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Vaughn Cooper

@vscooper.micropopbio.org
8K followers 1.6K following 1.7K posts

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

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Vaughn Cooper @vscooper.micropopbio.org · 8h
I like Once Upon a Time in Hollywood more with each watch
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Ignacio Gallup-Diaz @igallupd.bsky.social · 12h
"A 20-year-old Amish woman with leukemia got measles and died in Pa.’s largest outbreak in three decades: After measles swept through her household, the young woman wanted to get vaccinated. Her doctor said she couldn't because she had leukemia and the treatments had weakened her immune system."
share.inquirer.com
A 20-year-old Amish woman with leukemia got measles and died in Pa.’s largest outbreak in three decades
After measles swept through her household, the young woman wanted to get vaccinated. Her doctor said she couldn't because she had leukemia and the treatments had weakened her immune system.
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Alisa Bokulich @alisabokulich.bsky.social · 23h
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.org
The University of Texas at Austin - Assistant Professor (TT) – History of Science, Technology, and Medicine | H-Net
Preferred 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.
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Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 10h
🧪 "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.com
National Science Foundation Diverted $1.4 Billion in Science Funds Mandated by Congress
The 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.
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Costa Samaras @costasamaras.com · 9h
If they can ignore Congress and not spend 20% of the funds Congress told them to invest the country’s science capabilities, than all involved have lost the justification to remain in a position of public trust.
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Frog and Toad Bot @frogandtoadbot.bsky.social · 9h
Toad did not answer. He had fallen asleep.
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Sasha Gusev @sashagusevposts.bsky.social · 01/10/2026
A searchable mapping between NIH study sections and program officers that doesn't suck. (Claude one-shot) sashagusev.github.io/po-study-sec...
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Vaughn Cooper @vscooper.micropopbio.org · 01/10/2026
Enlightening synopsis, like a free minireview. Especially appreciate the graphic of the selection shadow for those of us in evolutionary medicine #EvMed
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Eric Topol @erictopol.bsky.social · 30/09/2026
Why do our cells age? It's not just wear and tear, accumulated damage. Loss of cell identity takes center stage. A new Nature paper and connection with prior work that substantially advances the science of aging. In the new Ground Truths. erictopol.substack.com/p/loss-of-ce...
erictopol.substack.com
Loss of Cell Identity Drives Human Aging
That’s What Biological (Epigenetic) Aging Clocks Are Measuring
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Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
In our brand new 🥳 review, @hemaa-selvakumar.bsky.social & team pull a scattered literature in phage biology into a coherent framework for scaling up to engineering complex communities. We poured our hearts into this to share challenges & future opportunities for the nextGen!
Next generation application space with systematic characterization of phage-host interaction landscapes.
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Josh Marshall @joshtpm.bsky.social · 29/09/2026
Best Sen Schmitt meme yet
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Carl Zimmer @carlzimmer.com · 28/09/2026
The human genome is part virus. And here's a virus that's part human, having picked up a human gene about 100,000 years ago. My story here: nyti.ms/4hRKNPC
nyti.ms
This Virus Stole a Human Gene and Won’t Let Go of It (Gift Article)
Scientists have found a human gene lurking in a virus that causes skin infections. It may be using our own DNA to infect us.
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Vaughn Cooper @vscooper.micropopbio.org · 28/09/2026
thank you, we agree!
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
We believe these findings show that bacterial evolution during chronic infections can follow predictable pathways that drive disease progression, which we hope can enable earlier detection, monitoring, and treatment (with Abx or phage!) of CF lung infections. Paper: www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
As various bacterial phenotypes changed in concert, due to common regulatory mutations, so too did the pattern of diversification AND the decline of lung function. Drivers of chronicity spawned several enduring lineages and the patient's health suffered.
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
We were stunned by the convergent evolution by different strains in each patient. In total, 108 genes acquired parallel mutations indicating common host selection. 55 genes had ≥4 independent mutations! Each infection gained a combination of 5 of the most frequent, like a winning hand of cards.
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
Led by Leonilde Moreira with 🤩 work by Mirela Ferreira, who visited us a few years go, we combine sequencing, lots of phenotyping, and host lung function data over 7-17 years per patient. @jameszlosnik.bsky.social Importantly, phylogenetic reconstructions show which mutations drive later success
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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The Ferrari Lab @theferrarilab.bsky.social · 27/09/2026
TT Assistant Professor position in Ecology and Evolution of Infectious Disease at University of Florida
explore.jobs.ufl.edu
University of Florida - Details - Assistant Professor of Biology
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
Brilliant. And haunting as I’ve already begun replacing some boards
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C. Brandon Ogbunu @cbo.bsky.social · 27/09/2026
In my latest for @undark.org, I compare AI adoption in science to the Ship of Theseus: "If you swap out every wooden plank on a ship over time, is it still the same vessel?" I argue that science derives authority from something more than data generation + publication. undark.org/2026/09/25/o...
undark.org
AI Presents Science with a ‘Ship of Theseus’ Problem
Opinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment.
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Kathleen Bachynski @bachynski.bsky.social · 27/09/2026
“Studying Paulinella, scientists hope, will elucidate one of the most fundamental transitions in the history of life on our planet — and possibly give clues to how it might happen elsewhere in the universe. It could also provide practical insights on how to engineer photosynthetic organisms”
nytimes.com
In an $80 Motel Room, a Discovery to Shed Light on the Origins of Life
A scrappy science project led to a significant discovery: two new species of a rare organism that could elucidate a fundamental transition in the history of life on our planet.
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Eric Topol @erictopol.bsky.social · 27/09/2026
The word of the day: Zombified www.nytimes.com/2026/09/26/h...
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
It is the case. The Biosketch has a certification so that happens when you generate the document. They updated the current certification to expire Sept 26. So you need new one
Action needed — Regenerate SciENcv documents before upcoming NIH and other federal submissions

