the 1930s if you want to nitpick]
But, with some data wrangling, my first NSF Funding Curves!
2/3
February 5, 2026 at 4:00 PM
Founded in 1950, NSF's mission is "To promote the progress of science; to advance the national health, prosperity, & welfare; & to secure the national defense; and for other purposes."
NSF discoveries underpin most modern technology from the US.
That scientific progress is ending. Tell your reps!
NSF discoveries underpin most modern technology from the US.
That scientific progress is ending. Tell your reps!
Reposted by Vaughn Cooper
Trump admin is "destroying medical research," Senate report finds arstechnica.com/health/2026/...
Trump admin is "destroying medical research," Senate report finds
In a Senate hearing Tuesday, NIH director dismissed concern about research chaos.
arstechnica.com
February 4, 2026 at 9:46 PM
Trump admin is "destroying medical research," Senate report finds arstechnica.com/health/2026/...
Reposted by Vaughn Cooper
Not quite: "NIH would not be required to cap the proportion of new multiyear awards at 2024 levels. Instead, the bill limits the amount of money for multiyear funding to the 2025 level, which means the total number of new awards could again drop by 2000 compared with 2024.
February 3, 2026 at 8:36 PM
Not quite: "NIH would not be required to cap the proportion of new multiyear awards at 2024 levels. Instead, the bill limits the amount of money for multiyear funding to the 2025 level, which means the total number of new awards could again drop by 2000 compared with 2024.
Reposted by Vaughn Cooper
Both chambers of Congress have now passed the FY26 minibus with NIH provisions. The President will sign.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
February 3, 2026 at 7:48 PM
Both chambers of Congress have now passed the FY26 minibus with NIH provisions. The President will sign.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
Reposted by Vaughn Cooper
All you want for christmas is.... transposon mutagenesis!
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
December 24, 2025 at 3:03 PM
All you want for christmas is.... transposon mutagenesis!
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Reposted by Vaughn Cooper
Trust does matter. Unfortunately HHS/NIH leadership is actively working to undermine trust in public health institutions and it's beginning to have an impact:
joshuasweitz.substack.com/p/confrontin...
joshuasweitz.substack.com/p/confrontin...
February 3, 2026 at 5:02 PM
Trust does matter. Unfortunately HHS/NIH leadership is actively working to undermine trust in public health institutions and it's beginning to have an impact:
joshuasweitz.substack.com/p/confrontin...
joshuasweitz.substack.com/p/confrontin...
PacBio folds its short-read sequencing hand.
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
PacBio Sells Short Read Tech To Illumina
PacBio has finally sold their short read sequencing assets to Illumina for ~$50M.
aseq.substack.com
February 2, 2026 at 5:23 PM
PacBio folds its short-read sequencing hand.
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
Reposted by Vaughn Cooper
There I fixed it
February 2, 2026 at 4:06 PM
There I fixed it
Reposted by Vaughn Cooper
“Remember,” she hissed, whip in hand, “the safe word is pierogi.”
buff.ly/Lu9Catr
buff.ly/Lu9Catr
Yinzerotica: Erotica for Pittsburghers
“Do you wanna get out of here?” she asked, Yuengling on her breath. “Do the Steelers have six Super Bowl trophies?” he responded, already putting o...
buff.ly
February 2, 2026 at 2:30 AM
“Remember,” she hissed, whip in hand, “the safe word is pierogi.”
buff.ly/Lu9Catr
buff.ly/Lu9Catr
Reposted by Vaughn Cooper
Reposted by Vaughn Cooper
HAPPENING NOW: Aerial view of a LARGE group of cyclists who have gathered in Minneapolis for an Alex Pretti memorial bike ride
📍Minneapolis, Minnesota
📍Minneapolis, Minnesota
January 31, 2026 at 7:23 PM
HAPPENING NOW: Aerial view of a LARGE group of cyclists who have gathered in Minneapolis for an Alex Pretti memorial bike ride
📍Minneapolis, Minnesota
📍Minneapolis, Minnesota
Reposted by Vaughn Cooper
New NIH funding strategy has been formalized.
I really do hope scientists understand what this means for the future of science (funding) - it's not subtle.
www.niaid.nih.gov/about/unifie...
I really do hope scientists understand what this means for the future of science (funding) - it's not subtle.
www.niaid.nih.gov/about/unifie...
NIH Unified Funding Strategy
Objective peer review, and HHS- and NIH- specific priorities, and a standardized, transparent process for incorporating NIAID-specific priorities will guide funding selections.
www.niaid.nih.gov
January 30, 2026 at 8:31 PM
New NIH funding strategy has been formalized.
I really do hope scientists understand what this means for the future of science (funding) - it's not subtle.
www.niaid.nih.gov/about/unifie...
I really do hope scientists understand what this means for the future of science (funding) - it's not subtle.
www.niaid.nih.gov/about/unifie...
Reposted by Vaughn Cooper
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!
asm.org/about-asm/as...
asm.org/about-asm/as...
Phage Therapy Coordination Network | ASM.org
ASM Health is unlocking bacteriophage therapies for antimicrobial resistance (AMR) through coordinated access and regulatory approvals.
asm.org
January 27, 2026 at 5:52 PM
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!
asm.org/about-asm/as...
asm.org/about-asm/as...
Reposted by Vaughn Cooper
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
January 27, 2026 at 8:23 PM
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!
asm.org/about-asm/as...
asm.org/about-asm/as...
Phage Therapy Coordination Network | ASM.org
ASM Health is unlocking bacteriophage therapies for antimicrobial resistance (AMR) through coordinated access and regulatory approvals.
asm.org
January 27, 2026 at 5:52 PM
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!
asm.org/about-asm/as...
asm.org/about-asm/as...
Reposted by Vaughn Cooper
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
January 26, 2026 at 7:00 PM
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
Reposted by Vaughn Cooper
More microbiologists need to think about goop! We only found 31 studies to compare our results to, mostly clinical gammaproteobacteria.
Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/
Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/
January 23, 2026 at 6:20 PM
More microbiologists need to think about goop! We only found 31 studies to compare our results to, mostly clinical gammaproteobacteria.
Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/
Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/
Reposted by Vaughn Cooper
Vaughn Cooper’s new Scientific American article offers a clear look at the potential threats posed by mirror‑life. He trained with MGI's Rich Lenski @relenski.bsky.social, whose contributions to the field are referenced in the piece. Important context for a complex topic.
What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them.
Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...
Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...
Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them
Researchers are close to making “reversed” cells that may wipe us off the planet
www.scientificamerican.com
January 22, 2026 at 8:27 PM
Vaughn Cooper’s new Scientific American article offers a clear look at the potential threats posed by mirror‑life. He trained with MGI's Rich Lenski @relenski.bsky.social, whose contributions to the field are referenced in the piece. Important context for a complex topic.