Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Toronto Blue Jays feeling Toronto blue, eh?
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
Lab’s 1st preprint!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
Agreed. A great game, but heart-wrenching ending.
That ball caromed off a Bucs DL's helmet too (despite remaining a perfect spiral). Not sure how much of that I'd hold against Darnold.
Announcement: Medical Microbiology & Immunology Seminar Series, September 26, 12:00 pm, MSB 1520. "The Evolution of Immunity and Pathogenesis within Environmental Microbial Battlegrounds". Dr. Tera Levin, University of Pittsburgh.
Join us on Friday at noon for a great seminar from Tera Levin @teralevin.bsky.social! @uwmadisonmmi.bsky.social
Great pun but sadly inaccurate (I liked it so much I read the methods section). Unfortunately, no Kelp chloroplasts were stolen in the making of this mind-melting manuscript.
Photosynthetic slugs ??!!??!
(also, I love the name 'kleptosome' for an organelle).
Congratulations @ching-hochang.bsky.social and @hsiehyp.bsky.social !! Excited for you both!
Come be my colleague!
I've been very happy at UTSW Micro. Why?
Its a supportive environment full of excellent people. There's strong ambition, reflexive empathy, and excellent resources.
Thanks, and good luck!
In the end, I am tickled that our lab’s first paper was also a first for Elsevier. At least we got a good story out of the situation.
Or two good stories, if you also count @luis840alberto.bsky.social’s first paper. And you should! You can read it for free right here: www.cell.com/cell-host-mi...
I suspect there may have options to avoid the open access fee or that allowed me to upload the author-accepted manuscript to PMC.
But I am a *cliché* assistant professor that wanted (and still want) no unnecessary enemies. I played it safe.
FWIW, I have read that any conflicting policies between the Federal Government and a publisher default to the Feds (see #5 in the link below, thanks to colleagues for this resource).
www.authorsalliance.org/2025/06/06/t...
I ❤️ open access so was always planning to pay the OA fee. If I had less (flexible) money or hadn’t been proactive and persistent with my emails, it would have been very easy to fall out of compliance.
I expect/hope that the path to compliance will become easier (and cheaper) in the months to come.
Everyone I emailed at Elsevier and the NIH were nothing but polite and – to the extent they could be – helpful.
As things stand, however, full compliance with both parties is tricky. For me, it required ~$9400, some clarifying, and careful maneuvering.
I emailed the NIH Office of Science Policy (who were amazing). I was assured that NIHMS processing times would not impact my compliance. I should just upload the version of record when it came.
A few more Elsevier emails and I had the VOR. I sent it to NIHMS and complied with everyone’s policies. 🤞
But the version of record is typically ready just days before online release. And NIHMS can take weeks to process manuscripts for PMC. How to comply?
But what about author-accepted manuscripts? I had read that I could upload that version.
Well, Elsevier only allows uploads of author-accepted manuscripts after a 12-month embargo period. So, it had to be the version-of-record (again, per Elsevier emails).
This NIH policy required our paper to be at PubMed Central without embargo upon its publication. Per emails with Elsevier, there was only one way to comply with the NIH AND their sharing policy:
Purchase Gold Open Access (~$9400) and self-upload my article’s version-of-record to PubMed Central.
Our paper was ‘accepted in principle’ in late June but not formally accepted until early July.
So, it was subject to the recently revised timeline on the NIH Public Access Policy, which impacted papers accepted for publication after July 1st.
grants.nih.gov/policy-and-c...
Our lab’s 1st manuscript was also Elsevier’s first test case for complying with the new NIH Public Access Policy.
It was a bit tricky to figure out how to make everybody happy (you could put that on my epitaph...)
A🧵 on how I threaded this needle of compliance!
Oh, and also! We happened to be the first authors in all of Elsevier to contend with the new NIH Public Access Policy.
Stay tuned for summary thread on that experience…
(3/3)
New content compared to the preprint:
> Dallas/TdgA likely block phages via abortive infection
> Escaper mutants implicate Terminase as a trigger of the Dallas defense system
> We show our functional selections can identify abortive infection defenses at rare (one per million) frequencies
(2/3)
Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social!
In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!
Congrats to first author @luis840alberto.bsky.social !
www.cell.com/cell-host-mi...
(1/3)
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