The Office of Sponsored Programs (OSP) has become aware of time-sensitive issues affecting SciENcv generated documents.

SciENcv updated the digital certificate used to sign Biosketch and Current & Pending (Other) Support (CPOS) documents without notification. The old certificate expires Saturday, September 26, 2026. Documents downloaded from SciENcv before that date may fail validation in eRA Commons and generate errors that delay or block submission.

This certificate change affects applications and RPPRs to NIH, AHRQ, CDC, NIOSH, FDA, and VA submitted on or after September 26, whether they are submitted in PERIS™ MyFunding/System-to-System, ASSIST, or Grants.gov Workspace. Because SciENcv is also used to prepare Biosketch and CPOS documents for NSF, DOE, NASA, and USDA proposals, investigators with imminent submissions to those agencies are encouraged to regenerate their documents as a precaution.

What to do

Investigators should log back into SciENcv and regenerate their Biosketch and CPOS documents. When 'Download PDF' is selected, SciENcv will prompt the investigator to certify. The new PDFs should replace any older versions in in-progress applications.

October 5 R01 deadline

Any in-progress application that already includes Biosketch or CPOS documents will need those documents regenerated and replaced this coming week.
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Vaughn Cooper @vscooper.micropopbio.org · 25/09/2026
FYI to everyone submitting this October NIH cycle You need to re-certify your ScienCV AFTER Sept 26 (tomorrow) for your application or it may not be accepted. Great timing!
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PLOS Biology @plosbiology.org · 25/09/2026
#PhageTherapy can fail when the immune system makes antibodies against therapeutic viruses. This study shows that fiber- and nozzle-specific antibodies block phage infection and promote aggregation-driven, Fc receptor-independent phagocytosis. 🧪 #ImmuneSky #structure #virus buff.ly/J0FOg9g
The image shows a reconstructed model of antibody-induced phage aggregation. Phage therapy, which uses bacteria-specific viruses to treat bacterial infections, is a highly promising therapeutic strategy in the era of precision medicine. Increasing evidence suggests that antibodies generated during phage therapy can affect the efficacy of phage therapy and, in some cases, even lead to treatment failure. However, the molecular mechanisms by which phage-specific antibodies cause phage therapy failure remain to be elucidated. Using Acinetobacter baumannii and its podovirus phage AbP20 as a model, the authors revealed the antibodies targeting phage fiber and nozzle proteins induced the formation of large-sized tail-to-tail phage aggregates which possess reduced infection and facilitated susceptibility to phagocytosis, providing a new clue to understand phage-specific antibodies induced therapy failure.  
This image was created by Heng Xue and Hang Yang.
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Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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NPR @npr.org · 24/09/2026
Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research. n.pr/4ycseLJ
n.pr
Under Trump, NIH funding disruptions have evolved. Here's what the numbers show
Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research.
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Joshua Weitz @joshuasweitz.bsky.social · 25/09/2026
FAI provides a window into a conservative re-imagining of science, one that might sound like it is focused on flourishing, but starts with vitriol and animus towards the very people who have driven US science forward and whose goal is the politicization of research (with a preferred winner).
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Joshua Weitz @joshuasweitz.bsky.social · 25/09/2026
He is not alone. Amidst 1.5+ years of attacks on science, there is well-funded, ascendant support for justifying the dismantling of America's leading scientific institutions from groups who will tell you, unmoored from evidence, that NIH, NSF, etc. were so flawed, that there was only one option.
FAI supporters

