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Reposted by Kevin Forsberg

Claus Wilke @clauswilke.com · 3d

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...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Reposted by Kevin Forsberg

Kara McKinley @karalmckinley.bsky.social · 16h

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!

Çağrı Çevrim @cagricevrim.bsky.social · 17h

I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵

Induction of menstruation in mice reveals the regulation of menstrual shedding

During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

www.biorxiv.org

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Reposted by Kevin Forsberg

Roni Odai @rodai.bsky.social · 8d

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/...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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Kevin Forsberg @kvnforsberg.bsky.social · 5d

Agreed. A great game, but heart-wrenching ending.

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Kevin Forsberg @kvnforsberg.bsky.social · 5d

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.

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Reposted by Kevin Forsberg

Mark Mandel @markjmandel.bsky.social · 16d

Join us on Friday at noon for a great seminar from Tera Levin @teralevin.bsky.social! @uwmadisonmmi.bsky.social

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.

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Kevin Forsberg @kvnforsberg.bsky.social · 23d

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.

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Kevin Forsberg @kvnforsberg.bsky.social · 23d

Photosynthetic slugs ??!!??!

(also, I love the name 'kleptosome' for an organelle).

Harmit Singh Malik @harmitmalik.bsky.social · 23d

www.cell.com/cell/abstrac...

A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis

A host organelle integrates stolen chloroplasts for animal photosynthesis

Sea slugs steal foreign chloroplasts and store them in specialized organelles that facilitate photosynthesis and eventual digestion to mediate starvation resistance.

www.cell.com

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Kevin Forsberg @kvnforsberg.bsky.social · Aug 26

Congratulations @ching-hochang.bsky.social and @hsiehyp.bsky.social !! Excited for you both!

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Kevin Forsberg @kvnforsberg.bsky.social · Aug 18

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.

Julie Pfeiffer @jkpfeiff.bsky.social · Aug 18

Faculty search announcement 2025: Tenure-Track Assistant Professor in Microbiology at UT Southwestern. We seek candidates working in microbial pathogenesis (some preference may be given to bacterial pathogens). Come join our community! (1/5) www.utsouthwestern.edu/departments/...

Department members sit at a very long table in the hallway eating a pre-Thanksgiving potluck feast.

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Kevin Forsberg @kvnforsberg.bsky.social · Aug 4

Thanks, and good luck!

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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...

Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes

Rodríguez-Rodríguez et al. use functional metagenomics to identify hundreds of sequences from diverse environmental bacteria that block phage infection when expressed in E. coli. Their discoveries inc...

www.cell.com

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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.

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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...

The NIH Public Access Policy: Q&A for Authors

We’ve received many questions from authors, librarians, and research administrators about the NIH decision to accelerate implementation of its public access plan, going into effect on July 1, 2025.…

www.authorsalliance.org

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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.

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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.

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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. 🤞

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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?

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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).

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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.

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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...

NIH Public Access Policy Overview | Grants & Funding

grants.nih.gov

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 30

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!

Kevin Forsberg @kvnforsberg.bsky.social · Jul 29

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…

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 29

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)

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 29

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

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Kevin Forsberg @kvnforsberg.bsky.social · Jul 29

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...

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