John Dennehy

Happy 134th birthday to humans knowing that viruses exist! OTD in 1892 Dmitri Ivanovsky presented his evidence of a tobacco mosaic disease caused by filterable agents (not bacteria!). Martinus Beijerinck confirmed this independently in 1898. And voila, virology is born!

FDA’s rejection of Moderna threatens to stifle broader vaccine industry Experts say the FDA "moved the goalposts" on Moderna, creating "a destructive precedent that will undermine the future of vaccine development" in the U.S.

FDA's decision not to accept Moderna's flu vaccine filing has sent shock waves through pharma. "When there’s uncertainty about the path to approval & the reliability of the process, that really has pretty serious consequences,” one player told @jasonmast.bsky.social. www.statnews.com/2026/02/12/f...

On delayed application review, the NIH grant terminations lawsuit appears to be headed for a settlement.

Both plaintiffs and defendants have submitted a joint document outlining their agreement. Judge Young must sign off on it before it takes effect.

Here's what it says and what all this means 🧵

The host range of generalist and specialist phages in capsule-diverse Klebsiella hosts is driven by the evolvability of receptor-binding proteins Capsule diversity limits phage host range by affecting RBP interactions in capsulated bacteria. This study shows that generalist phages evolve host range through RBP mutations and recombination, while...

journals.plos.org/plosbiology/...

The Lysis Genes of the Paradigm Phage SP6 | PHAGE Background: The Salmonella podophage SP6 has been extensively studied as a divergent relative of T7 and as a prototype for therapeutic applications. Two decades ago, it underwent two comprehensive gen...

We recently revised the genome of the paradigm phage SP6 and characterize its lysis genes: www.liebertpub.com/doi/10.1177/...

Vampire bats may have contracted H5N1 bird flu in Peru, raising worries about further spread Bats could form a bridge between marine and terrestrial mammals, scientists say

Fascinating story about evidence that #H5N1 #birdflu infected vampire bats in South America, raising the prospect of a potential new & dangerous host for the virus. Some good news: The virus didn't appear to spread well among the bats. By @martinenserink.bsky.social. www.science.org/content/arti...

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky

Disability in ecology and evolution In this TrendsTalk series 'Disability in ecology and evolution' in Trends in Ecology and Evolution, we will be hearing from people about their experiences being disabled in ecology and evolution. We a...

www.cell.com/trends/ecolo...

New entry into the Disability in Ecology and Evolution series in TREE featuring me :)

STAND WITH YOUR SCHOOL: Trump attacks 9 universities. Sign the alumni petition now. Are you an alum from one of the 9 schools Trump just attacked? Sign this alumni petition now to support your school, defend democracy, and build a grassroots movement for campus freedom across America...

Are you an alum from one of the 9 schools Trump just attacked? Sign this alumni petition now to support your school, defend democracy, and build a grassroots movement for campus freedom across America. alumni.controlshift.app/petitions/tr...

The NIH ordered me to stop my ‘dangerous’ gain-of-function research. It isn’t dangerous at all Safe gain-of-function research is necessary to identify new treatments for diseases like for tuberculosis — but the NIH has imposed unfounded stops.

www.statnews.com/2025/10/06/g...

TB research flagged as GoF for knocking out genes and introducing Kan resistance!

"Decisions designating research as “dangerous” must be transparent, deliberative, and scientifically informed."

www.hud.gov#openModal

Official US Gov site with blatantly partisan banner? Another milestone in the USA's slide into fascism.

jasonjwilliamsny.github.io/grfp2025/

"Weeks ago, the NSF asked the impossible—posting NSF [GRFP] application deadlines without providing a way to apply and without issuing an official solicitation or guidelines..."

Queens College's episode of The College Tour is live on our website! Highlights include campus life, academics, housing, sports and activities through the eyes of ten students.

▶️Watch the episode to see why QC might be the perfect fit for you: www.qc.cuny.edu/admissions/t...

New in Evolution:
Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae,
by Joleen Khey and Mike Travisano
academic.oup.com/evolut/artic...

I stand with PBS.

I stand with NPR.

I stand with Stephen Colbert.

I stand with Jimmy Kimmel.

I stand with the First Amendment.

PERIOD.*

*Also #ReleaseTheEPSTEIN_Files

Join us for the exciting Hispanic Heritage Month Kick-off Event! 🎉

Happening today, Monday, September 15, 2025
From 12:15 PM to 1:00 PM (Free Hour)
Room: Quad (Rain Location: Dining Hall 800)

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

RFK Jr. is a public disgrace. He should resign immediately!

All of these professional infectious disease organizations think so too!

asm.org/press-releas...

I just sent a Quack-o-Gram to Congress because RFK JR is America's Public Health Enemy #1 and needs to be removed!

act.standupforscience.net/fundraising/...

@standupforscience.bsky.social

So, kudos to both #Democrats & #Republicans in the House for their draft mark-up for next year's #budget, which maintains funding for #NIH (just like the Senate). This is rare, true #bipartisanship and should be praised. But #RussellVought will not be stopped by an appropriations bill. Why? 1/

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

RFK Jr.’s HHS Orders Lab Studying Deadly Infectious Diseases to Stop Research NIAID’s Integrated Research Facility is one of the few federal facilities charged with studying Ebola. Tuesday afternoon, all of its work was put on indefinite pause by Robert F. Kennedy Jr.’s departm...

What will be the deranged reason given for this idiotic move? That they might recommend vaccine research or something? RFK Jr. must be removed from office. It’s him or us.

Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage? The rise of antibiotic-resistant bacteria, particularly multidrug-resistant Pseudomonas aeruginosa (P. aeruginosa), represents a critical challenge to…

Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?

#phage #phagesky #mevosky

www.sciencedirect.com/science/arti...

I made a video about my new paper. I hope you enjoy it!

vimeo.com/1113132836?s...

Tweet by RFK Jr: "X posts that erroneously attribute Biden-era tweets supporting masks, lockdowns, vaccine mandates, etc. to my @CDCgov Director nominee, Susan Monarez, have understandably provoked agita within the MAHA movement. I handpicked Susan for this job because she is a longtime champion of MAHA values, and a caring, compassionate and brilliant microbiologist and a tech wizard who will reorient CDC toward public health and gold-standard science. I’m so grateful to President Trump for making this appointment."

There's some disinformation going around that the ousted CDC director wasn't really chosen by RFK Jr/Trump

But he tweeted this earlier this year...

Breaking News: Read three top CDC officials' resignation emails. The end of an era.

Enough is enough. The health of the country is in danger. Read our resignation letters: insidemedicine.substack.com/p/breaking-n...

"Their desire to please a political base will result in death and disability of vulnerable children and adults."

Powerful words. Our government is killing people.

Anti-vaccine misinformation can terrorize new parents, but science leads to truth | Defend Public Health Elizabeth Jacobs, PhD, shares her story of encountering online vaccine misinformation in the early 2000's, and how she used her scientific training to uncover the truth.

RFK Jr. continues to falsely claim that vaccines cause autism, and this will likely be among the propaganda he spreads in September, when he says he will “reveal the causes of autism”.

I wrote about my experience with encountering vaccine lies online and how I used science to find the truth.

In my discussions with various stakeholders, it was clear that we are adrift with no clear guidelines. I'm not optimistic that the administration will rise to the challenge to fill the "biosecurity policy vacuum after this EO". In my view, I see destructive policy to make political points.