Our major philanthropic supporters have included Arnold Ventures, the Arthur N. Rupe Foundation, the Beth and Ravenel Curry Foundation, Coefficient Giving, the David and Lucile Packard Foundation, the Diana Davis Spencer Foundation, DonorsTrust, the Doris Duke Foundation, the Ethereum Foundation, the Filecoin Foundation for the Decentralized Web, the John S. and James L. Knight Foundation, the John Templeton Foundation, the Lynde and Harry Bradley Foundation, the Miles Foundation, the Proton Foundation, Recoding America Fund, Renaissance Philanthropy, the Sarah Scaife Foundation, the Searle Freedom Trust, the Silicon Valley Community Foundation, Stand Together Trust, Survival and Flourishing Fund, the Walton Family Foundation, the William and Flora Hewlett Foundation, and many others. Our corporate supporters and event sponsors have included a16z, Alphabet, Amazon, Anthropic, Astro Mechanica, Boom Supersonic, Cognition AI, DuckDuckGo, ExxonMobil, First Solar, Hadrian, Lightspeed Venture Partners, Meta, Microsoft, Mozilla, Narya Capital, New American Industrial Alliance, NRG Energy, Oklo, OpenAI, Paradigm Capital, Playground Global, Qualcomm, Rainmaker, Reflection AI, Shopify, Southern Company, T-Mobile, Uber, Ulysses, Variance, Waymo, XYZ Venture Capital, YCombinator, Yelp, Zanskar Geothermal, and various others. We are also grateful to our generous individual supporters who have chosen to remain anonymous.
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Erin Hotchkiss @fluvialbenthos.bsky.social · 24/09/2026
We (Biological Sciences at Virginia Tech) are #hiring TWO tenure-track Molecular Microbiology professors! Review of applications starts 1 Nov. I'm happy to answer questions about the department, VT, life in Blacksburg, etc.! More info / to apply: jobs.apply.vt.edu/jobs/assista... 🧪👩‍🔬🦠 #academicjobs
jobs.apply.vt.edu
Assistant/Associate Professor - Blacksburg, Virginia, United States
Job Description The Department of Biological Sciences in the College of Science at Virginia Tech seeks applicants for two (2) tenure-track research and teaching positions at the Assistant/Associate ...
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
This is so awesome
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Vaughn Cooper @vscooper.micropopbio.org · 23/09/2026
<shots fired> Why are consensus reviews authored by field leaders published in for-profit journals, instead of those run by the societies that serve those fields (and may have sponsored the workshop)? Disclosure: I’m a middle author of at least one, and it burns me.
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Vaughn Cooper @vscooper.micropopbio.org · 23/09/2026
Fantastic, comprehensive, useful review if you care about RNA modifications in bacteria: @asm.org @csdetweiler.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews
SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modificat...
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Harmit Singh Malik @harmitmalik.bsky.social · 21/09/2026
Thanks to the generosity of the Bezos Family Foundation, @basicsci.fredhutch.org is excited to announce a new search to recruit a Bezos Family Distinguished Scholar : apply.interfolio.com/193655
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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tracey depellegrin @traceydepellegrin.bsky.social · 21/09/2026
The @c4lifesciences.bsky.social is seeking an Executive Director. CLS is a terrific group of engaged scientific & scholarly society leaders. Check out the position (ideal for a person experienced in policy & advocacy + Capitol Hill) & share w/interested, qualified folks.
ascb.applytojob.com
Executive Director, Coalition for the Life Sciences - American Society for Cell Biology (ASCB) - Career Page
Apply to Executive Director, Coalition for the Life Sciences at American Society for Cell Biology (ASCB) in Bethesda, MD.
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Mozammel Hoque @mozammel.bsky.social · 20/09/2026
1/ New paper out in ISME Communications now in full version. Bacteria rarely live alone in nature, so we ran a 6-month evolution experiment asking what happens when species are forced to share the same biofilm. Turns out, company changes everything. 🧵 doi.org/10.1093/isme...
doi.org
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Mozammel Hoque @mozammel.bsky.social · 20/09/2026
5/ Personal note, this is my first paper as last author, from my time at AIMI, UTS. Great collaboration with @vscooper.micropopbio.org, and huge thanks to my supervisors Diane McDougald and Scott Rice for their mentorship. This work was supported by the ARC. @arc-gov-au.bsky.social
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Vaughn Cooper @vscooper.micropopbio.org · 20/09/2026
Now published from a fun collaboration, please see 🧵 academic.oup.com/ismecommun/a...
academic.oup.com
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Ákos T Kovács @evolvedbiofilm.bsky.social · 19/09/2026
Mixed-species interactions constrain diversification and shape biofilm evolution Klebsiella pneumoniae + Pseudomonas protegens + Pseudomonas aeruginosa in ISME Communications from Mozammel Hoque, with Diane McDougald, Scott Rice, @vscooper.micropopbio.org academic.oup.com/ismecommun/a...
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Carl Zimmer @carlzimmer.com · 17/09/2026
I wrote about what came before CRISPR 4 billion years ago: a war among viruses. Gift link: nyti.ms/3TBq4q0
nyti.ms
The Next Gene-Editing Technology May Also Be the Oldest (Gift Article)
Scientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more powerful.
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Carl Zimmer @carlzimmer.com · 17/09/2026
Pennsylvania measles outbreak now up to 731 cases and 4 deaths www.pa.gov/agencies/hea...
pa.gov
Measles
Measles is a disease that spreads easily from person to person and can make you sick. People who are not vaccinated are at the highest risk. The best protection against measles is vaccination. DOH is ...
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David Ho @davidho.bsky.social · 15/09/2026
NSF has reduced the research budget for all atmospheric, ocean, and earth sciences by ~80%. 80%! A lot of us will not be conducting new research or training new students for the foreseeable future.
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Vaughn Cooper @vscooper.micropopbio.org · 17/09/2026
www.ce-strategy.com/the-brief/gr...
ce-strategy.com
Growth | Clarke & Esposito
Publishers appear to be doing just fine despite AI fears. Two associations run into member backlash for very different reasons.
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Vaughn Cooper @vscooper.micropopbio.org · 21/12/2023
Friends don't let friends publish in MDPI journals. Pass it on. For more info, check out the Wikipedia page: en.wikipedia.org/wiki/MDPI 🔥
en.wikipedia.org
MDPI - Wikipedia
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Asher Leeks @asherleeks.bsky.social · 16/09/2026
Come work with @viromehunter.bsky.social and myself at UBC! We have a postdoctoral position available for someone with an interest in bioinformatics and genomics, using sociovirology to understand disease dynamics in plant viruses. Advert: ppvlab.sites.olt.ubc.ca/files/2026/0...
ppvlab.sites.olt.ubc.ca
Browser Verification | UBC Cybersecurity
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Nature Microbiology @natmicrobiol.nature.com · 16/09/2026
Out Now! Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice #MicroSky
go.nature.com
Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice
Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.
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Vaughn Cooper @vscooper.micropopbio.org · 16/09/2026
Authors!🚨 While you scramble for scarce $ 🤔 “Springer Nature reports revenue growth of 6.2%..and adjusted operating profit growth of 7.7%. They reported even more stunning submission growth of 30% and published article growth of 13%.” Publishing in society journals helps YOU not them👇🏻. Pass it on.
static.klipy.com
Man Lying on a Pile of Money
ALT: Man Lying on a Pile of Money
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Hiten Madhani @hitenmadhani.bsky.social · 16/09/2026
Spot on piece about the relationship between Federally funded science and the development of therapies. Investors want ‘de-risked’ assets. It’s their favorite word.
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